WorldWideScience

Sample records for genomics visualization applications

  1. IVAG: An Integrative Visualization Application for Various Types of Genomic Data Based on R-Shiny and the Docker Platform.

    Science.gov (United States)

    Lee, Tae-Rim; Ahn, Jin Mo; Kim, Gyuhee; Kim, Sangsoo

    2017-12-01

    Next-generation sequencing (NGS) technology has become a trend in the genomics research area. There are many software programs and automated pipelines to analyze NGS data, which can ease the pain for traditional scientists who are not familiar with computer programming. However, downstream analyses, such as finding differentially expressed genes or visualizing linkage disequilibrium maps and genome-wide association study (GWAS) data, still remain a challenge. Here, we introduce a dockerized web application written in R using the Shiny platform to visualize pre-analyzed RNA sequencing and GWAS data. In addition, we have integrated a genome browser based on the JBrowse platform and an automated intermediate parsing process required for custom track construction, so that users can easily build and navigate their personal genome tracks with in-house datasets. This application will help scientists perform series of downstream analyses and obtain a more integrative understanding about various types of genomic data by interactively visualizing them with customizable options.

  2. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

  3. Applications of the pipeline environment for visual informatics and genomics computations

    Directory of Open Access Journals (Sweden)

    Genco Alex

    2011-07-01

    Full Text Available Abstract Background Contemporary informatics and genomics research require efficient, flexible and robust management of large heterogeneous data, advanced computational tools, powerful visualization, reliable hardware infrastructure, interoperability of computational resources, and detailed data and analysis-protocol provenance. The Pipeline is a client-server distributed computational environment that facilitates the visual graphical construction, execution, monitoring, validation and dissemination of advanced data analysis protocols. Results This paper reports on the applications of the LONI Pipeline environment to address two informatics challenges - graphical management of diverse genomics tools, and the interoperability of informatics software. Specifically, this manuscript presents the concrete details of deploying general informatics suites and individual software tools to new hardware infrastructures, the design, validation and execution of new visual analysis protocols via the Pipeline graphical interface, and integration of diverse informatics tools via the Pipeline eXtensible Markup Language syntax. We demonstrate each of these processes using several established informatics packages (e.g., miBLAST, EMBOSS, mrFAST, GWASS, MAQ, SAMtools, Bowtie for basic local sequence alignment and search, molecular biology data analysis, and genome-wide association studies. These examples demonstrate the power of the Pipeline graphical workflow environment to enable integration of bioinformatics resources which provide a well-defined syntax for dynamic specification of the input/output parameters and the run-time execution controls. Conclusions The LONI Pipeline environment http://pipeline.loni.ucla.edu provides a flexible graphical infrastructure for efficient biomedical computing and distributed informatics research. The interactive Pipeline resource manager enables the utilization and interoperability of diverse types of informatics resources. The

  4. Visualization for genomics: the Microbial Genome Viewer.

    Science.gov (United States)

    Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

    2004-07-22

    A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

  5. Family genome browser: visualizing genomes with pedigree information.

    Science.gov (United States)

    Juan, Liran; Liu, Yongzhuang; Wang, Yongtian; Teng, Mingxiang; Zang, Tianyi; Wang, Yadong

    2015-07-15

    Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge. We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage disequilibriums, genes, variant effects, potential phenotypes, etc., are illustrated as well. Moreover, the FGB can automatically search de novo mutations and compound heterozygous variants for a selected individual, and guide investigators to find high-risk genes with flexible navigation options. These features enable users to investigate and understand family genomes intuitively and systematically. The FGB is available at http://mlg.hit.edu.cn/FGB/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  6. Genome U-Plot: a whole genome visualization.

    Science.gov (United States)

    Gaitatzes, Athanasios; Johnson, Sarah H; Smadbeck, James B; Vasmatzis, George

    2018-05-15

    The ability to produce and analyze whole genome sequencing (WGS) data from samples with structural variations (SV) generated the need to visualize such abnormalities in simplified plots. Conventional two-dimensional representations of WGS data frequently use either circular or linear layouts. There are several diverse advantages regarding both these representations, but their major disadvantage is that they do not use the two-dimensional space very efficiently. We propose a layout, termed the Genome U-Plot, which spreads the chromosomes on a two-dimensional surface and essentially quadruples the spatial resolution. We present the Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution and its improved aesthetic qualities. We compare conventional visualization schemas with the Genome U-Plot using visualization metrics such as number of line crossings and crossing angle resolution measures. Based on our metrics, we improve the readability of the resulting graph by at least 2-fold, making apparent important features and making it easy to identify important genomic changes. A whole genome visualization tool with high spatial resolution and improved aesthetic qualities. An implementation and documentation of the Genome U-Plot is publicly available at https://github.com/gaitat/GenomeUPlot. vasmatzis.george@mayo.edu. Supplementary data are available at Bioinformatics online.

  7. Visualizing conserved gene location across microbe genomes

    Science.gov (United States)

    Shaw, Chris D.

    2009-01-01

    This paper introduces an analysis-based zoomable visualization technique for displaying the location of genes across many related species of microbes. The purpose of this visualizatiuon is to enable a biologist to examine the layout of genes in the organism of interest with respect to the gene organization of related organisms. During the genomic annotation process, the ability to observe gene organization in common with previously annotated genomes can help a biologist better confirm the structure and function of newly analyzed microbe DNA sequences. We have developed a visualization and analysis tool that enables the biologist to observe and examine gene organization among genomes, in the context of the primary sequence of interest. This paper describes the visualization and analysis steps, and presents a case study using a number of Rickettsia genomes.

  8. Barcode server: a visualization-based genome analysis system.

    Directory of Open Access Journals (Sweden)

    Fenglou Mao

    Full Text Available We have previously developed a computational method for representing a genome as a barcode image, which makes various genomic features visually apparent. We have demonstrated that this visual capability has made some challenging genome analysis problems relatively easy to solve. We have applied this capability to a number of challenging problems, including (a identification of horizontally transferred genes, (b identification of genomic islands with special properties and (c binning of metagenomic sequences, and achieved highly encouraging results. These application results inspired us to develop this barcode-based genome analysis server for public service, which supports the following capabilities: (a calculation of the k-mer based barcode image for a provided DNA sequence; (b detection of sequence fragments in a given genome with distinct barcodes from those of the majority of the genome, (c clustering of provided DNA sequences into groups having similar barcodes; and (d homology-based search using Blast against a genome database for any selected genomic regions deemed to have interesting barcodes. The barcode server provides a job management capability, allowing processing of a large number of analysis jobs for barcode-based comparative genome analyses. The barcode server is accessible at http://csbl1.bmb.uga.edu/Barcode.

  9. Visual languages and applications

    CERN Document Server

    Zhang, Kang

    2010-01-01

    Visual languages have long been a pursuit of effective communication between human and machine. With rapid advances of the Internet and Web technology, human-human communication through the Web or electronic mobile devices is becoming more and more prevalent. Visual Languages and Applications is a comprehensive introduction to diagrammatical visual languages. This book discusses what visual programming languages are, and how such languages and their underlying foundations can be usefully applied to other fields in computer science. It also covers a broad range of contents from the underlying t

  10. Next generation tools for genomic data generation, distribution, and visualization

    Directory of Open Access Journals (Sweden)

    Nix David A

    2010-09-01

    Full Text Available Abstract Background With the rapidly falling cost and availability of high throughput sequencing and microarray technologies, the bottleneck for effectively using genomic analysis in the laboratory and clinic is shifting to one of effectively managing, analyzing, and sharing genomic data. Results Here we present three open-source, platform independent, software tools for generating, analyzing, distributing, and visualizing genomic data. These include a next generation sequencing/microarray LIMS and analysis project center (GNomEx; an application for annotating and programmatically distributing genomic data using the community vetted DAS/2 data exchange protocol (GenoPub; and a standalone Java Swing application (GWrap that makes cutting edge command line analysis tools available to those who prefer graphical user interfaces. Both GNomEx and GenoPub use the rich client Flex/Flash web browser interface to interact with Java classes and a relational database on a remote server. Both employ a public-private user-group security model enabling controlled distribution of patient and unpublished data alongside public resources. As such, they function as genomic data repositories that can be accessed manually or programmatically through DAS/2-enabled client applications such as the Integrated Genome Browser. Conclusions These tools have gained wide use in our core facilities, research laboratories and clinics and are freely available for non-profit use. See http://sourceforge.net/projects/gnomex/, http://sourceforge.net/projects/genoviz/, and http://sourceforge.net/projects/useq.

  11. Next generation tools for genomic data generation, distribution, and visualization.

    Science.gov (United States)

    Nix, David A; Di Sera, Tonya L; Dalley, Brian K; Milash, Brett A; Cundick, Robert M; Quinn, Kevin S; Courdy, Samir J

    2010-09-09

    With the rapidly falling cost and availability of high throughput sequencing and microarray technologies, the bottleneck for effectively using genomic analysis in the laboratory and clinic is shifting to one of effectively managing, analyzing, and sharing genomic data. Here we present three open-source, platform independent, software tools for generating, analyzing, distributing, and visualizing genomic data. These include a next generation sequencing/microarray LIMS and analysis project center (GNomEx); an application for annotating and programmatically distributing genomic data using the community vetted DAS/2 data exchange protocol (GenoPub); and a standalone Java Swing application (GWrap) that makes cutting edge command line analysis tools available to those who prefer graphical user interfaces. Both GNomEx and GenoPub use the rich client Flex/Flash web browser interface to interact with Java classes and a relational database on a remote server. Both employ a public-private user-group security model enabling controlled distribution of patient and unpublished data alongside public resources. As such, they function as genomic data repositories that can be accessed manually or programmatically through DAS/2-enabled client applications such as the Integrated Genome Browser. These tools have gained wide use in our core facilities, research laboratories and clinics and are freely available for non-profit use. See http://sourceforge.net/projects/gnomex/, http://sourceforge.net/projects/genoviz/, and http://sourceforge.net/projects/useq.

  12. Microreact: visualizing and sharing data for genomic epidemiology and phylogeography.

    Science.gov (United States)

    Argimón, Silvia; Abudahab, Khalil; Goater, Richard J E; Fedosejev, Artemij; Bhai, Jyothish; Glasner, Corinna; Feil, Edward J; Holden, Matthew T G; Yeats, Corin A; Grundmann, Hajo; Spratt, Brian G; Aanensen, David M

    2016-11-01

    Visualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple genomes as a tree provides a framework onto which associated data (geographical, temporal, phenotypic and epidemiological) are added to generate hypotheses and to explore the dynamics of the system under investigation. Selected static images are then used within publications to highlight the key findings to a wider audience. However, these images are a very inadequate way of exploring and interpreting the richness of the data. There is, therefore, a need for flexible, interactive software that presents the population genomic outputs and associated data in a user-friendly manner for a wide range of end users, from trained bioinformaticians to front-line epidemiologists and health workers. Here, we present Microreact, a web application for the easy visualization of datasets consisting of any combination of trees, geographical, temporal and associated metadata. Data files can be uploaded to Microreact directly via the web browser or by linking to their location (e.g. from Google Drive/Dropbox or via API), and an integrated visualization via trees, maps, timelines and tables provides interactive querying of the data. The visualization can be shared as a permanent web link among collaborators, or embedded within publications to enable readers to explore and download the data. Microreact can act as an end point for any tool or bioinformatic pipeline that ultimately generates a tree, and provides a simple, yet powerful, visualization method that will aid research and discovery and the open sharing of datasets.

  13. CrusView: a Java-based visualization platform for comparative genomics analyses in Brassicaceae species.

    Science.gov (United States)

    Chen, Hao; Wang, Xiangfeng

    2013-09-01

    In plants and animals, chromosomal breakage and fusion events based on conserved syntenic genomic blocks lead to conserved patterns of karyotype evolution among species of the same family. However, karyotype information has not been well utilized in genomic comparison studies. We present CrusView, a Java-based bioinformatic application utilizing Standard Widget Toolkit/Swing graphics libraries and a SQLite database for performing visualized analyses of comparative genomics data in Brassicaceae (crucifer) plants. Compared with similar software and databases, one of the unique features of CrusView is its integration of karyotype information when comparing two genomes. This feature allows users to perform karyotype-based genome assembly and karyotype-assisted genome synteny analyses with preset karyotype patterns of the Brassicaceae genomes. Additionally, CrusView is a local program, which gives its users high flexibility when analyzing unpublished genomes and allows users to upload self-defined genomic information so that they can visually study the associations between genome structural variations and genetic elements, including chromosomal rearrangements, genomic macrosynteny, gene families, high-frequency recombination sites, and tandem and segmental duplications between related species. This tool will greatly facilitate karyotype, chromosome, and genome evolution studies using visualized comparative genomics approaches in Brassicaceae species. CrusView is freely available at http://www.cmbb.arizona.edu/CrusView/.

  14. CAGO: a software tool for dynamic visual comparison and correlation measurement of genome organization.

    Directory of Open Access Journals (Sweden)

    Yi-Feng Chang

    Full Text Available CAGO (Comparative Analysis of Genome Organization is developed to address two critical shortcomings of conventional genome atlas plotters: lack of dynamic exploratory functions and absence of signal analysis for genomic properties. With dynamic exploratory functions, users can directly manipulate chromosome tracks of a genome atlas and intuitively identify distinct genomic signals by visual comparison. Signal analysis of genomic properties can further detect inconspicuous patterns from noisy genomic properties and calculate correlations between genomic properties across various genomes. To implement dynamic exploratory functions, CAGO presents each genome atlas in Scalable Vector Graphics (SVG format and allows users to interact with it using a SVG viewer through JavaScript. Signal analysis functions are implemented using R statistical software and a discrete wavelet transformation package waveslim. CAGO is not only a plotter for generating complex genome atlases, but also a platform for exploring genome atlases with dynamic exploratory functions for visual comparison and with signal analysis for comparing genomic properties across multiple organisms. The web-based application of CAGO, its source code, user guides, video demos, and live examples are publicly available and can be accessed at http://cbs.ym.edu.tw/cago.

  15. GenoSets: visual analytic methods for comparative genomics.

    Directory of Open Access Journals (Sweden)

    Aurora A Cain

    Full Text Available Many important questions in biology are, fundamentally, comparative, and this extends to our analysis of a growing number of sequenced genomes. Existing genomic analysis tools are often organized around literal views of genomes as linear strings. Even when information is highly condensed, these views grow cumbersome as larger numbers of genomes are added. Data aggregation and summarization methods from the field of visual analytics can provide abstracted comparative views, suitable for sifting large multi-genome datasets to identify critical similarities and differences. We introduce a software system for visual analysis of comparative genomics data. The system automates the process of data integration, and provides the analysis platform to identify and explore features of interest within these large datasets. GenoSets borrows techniques from business intelligence and visual analytics to provide a rich interface of interactive visualizations supported by a multi-dimensional data warehouse. In GenoSets, visual analytic approaches are used to enable querying based on orthology, functional assignment, and taxonomic or user-defined groupings of genomes. GenoSets links this information together with coordinated, interactive visualizations for both detailed and high-level categorical analysis of summarized data. GenoSets has been designed to simplify the exploration of multiple genome datasets and to facilitate reasoning about genomic comparisons. Case examples are included showing the use of this system in the analysis of 12 Brucella genomes. GenoSets software and the case study dataset are freely available at http://genosets.uncc.edu. We demonstrate that the integration of genomic data using a coordinated multiple view approach can simplify the exploration of large comparative genomic data sets, and facilitate reasoning about comparisons and features of interest.

  16. Genome Writing: Current Progress and Related Applications

    Directory of Open Access Journals (Sweden)

    Yueqiang Wang

    2018-02-01

    Full Text Available The ultimate goal of synthetic biology is to build customized cells or organisms to meet specific industrial or medical needs. The most important part of the customized cell is a synthetic genome. Advanced genomic writing technologies are required to build such an artificial genome. Recently, the partially-completed synthetic yeast genome project represents a milestone in this field. In this mini review, we briefly introduce the techniques for de novo genome synthesis and genome editing. Furthermore, we summarize recent research progresses and highlight several applications in the synthetic genome field. Finally, we discuss current challenges and future prospects. Keywords: Synthetic biology, Genome writing, Genome editing, Bioethics, Biosafety

  17. Application of Genomic In Situ Hybridization in Horticultural Science

    Directory of Open Access Journals (Sweden)

    Fahad Ramzan

    2017-01-01

    Full Text Available Molecular cytogenetic techniques, such as in situ hybridization methods, are admirable tools to analyze the genomic structure and function, chromosome constituents, recombination patterns, alien gene introgression, genome evolution, aneuploidy, and polyploidy and also genome constitution visualization and chromosome discrimination from different genomes in allopolyploids of various horticultural crops. Using GISH advancement as multicolor detection is a significant approach to analyze the small and numerous chromosomes in fruit species, for example, Diospyros hybrids. This analytical technique has proved to be the most exact and effective way for hybrid status confirmation and helps remarkably to distinguish donor parental genomes in hybrids such as Clivia, Rhododendron, and Lycoris ornamental hybrids. The genome characterization facilitates in hybrid selection having potential desirable characteristics during the early hybridization breeding, as this technique expedites to detect introgressed sequence chromosomes. This review study epitomizes applications and advancements of genomic in situ hybridization (GISH techniques in horticultural plants.

  18. Intervene: a tool for intersection and visualization of multiple gene or genomic region sets.

    Science.gov (United States)

    Khan, Aziz; Mathelier, Anthony

    2017-05-31

    A common task for scientists relies on comparing lists of genes or genomic regions derived from high-throughput sequencing experiments. While several tools exist to intersect and visualize sets of genes, similar tools dedicated to the visualization of genomic region sets are currently limited. To address this gap, we have developed the Intervene tool, which provides an easy and automated interface for the effective intersection and visualization of genomic region or list sets, thus facilitating their analysis and interpretation. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. Intervene, and its interactive web ShinyApp companion, generate publication-quality figures for the interpretation of genomic region and list sets. Intervene and its web application companion provide an easy command line and an interactive web interface to compute intersections of multiple genomic and list sets. They have the capacity to plot intersections using easy-to-interpret visual approaches. Intervene is developed and designed to meet the needs of both computer scientists and biologists. The source code is freely available at https://bitbucket.org/CBGR/intervene , with the web application available at https://asntech.shinyapps.io/intervene .

  19. The genome BLASTatlas - a GeneWiz extension for visualization of whole-genome homology

    DEFF Research Database (Denmark)

    Hallin, Peter Fischer; Binnewies, Tim Terence; Ussery, David

    2008-01-01

    ://www.cbs.dtu.dk/ws/BLASTatlas), where programming examples are available in Perl. By providing an interoperable method to carry out whole genome visualization of homology, this service offers bioinformaticians as well as biologists an easy-to-adopt workflow that can be directly called from the programming language of the user, hence......The development of fast and inexpensive methods for sequencing bacterial genomes has led to a wealth of data, often with many genomes being sequenced of the same species or closely related organisms. Thus, there is a need for visualization methods that will allow easy comparison of many sequenced...... genomes to a defined reference strain. The BLASTatlas is one such tool that is useful for mapping and visualizing whole genome homology of genes and proteins within a reference strain compared to other strains or species of one or more prokaryotic organisms. We provide examples of BLASTatlases, including...

  20. GeneViTo: Visualizing gene-product functional and structural features in genomic datasets

    Directory of Open Access Journals (Sweden)

    Promponas Vasilis J

    2003-10-01

    Full Text Available Abstract Background The availability of increasing amounts of sequence data from completely sequenced genomes boosts the development of new computational methods for automated genome annotation and comparative genomics. Therefore, there is a need for tools that facilitate the visualization of raw data and results produced by bioinformatics analysis, providing new means for interactive genome exploration. Visual inspection can be used as a basis to assess the quality of various analysis algorithms and to aid in-depth genomic studies. Results GeneViTo is a JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction. The application deals with various experimental information concerning both DNA and protein sequences (derived from public sequence databases or proprietary data sources and meta-data obtained by various prediction algorithms, classification schemes or user-defined features. Interaction with a Graphical User Interface (GUI allows easy extraction of genomic and proteomic data referring to the sequence itself, sequence features, or general structural and functional features. Emphasis is laid on the potential comparison between annotation and prediction data in order to offer a supplement to the provided information, especially in cases of "poor" annotation, or an evaluation of available predictions. Moreover, desired information can be output in high quality JPEG image files for further elaboration and scientific use. A compilation of properly formatted GeneViTo input data for demonstration is available to interested readers for two completely sequenced prokaryotes, Chlamydia trachomatis and Methanococcus jannaschii. Conclusions GeneViTo offers an inspectional view of genomic functional elements, concerning data stemming both from database annotation and analysis tools for an overall analysis of existing genomes. The application is compatible with Linux or Windows ME-2000-XP operating

  1. CrusView: A Java-Based Visualization Platform for Comparative Genomics Analyses in Brassicaceae Species[OPEN

    Science.gov (United States)

    Chen, Hao; Wang, Xiangfeng

    2013-01-01

    In plants and animals, chromosomal breakage and fusion events based on conserved syntenic genomic blocks lead to conserved patterns of karyotype evolution among species of the same family. However, karyotype information has not been well utilized in genomic comparison studies. We present CrusView, a Java-based bioinformatic application utilizing Standard Widget Toolkit/Swing graphics libraries and a SQLite database for performing visualized analyses of comparative genomics data in Brassicaceae (crucifer) plants. Compared with similar software and databases, one of the unique features of CrusView is its integration of karyotype information when comparing two genomes. This feature allows users to perform karyotype-based genome assembly and karyotype-assisted genome synteny analyses with preset karyotype patterns of the Brassicaceae genomes. Additionally, CrusView is a local program, which gives its users high flexibility when analyzing unpublished genomes and allows users to upload self-defined genomic information so that they can visually study the associations between genome structural variations and genetic elements, including chromosomal rearrangements, genomic macrosynteny, gene families, high-frequency recombination sites, and tandem and segmental duplications between related species. This tool will greatly facilitate karyotype, chromosome, and genome evolution studies using visualized comparative genomics approaches in Brassicaceae species. CrusView is freely available at http://www.cmbb.arizona.edu/CrusView/. PMID:23898041

  2. Savant Genome Browser 2: visualization and analysis for population-scale genomics.

    Science.gov (United States)

    Fiume, Marc; Smith, Eric J M; Brook, Andrew; Strbenac, Dario; Turner, Brian; Mezlini, Aziz M; Robinson, Mark D; Wodak, Shoshana J; Brudno, Michael

    2012-07-01

    High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data exploration and analysis capabilities. Although most existing tools for HTS data analysis are developed for either automated (e.g. genotyping) or visualization (e.g. genome browsing) purposes, such tools are most powerful when combined. For example, integration of visualization and computation allows users to iteratively refine their analyses by updating computational parameters within the visual framework in real-time. Here we introduce the second version of the Savant Genome Browser, a standalone program for visual and computational analysis of HTS data. Savant substantially improves upon its predecessor and existing tools by introducing innovative visualization modes and navigation interfaces for several genomic datatypes, and synergizing visual and automated analyses in a way that is powerful yet easy even for non-expert users. We also present a number of plugins that were developed by the Savant Community, which demonstrate the power of integrating visual and automated analyses using Savant. The Savant Genome Browser is freely available (open source) at www.savantbrowser.com.

  3. Meeting Report: Towards the Visualization of Genome Activity at Nanoscale Dimensions

    International Nuclear Information System (INIS)

    Ritland Politz, Joan C.

    2006-01-01

    A report on the Fifth Annual Nanostructural Genomics meeting, Bar Harbor, USA, 7-10 September 2005. It is a rare meeting where one can hear the latest developments in comparative genome analysis, relate these findings to advances in understanding both the linear and three-dimensional organization of the eukaryotic genome, and see it all beginning to fit into the context of the structure and function of the nucleus, visualized using state-of-the art labeling and microscopic techniques. These cross-disciplinary areas of research have been presented by a diverse group of scientists for the past five years at the Nanostructural Genomics meeting at the Jackson Laboratory in Bar Harbor, and the 2005 meeting again gave attendees much food for thought. In summary, the meeting provided a delightfully unique perspective on the application of exciting experimental breakthroughs at the interface of genomics, cell biology and optical physics.

  4. Visualizing the application of filters

    DEFF Research Database (Denmark)

    Rasmussen, Rasmus; Hertzum, Morten

    2013-01-01

    Through a mixed-design experiment we compare how emergency-department clinicians perform when solving realistic work tasks with an electronic whiteboard where the application of information filters is visualized either by blocking, colour-coding or blurring information. We find that clinicians...... perform significantly faster and with less effort and temporal demand when using the blocking interface. However, we also find that the colour-coding interface provides clinicians with a better overview of the information displayed by the electronic whiteboard. The blurring interface did not perform...

  5. Visualization of RNA structure models within the Integrative Genomics Viewer.

    Science.gov (United States)

    Busan, Steven; Weeks, Kevin M

    2017-07-01

    Analyses of the interrelationships between RNA structure and function are increasingly important components of genomic studies. The SHAPE-MaP strategy enables accurate RNA structure probing and realistic structure modeling of kilobase-length noncoding RNAs and mRNAs. Existing tools for visualizing RNA structure models are not suitable for efficient analysis of long, structurally heterogeneous RNAs. In addition, structure models are often advantageously interpreted in the context of other experimental data and gene annotation information, for which few tools currently exist. We have developed a module within the widely used and well supported open-source Integrative Genomics Viewer (IGV) that allows visualization of SHAPE and other chemical probing data, including raw reactivities, data-driven structural entropies, and data-constrained base-pair secondary structure models, in context with linear genomic data tracks. We illustrate the usefulness of visualizing RNA structure in the IGV by exploring structure models for a large viral RNA genome, comparing bacterial mRNA structure in cells with its structure under cell- and protein-free conditions, and comparing a noncoding RNA structure modeled using SHAPE data with a base-pairing model inferred through sequence covariation analysis. © 2017 Busan and Weeks; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  6. The Application of Visual Illusion in the Visual Communication Design

    Science.gov (United States)

    Xin, Tao; You Ye, Han

    2018-03-01

    With the development of our national reform, opening up and modernization, the science and technology has also been well developed and it has been applied in every wall of life, the development of visual illusion industry is represented in the widespread use of advanced technology in it. Ultimately, the visual illusion is a phenomenon, it should be analyzed from the angles of physics and philosophy. The widespread application of visual illusion not only can improve the picture quality, but also could maximize peoples’ sense degree through the visual communication design works, expand people’s horizons and promote the diversity of visual communication design works.

  7. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.

    Science.gov (United States)

    Thorvaldsdóttir, Helga; Robinson, James T; Mesirov, Jill P

    2013-03-01

    Data visualization is an essential component of genomic data analysis. However, the size and diversity of the data sets produced by today's sequencing and array-based profiling methods present major challenges to visualization tools. The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of IGV is its focus on the integrative nature of genomic studies, with support for both array-based and next-generation sequencing data, and the integration of clinical and phenotypic data. Although IGV is often used to view genomic data from public sources, its primary emphasis is to support researchers who wish to visualize and explore their own data sets or those from colleagues. To that end, IGV supports flexible loading of local and remote data sets, and is optimized to provide high-performance data visualization and exploration on standard desktop systems. IGV is freely available for download from http://www.broadinstitute.org/igv, under a GNU LGPL open-source license.

  8. KENeV: A web-application for the automated reconstruction and visualization of the enriched metabolic and signaling super-pathways deriving from genomic experiments

    Directory of Open Access Journals (Sweden)

    Eleftherios Pilalis

    2015-01-01

    In conclusion, KENeV (available online at http://www.grissom.gr/kenev provides an integrative tool, suitable for users with no programming experience, for the functional interpretation, at both the metabolic and signaling level, of differentially expressed gene subsets deriving from genomic experiments.

  9. Genovar: a detection and visualization tool for genomic variants.

    Science.gov (United States)

    Jung, Kwang Su; Moon, Sanghoon; Kim, Young Jin; Kim, Bong-Jo; Park, Kiejung

    2012-05-08

    Along with single nucleotide polymorphisms (SNPs), copy number variation (CNV) is considered an important source of genetic variation associated with disease susceptibility. Despite the importance of CNV, the tools currently available for its analysis often produce false positive results due to limitations such as low resolution of array platforms, platform specificity, and the type of CNV. To resolve this problem, spurious signals must be separated from true signals by visual inspection. None of the previously reported CNV analysis tools support this function and the simultaneous visualization of comparative genomic hybridization arrays (aCGH) and sequence alignment. The purpose of the present study was to develop a useful program for the efficient detection and visualization of CNV regions that enables the manual exclusion of erroneous signals. A JAVA-based stand-alone program called Genovar was developed. To ascertain whether a detected CNV region is a novel variant, Genovar compares the detected CNV regions with previously reported CNV regions using the Database of Genomic Variants (DGV, http://projects.tcag.ca/variation) and the Single Nucleotide Polymorphism Database (dbSNP). The current version of Genovar is capable of visualizing genomic data from sources such as the aCGH data file and sequence alignment format files. Genovar is freely accessible and provides a user-friendly graphic user interface (GUI) to facilitate the detection of CNV regions. The program also provides comprehensive information to help in the elimination of spurious signals by visual inspection, making Genovar a valuable tool for reducing false positive CNV results. http://genovar.sourceforge.net/.

  10. Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web.

    Science.gov (United States)

    Miller, Chase A; Anthony, Jon; Meyer, Michelle M; Marth, Gabor

    2013-02-01

    High-throughput biological research requires simultaneous visualization as well as analysis of genomic data, e.g. read alignments, variant calls and genomic annotations. Traditionally, such integrative analysis required desktop applications operating on locally stored data. Many current terabyte-size datasets generated by large public consortia projects, however, are already only feasibly stored at specialist genome analysis centers. As even small laboratories can afford very large datasets, local storage and analysis are becoming increasingly limiting, and it is likely that most such datasets will soon be stored remotely, e.g. in the cloud. These developments will require web-based tools that enable users to access, analyze and view vast remotely stored data with a level of sophistication and interactivity that approximates desktop applications. As rapidly dropping cost enables researchers to collect data intended to answer questions in very specialized contexts, developers must also provide software libraries that empower users to implement customized data analyses and data views for their particular application. Such specialized, yet lightweight, applications would empower scientists to better answer specific biological questions than possible with general-purpose genome browsers currently available. Using recent advances in core web technologies (HTML5), we developed Scribl, a flexible genomic visualization library specifically targeting coordinate-based data such as genomic features, DNA sequence and genetic variants. Scribl simplifies the development of sophisticated web-based graphical tools that approach the dynamism and interactivity of desktop applications. Software is freely available online at http://chmille4.github.com/Scribl/ and is implemented in JavaScript with all modern browsers supported.

  11. Tetrahedral gray code for visualization of genome information.

    Directory of Open Access Journals (Sweden)

    Natsuhiro Ichinose

    Full Text Available We propose a tetrahedral Gray code that facilitates visualization of genome information on the surfaces of a tetrahedron, where the relative abundance of each [Formula: see text]-mer in the genomic sequence is represented by a color of the corresponding cell of a triangular lattice. For biological significance, the code is designed such that the [Formula: see text]-mers corresponding to any adjacent pair of cells differ from each other by only one nucleotide. We present a simple procedure to draw such a pattern on the development surfaces of a tetrahedron. The thus constructed tetrahedral Gray code can demonstrate evolutionary conservation and variation of the genome information of many organisms at a glance. We also apply the tetrahedral Gray code to the honey bee (Apis mellifera genome to analyze its methylation structure. The results indicate that the honey bee genome exhibits CpG overrepresentation in spite of its methylation ability and that two conserved motifs, CTCGAG and CGCGCG, in the unmethylated regions are responsible for the overrepresentation of CpG.

  12. Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny.

    Science.gov (United States)

    Cleary, Alan; Farmer, Andrew

    2018-05-01

    The Genome Context Viewer is a visual data-mining tool that allows users to search across multiple providers of genome data for regions with similarly annotated content that may be aligned and visualized at the level of their shared functional elements. By handling ordered sequences of gene family memberships as a unit of search and comparison, the user interface enables quick and intuitive assessment of the degree of gene content divergence and the presence of various types of structural events within syntenic contexts. Insights into functionally significant differences seen at this level of abstraction can then serve to direct the user to more detailed explorations of the underlying data in other interconnected, provider-specific tools. GCV is provided under the GNU General Public License version 3 (GPL-3.0). Source code is available at https://github.com/legumeinfo/lis_context_viewer. adf@ncgr.org. Supplementary data are available at Bioinformatics online.

  13. Live visualization of genomic loci with BiFC-TALE.

    Science.gov (United States)

    Hu, Huan; Zhang, Hongmin; Wang, Sheng; Ding, Miao; An, Hui; Hou, Yingping; Yang, Xiaojing; Wei, Wensheng; Sun, Yujie; Tang, Chao

    2017-01-11

    Tracking the dynamics of genomic loci is important for understanding the mechanisms of fundamental intracellular processes. However, fluorescent labeling and imaging of such loci in live cells have been challenging. One of the major reasons is the low signal-to-background ratio (SBR) of images mainly caused by the background fluorescence from diffuse full-length fluorescent proteins (FPs) in the living nucleus, hampering the application of live cell genomic labeling methods. Here, combining bimolecular fluorescence complementation (BiFC) and transcription activator-like effector (TALE) technologies, we developed a novel method for labeling genomic loci (BiFC-TALE), which largely reduces the background fluorescence level. Using BiFC-TALE, we demonstrated a significantly improved SBR by imaging telomeres and centromeres in living cells in comparison with the methods using full-length FP.

  14. GFFview: A Web Server for Parsing and Visualizing Annotation Information of Eukaryotic Genome.

    Science.gov (United States)

    Deng, Feilong; Chen, Shi-Yi; Wu, Zhou-Lin; Hu, Yongsong; Jia, Xianbo; Lai, Song-Jia

    2017-10-01

    Owing to wide application of RNA sequencing (RNA-seq) technology, more and more eukaryotic genomes have been extensively annotated, such as the gene structure, alternative splicing, and noncoding loci. Annotation information of genome is prevalently stored as plain text in General Feature Format (GFF), which could be hundreds or thousands Mb in size. Therefore, it is a challenge for manipulating GFF file for biologists who have no bioinformatic skill. In this study, we provide a web server (GFFview) for parsing the annotation information of eukaryotic genome and then generating statistical description of six indices for visualization. GFFview is very useful for investigating quality and difference of the de novo assembled transcriptome in RNA-seq studies.

  15. SPOCS: Software for Predicting and Visualizing Orthology/Paralogy Relationships Among Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Curtis, Darren S.; Phillips, Aaron R.; Callister, Stephen J.; Conlan, Sean; McCue, Lee Ann

    2013-10-15

    At the rate that prokaryotic genomes can now be generated, comparative genomics studies require a flexible method for quickly and accurately predicting orthologs among the rapidly changing set of genomes available. SPOCS implements a graph-based ortholog prediction method to generate a simple tab-delimited table of orthologs and in addition, html files that provide a visualization of the predicted ortholog/paralog relationships to which gene/protein expression metadata may be overlaid. AVAILABILITY AND IMPLEMENTATION: A SPOCS web application is freely available at http://cbb.pnnl.gov/portal/tools/spocs.html. Source code for Linux systems is also freely available under an open source license at http://cbb.pnnl.gov/portal/software/spocs.html; the Boost C++ libraries and BLAST are required.

  16. Genomic applications in forensic medicine

    DEFF Research Database (Denmark)

    Børsting, Claus; Morling, Niels

    2016-01-01

    Since the 1980s, advances in DNA technology have revolutionized the scope and practice of forensic medicine. From the days of restriction fragment length polymorphisms (RFLPs) to short tandem repeats (STRs), the current focus is on the next generation genome sequencing. It has been almost a decad...

  17. Interactive data visualization foundations, techniques, and applications

    CERN Document Server

    Ward, Matthew; Keim, Daniel

    2010-01-01

    Visualization is the process of representing data, information, and knowledge in a visual form to support the tasks of exploration, confirmation, presentation, and understanding. This book is designed as a textbook for students, researchers, analysts, professionals, and designers of visualization techniques, tools, and systems. It covers the full spectrum of the field, including mathematical and analytical aspects, ranging from its foundations to human visual perception; from coded algorithms for different types of data, information and tasks to the design and evaluation of new visualization techniques. Sample programs are provided as starting points for building one's own visualization tools. Numerous data sets have been made available that highlight different application areas and allow readers to evaluate the strengths and weaknesses of different visualization methods. Exercises, programming projects, and related readings are given for each chapter. The book concludes with an examination of several existin...

  18. Visual Attention and Applications in Multimedia Technologies

    OpenAIRE

    Le Callet, Patrick; Niebur, Ernst

    2013-01-01

    Making technological advances in the field of human-machine interactions requires that the capabilities and limitations of the human perceptual system are taken into account. The focus of this report is an important mechanism of perception, visual selective attention, which is becoming more and more important for multimedia applications. We introduce the concept of visual attention and describe its underlying mechanisms. In particular, we introduce the concepts of overt and covert visual atte...

  19. Applications of visual soil evaluation

    DEFF Research Database (Denmark)

    Ball, Bruce C; Munkholm, Lars Juhl; Batey, Tom

    2013-01-01

    Working Group F “Visual Soil Examination and Evaluation” (VSEE) was formed over 30 years ago within the International Soil & Tillage Research Organisation (ISTRO) on the initiative of Tom Batey. The objectives of the Working Group are to stimulate interest in field methods of visual-tactile soil...... assessment, to encourage their wider use and to foster international cooperation. The previous main meeting of the group in 2005 at Peronne, France, brought together, for the first time, a group of soil scientists who had each developed a method to evaluate soil structure directly in the field (Boizard et al...... to the re-development of the Peerlkamp numeric method of assessment of soil structure into the Visual Evaluation of Soil Structure (VESS) spade test (Ball et al., 2007 and Guimarães et al., 2011). The meeting also recommended further cooperation between members of the Working Group. The evaluation...

  20. Visual Learning in Application of Integration

    Science.gov (United States)

    Bt Shafie, Afza; Barnachea Janier, Josefina; Bt Wan Ahmad, Wan Fatimah

    Innovative use of technology can improve the way how Mathematics should be taught. It can enhance student's learning the concepts through visualization. Visualization in Mathematics refers to us of texts, pictures, graphs and animations to hold the attention of the learners in order to learn the concepts. This paper describes the use of a developed multimedia courseware as an effective tool for visual learning mathematics. The focus is on the application of integration which is a topic in Engineering Mathematics 2. The course is offered to the foundation students in the Universiti Teknologi of PETRONAS. Questionnaire has been distributed to get a feedback on the visual representation and students' attitudes towards using visual representation as a learning tool. The questionnaire consists of 3 sections: Courseware Design (Part A), courseware usability (Part B) and attitudes towards using the courseware (Part C). The results showed that students demonstrated the use of visual representation has benefited them in learning the topic.

  1. [Genomic selection and its application].

    Science.gov (United States)

    Li, Heng-De; Bao, Zhen-Min; Sun, Xiao-Wen

    2011-12-01

    Selective breeding is very important in agricultural production and breeding value estimation is the core of selective breeding. With the development of genetic markers, especially high throughput genotyping technology, it becomes available to estimate breeding value at genome level, i.e. genomic selection (GS). In this review, the methods of GS was categorized into two groups: one is to predict genomic estimated breeding value (GEBV) based on the allele effect, such as least squares, random regression - best linear unbiased prediction (RR-BLUP), Bayes and principle component analysis, etc; the other is to predict GEBV with genetic relationship matrix, which constructs genetic relationship matrix via high throughput genetic markers and then predicts GEBV through linear mixed model, i.e. GBLUP. The basic principles of these methods were also introduced according to the above two classifications. Factors affecting GS accuracy include markers of type and density, length of haplotype, the size of reference population, the extent between marker-QTL and so on. Among the methods of GS, Bayes and GBLUP are usually more accurate than the others and least squares is the worst. GBLUP is time-efficient and can combine pedigree with genotypic information, hence it is superior to other methods. Although progress was made in GS, there are still some challenges, for examples, united breeding, long-term genetic gain with GS, and disentangling markers with and without contribution to the traits. GS has been applied in animal and plant breeding practice and also has the potential to predict genetic predisposition in humans and study evolutionary dynamics. GS, which is more precise than the traditional method, is a breakthrough at measuring genetic relationship. Therefore, GS will be a revolutionary event in the history of animal and plant breeding.

  2. LocusTrack: Integrated visualization of GWAS results and genomic annotation.

    Science.gov (United States)

    Cuellar-Partida, Gabriel; Renteria, Miguel E; MacGregor, Stuart

    2015-01-01

    Genome-wide association studies (GWAS) are an important tool for the mapping of complex traits and diseases. Visual inspection of genomic annotations may be used to generate insights into the biological mechanisms underlying GWAS-identified loci. We developed LocusTrack, a web-based application that annotates and creates plots of regional GWAS results and incorporates user-specified tracks that display annotations such as linkage disequilibrium (LD), phylogenetic conservation, chromatin state, and other genomic and regulatory elements. Currently, LocusTrack can integrate annotation tracks from the UCSC genome-browser as well as from any tracks provided by the user. LocusTrack is an easy-to-use application and can be accessed at the following URL: http://gump.qimr.edu.au/general/gabrieC/LocusTrack/. Users can upload and manage GWAS results and select from and/or provide annotation tracks using simple and intuitive menus. LocusTrack scripts and associated data can be downloaded from the website and run locally.

  3. Cytoscape: the network visualization tool for GenomeSpace workflows [v2; ref status: indexed, http://f1000r.es/47f

    Directory of Open Access Journals (Sweden)

    Barry Demchak

    2014-08-01

    Full Text Available Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013.

  4. Cytoscape: the network visualization tool for GenomeSpace workflows [v1; ref status: indexed, http://f1000r.es/3ph

    Directory of Open Access Journals (Sweden)

    Barry Demchak

    2014-07-01

    Full Text Available Modern genomic analysis often requires workflows incorporating multiple best-ofbreed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded it over 850 times since the release of its first version in September, 2013.

  5. GAViT: Genome Assembly Visualization Tool for Short Read Data

    Energy Technology Data Exchange (ETDEWEB)

    Syed, Aijazuddin; Shapiro, Harris; Tu, Hank; Pangilinan, Jasmyn; Trong, Stephan

    2008-03-14

    It is a challenging job for genome analysts to accurately debug, troubleshoot, and validate genome assembly results. Genome analysts rely on visualization tools to help validate and troubleshoot assembly results, including such problems as mis-assemblies, low-quality regions, and repeats. Short read data adds further complexity and makes it extremely challenging for the visualization tools to scale and to view all needed assembly information. As a result, there is a need for a visualization tool that can scale to display assembly data from the new sequencing technologies. We present Genome Assembly Visualization Tool (GAViT), a highly scalable and interactive assembly visualization tool developed at the DOE Joint Genome Institute (JGI).

  6. Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

    DEFF Research Database (Denmark)

    King, Zachary A.; Draeger, Andreas; Ebrahim, Ali

    2015-01-01

    Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users c...... of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools....

  7. FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context.

    Science.gov (United States)

    Mader, Malte; Simon, Ronald; Steinbiss, Sascha; Kurtz, Stefan

    2011-07-28

    The rapidly growing amount of array CGH data requires improved visualization software supporting the process of identifying candidate cancer genes. Optimally, such software should work across multiple microarray platforms, should be able to cope with data from different sources and should be easy to operate. We have developed a web-based software FISH Oracle to visualize data from multiple array CGH experiments in a genomic context. Its fast visualization engine and advanced web and database technology supports highly interactive use. FISH Oracle comes with a convenient data import mechanism, powerful search options for genomic elements (e.g. gene names or karyobands), quick navigation and zooming into interesting regions, and mechanisms to export the visualization into different high quality formats. These features make the software especially suitable for the needs of life scientists. FISH Oracle offers a fast and easy to use visualization tool for array CGH and SNP array data. It allows for the identification of genomic regions representing minimal common changes based on data from one or more experiments. FISH Oracle will be instrumental to identify candidate onco and tumor suppressor genes based on the frequency and genomic position of DNA copy number changes. The FISH Oracle application and an installed demo web server are available at http://www.zbh.uni-hamburg.de/fishoracle.

  8. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.

    Science.gov (United States)

    Treangen, Todd J; Ondov, Brian D; Koren, Sergey; Phillippy, Adam M

    2014-01-01

    Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of multiple sequences simultaneously. Here we present the Harvest suite of core-genome alignment and visualization tools for the rapid and simultaneous analysis of thousands of intraspecific microbial strains. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Together they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees. Using simulated and real data we demonstrate that our approach exhibits unrivaled speed while maintaining the accuracy of existing methods. The Harvest suite is open-source and freely available from: http://github.com/marbl/harvest.

  9. Machine learning applications in genetics and genomics.

    Science.gov (United States)

    Libbrecht, Maxwell W; Noble, William Stafford

    2015-06-01

    The field of machine learning, which aims to develop computer algorithms that improve with experience, holds promise to enable computers to assist humans in the analysis of large, complex data sets. Here, we provide an overview of machine learning applications for the analysis of genome sequencing data sets, including the annotation of sequence elements and epigenetic, proteomic or metabolomic data. We present considerations and recurrent challenges in the application of supervised, semi-supervised and unsupervised machine learning methods, as well as of generative and discriminative modelling approaches. We provide general guidelines to assist in the selection of these machine learning methods and their practical application for the analysis of genetic and genomic data sets.

  10. A New Approach to Dissect Nuclear Organization: TALE-Mediated Genome Visualization (TGV).

    Science.gov (United States)

    Miyanari, Yusuke

    2016-01-01

    Spatiotemporal organization of chromatin within the nucleus has so far remained elusive. Live visualization of nuclear remodeling could be a promising approach to understand its functional relevance in genome functions and mechanisms regulating genome architecture. Recent technological advances in live imaging of chromosomes begun to explore the biological roles of the movement of the chromatin within the nucleus. Here I describe a new technique, called TALE-mediated genome visualization (TGV), which allows us to visualize endogenous repetitive sequence including centromeric, pericentromeric, and telomeric repeats in living cells.

  11. Visual Basic Applications to Physics Teaching

    Science.gov (United States)

    Chitu, Catalin; Inpuscatu, Razvan Constantin; Viziru, Marilena

    2011-01-01

    Derived from basic language, VB (Visual Basic) is a programming language focused on the video interface component. With graphics and functional components implemented, the programmer is able to bring and use their components to achieve the desired application in a relatively short time. Language VB is a useful tool in physics teaching by creating…

  12. GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants.

    Science.gov (United States)

    Tebel, Katrin; Boldt, Vivien; Steininger, Anne; Port, Matthias; Ebert, Grit; Ullmann, Reinhard

    2017-01-06

    The analysis of DNA copy number variants (CNV) has increasing impact in the field of genetic diagnostics and research. However, the interpretation of CNV data derived from high resolution array CGH or NGS platforms is complicated by the considerable variability of the human genome. Therefore, tools for multidimensional data analysis and comparison of patient cohorts are needed to assist in the discrimination of clinically relevant CNVs from others. We developed GenomeCAT, a standalone Java application for the analysis and integrative visualization of CNVs. GenomeCAT is composed of three modules dedicated to the inspection of single cases, comparative analysis of multidimensional data and group comparisons aiming at the identification of recurrent aberrations in patients sharing the same phenotype, respectively. Its flexible import options ease the comparative analysis of own results derived from microarray or NGS platforms with data from literature or public depositories. Multidimensional data obtained from different experiment types can be merged into a common data matrix to enable common visualization and analysis. All results are stored in the integrated MySQL database, but can also be exported as tab delimited files for further statistical calculations in external programs. GenomeCAT offers a broad spectrum of visualization and analysis tools that assist in the evaluation of CNVs in the context of other experiment data and annotations. The use of GenomeCAT does not require any specialized computer skills. The various R packages implemented for data analysis are fully integrated into GenomeCATs graphical user interface and the installation process is supported by a wizard. The flexibility in terms of data import and export in combination with the ability to create a common data matrix makes the program also well suited as an interface between genomic data from heterogeneous sources and external software tools. Due to the modular architecture the functionality of

  13. Explorative visual analytics on interval-based genomic data and their metadata.

    Science.gov (United States)

    Jalili, Vahid; Matteucci, Matteo; Masseroli, Marco; Ceri, Stefano

    2017-12-04

    With the wide-spreading of public repositories of NGS processed data, the availability of user-friendly and effective tools for data exploration, analysis and visualization is becoming very relevant. These tools enable interactive analytics, an exploratory approach for the seamless "sense-making" of data through on-the-fly integration of analysis and visualization phases, suggested not only for evaluating processing results, but also for designing and adapting NGS data analysis pipelines. This paper presents abstractions for supporting the early analysis of NGS processed data and their implementation in an associated tool, named GenoMetric Space Explorer (GeMSE). This tool serves the needs of the GenoMetric Query Language, an innovative cloud-based system for computing complex queries over heterogeneous processed data. It can also be used starting from any text files in standard BED, BroadPeak, NarrowPeak, GTF, or general tab-delimited format, containing numerical features of genomic regions; metadata can be provided as text files in tab-delimited attribute-value format. GeMSE allows interactive analytics, consisting of on-the-fly cycling among steps of data exploration, analysis and visualization that help biologists and bioinformaticians in making sense of heterogeneous genomic datasets. By means of an explorative interaction support, users can trace past activities and quickly recover their results, seamlessly going backward and forward in the analysis steps and comparative visualizations of heatmaps. GeMSE effective application and practical usefulness is demonstrated through significant use cases of biological interest. GeMSE is available at http://www.bioinformatics.deib.polimi.it/GeMSE/ , and its source code is available at https://github.com/Genometric/GeMSE under GPLv3 open-source license.

  14. Normalization of Complete Genome Characteristics: Application to Evolution from Primitive Organisms to Homo sapiens.

    Science.gov (United States)

    Sorimachi, Kenji; Okayasu, Teiji; Ohhira, Shuji

    2015-04-01

    Normalized nucleotide and amino acid contents of complete genome sequences can be visualized as radar charts. The shapes of these charts depict the characteristics of an organism's genome. The normalized values calculated from the genome sequence theoretically exclude experimental errors. Further, because normalization is independent of both target size and kind, this procedure is applicable not only to single genes but also to whole genomes, which consist of a huge number of different genes. In this review, we discuss the applications of the normalization of the nucleotide and predicted amino acid contents of complete genomes to the investigation of genome structure and to evolutionary research from primitive organisms to Homo sapiens. Some of the results could never have been obtained from the analysis of individual nucleotide or amino acid sequences but were revealed only after the normalization of nucleotide and amino acid contents was applied to genome research. The discovery that genome structure was homogeneous was obtained only after normalization methods were applied to the nucleotide or predicted amino acid contents of genome sequences. Normalization procedures are also applicable to evolutionary research. Thus, normalization of the contents of whole genomes is a useful procedure that can help to characterize organisms.

  15. Zipper plot: visualizing transcriptional activity of genomic regions.

    Science.gov (United States)

    Avila Cobos, Francisco; Anckaert, Jasper; Volders, Pieter-Jan; Everaert, Celine; Rombaut, Dries; Vandesompele, Jo; De Preter, Katleen; Mestdagh, Pieter

    2017-05-02

    Reconstructing transcript models from RNA-sequencing (RNA-seq) data and establishing these as independent transcriptional units can be a challenging task. Current state-of-the-art tools for long non-coding RNA (lncRNA) annotation are mainly based on evolutionary constraints, which may result in false negatives due to the overall limited conservation of lncRNAs. To tackle this problem we have developed the Zipper plot, a novel visualization and analysis method that enables users to simultaneously interrogate thousands of human putative transcription start sites (TSSs) in relation to various features that are indicative for transcriptional activity. These include publicly available CAGE-sequencing, ChIP-sequencing and DNase-sequencing datasets. Our method only requires three tab-separated fields (chromosome, genomic coordinate of the TSS and strand) as input and generates a report that includes a detailed summary table, a Zipper plot and several statistics derived from this plot. Using the Zipper plot, we found evidence of transcription for a set of well-characterized lncRNAs and observed that fewer mono-exonic lncRNAs have CAGE peaks overlapping with their TSSs compared to multi-exonic lncRNAs. Using publicly available RNA-seq data, we found more than one hundred cases where junction reads connected protein-coding gene exons with a downstream mono-exonic lncRNA, revealing the need for a careful evaluation of lncRNA 5'-boundaries. Our method is implemented using the statistical programming language R and is freely available as a webtool.

  16. Genomics and proteomics: Applications in autoimmune diseases

    Directory of Open Access Journals (Sweden)

    Wolfgang Hueber

    2009-08-01

    Full Text Available Wolfgang Hueber1,2,3, William H Robinson1,21VA Palo Alto Health Care System, Palo Alto, CA, USA; 2Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA; 3Novartis Institutes of Biomedical Research, Novartis, Basle, SwitzerlandAbstract: Tremendous progress has been made over the past decade in the development and refinement of genomic and proteomic technologies for the identification of novel drug targets and molecular signatures associated with clinically important disease states, disease subsets, or differential responses to therapies. The rapid progress in high-throughput technologies has been preceded and paralleled by the elucidation of cytokine networks, followed by the stepwise clinical development of pathway-specific biological therapies that revolutionized the treatment of autoimmune diseases. Together, these advances provide opportunities for a long-anticipated personalized medicine approach to the treatment of autoimmune disease. The ever-increasing numbers of novel, innovative therapies will need to be harnessed wisely to achieve optimal long-term outcomes in as many patients as possible while complying with the demands of health authorities and health care providers for evidence-based, economically sound prescription of these expensive drugs. Genomic and proteomic profiling of patients with autoimmune diseases holds great promise in two major clinical areas: (1 rapid identification of new targets for the development of innovative therapies and (2 identification of patients who will experience optimal benefit and minimal risk from a specific (targeted therapy. In this review, we attempt to capture important recent developments in the application of genomic and proteomic technologies to translational research by discussing informative examples covering a diversity of autoimmune diseases.Keywords: proteomics, genomics, autoimmune diseases, antigen microarrays, 2-Dih, rheumatoid arthritis

  17. FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research.

    Science.gov (United States)

    Mader, Malte; Simon, Ronald; Kurtz, Stefan

    2014-03-31

    A comprehensive view on all relevant genomic data is instrumental for understanding the complex patterns of molecular alterations typically found in cancer cells. One of the most effective ways to rapidly obtain an overview of genomic alterations in large amounts of genomic data is the integrative visualization of genomic events. We developed FISH Oracle 2, a web server for the interactive visualization of different kinds of downstream processed genomics data typically available in cancer research. A powerful search interface and a fast visualization engine provide a highly interactive visualization for such data. High quality image export enables the life scientist to easily communicate their results. A comprehensive data administration allows to keep track of the available data sets. We applied FISH Oracle 2 to published data and found evidence that, in colorectal cancer cells, the gene TTC28 may be inactivated in two different ways, a fact that has not been published before. The interactive nature of FISH Oracle 2 and the possibility to store, select and visualize large amounts of downstream processed data support life scientists in generating hypotheses. The export of high quality images supports explanatory data visualization, simplifying the communication of new biological findings. A FISH Oracle 2 demo server and the software is available at http://www.zbh.uni-hamburg.de/fishoracle.

  18. VarB Plus: An Integrated Tool for Visualization of Genome Variation Datasets

    KAUST Repository

    Hidayah, Lailatul

    2012-07-01

    Research on genomic sequences has been improving significantly as more advanced technology for sequencing has been developed. This opens enormous opportunities for sequence analysis. Various analytical tools have been built for purposes such as sequence assembly, read alignments, genome browsing, comparative genomics, and visualization. From the visualization perspective, there is an increasing trend towards use of large-scale computation. However, more than power is required to produce an informative image. This is a challenge that we address by providing several ways of representing biological data in order to advance the inference endeavors of biologists. This thesis focuses on visualization of variations found in genomic sequences. We develop several visualization functions and embed them in an existing variation visualization tool as extensions. The tool we improved is named VarB, hence the nomenclature for our enhancement is VarB Plus. To the best of our knowledge, besides VarB, there is no tool that provides the capability of dynamic visualization of genome variation datasets as well as statistical analysis. Dynamic visualization allows users to toggle different parameters on and off and see the results on the fly. The statistical analysis includes Fixation Index, Relative Variant Density, and Tajima’s D. Hence we focused our efforts on this tool. The scope of our work includes plots of per-base genome coverage, Principal Coordinate Analysis (PCoA), integration with a read alignment viewer named LookSeq, and visualization of geo-biological data. In addition to description of embedded functionalities, significance, and limitations, future improvements are discussed. The result is four extensions embedded successfully in the original tool, which is built on the Qt framework in C++. Hence it is portable to numerous platforms. Our extensions have shown acceptable execution time in a beta testing with various high-volume published datasets, as well as positive

  19. Visualization of Genome Diversity in German Shepherd Dogs

    OpenAIRE

    Sally-Anne Mortlock; Rachel Booth; Hamutal Mazrier; Mehar S. Khatkar; Peter Williamson

    2016-01-01

    A loss of genetic diversity may lead to increased disease risks in subpopulations of dogs. The canine breed structure has contributed to relatively small effective population size in many breeds and can limit the options for selective breeding strategies to maintain diversity. With the completion of the canine genome sequencing project, and the subsequent reduction in the cost of genotyping on a genomic scale, evaluating diversity in dogs has become much more accurate and accessible. This pro...

  20. A Stereographic Visualization Environment and its Applications

    Energy Technology Data Exchange (ETDEWEB)

    Peskin, A.M.; Andrews, A.B.

    1999-04-12

    The data visualization activity at Brookhaven National Laboratory is rooted in programs extending back several decades to develop, evaluate and deploy imaging instruments. Several of these developments, such as Magnetic Resonance Imaging (MRI) and Positron Emission Tomography (PET) technology, were targeted for medical imaging. Other applications made use of images derived from larger, general purpose scientific instruments such as the Laboratory's nuclear reactors and particle accelerators. The most recent impetus to the program has been from a cooperative research and development project between BNL and two industrial companies, GTE and Mobil Oil involving microtomographic imaging of oil reservoir rock, which included development of a novel stereoscopic visualization theatre. This 'Vis Theatre' has been subsequently used for research in other scientific disciplines, and has attracted considerable attention in both the technical literature and even the popular press.

  1. Cloud Based Resource for Data Hosting, Visualization and Analysis Using UCSC Cancer Genomics Browser | Informatics Technology for Cancer Research (ITCR)

    Science.gov (United States)

    The Cancer Analysis Virtual Machine (CAVM) project will leverage cloud technology, the UCSC Cancer Genomics Browser, and the Galaxy analysis workflow system to provide investigators with a flexible, scalable platform for hosting, visualizing and analyzing their own genomic data.

  2. Visualization of genome signatures of eukaryote genomes by batch-learning self-organizing map with a special emphasis on Drosophila genomes.

    Science.gov (United States)

    Abe, Takashi; Hamano, Yuta; Ikemura, Toshimichi

    2014-01-01

    A strategy of evolutionary studies that can compare vast numbers of genome sequences is becoming increasingly important with the remarkable progress of high-throughput DNA sequencing methods. We previously established a sequence alignment-free clustering method "BLSOM" for di-, tri-, and tetranucleotide compositions in genome sequences, which can characterize sequence characteristics (genome signatures) of a wide range of species. In the present study, we generated BLSOMs for tetra- and pentanucleotide compositions in approximately one million sequence fragments derived from 101 eukaryotes, for which almost complete genome sequences were available. BLSOM recognized phylotype-specific characteristics (e.g., key combinations of oligonucleotide frequencies) in the genome sequences, permitting phylotype-specific clustering of the sequences without any information regarding the species. In our detailed examination of 12 Drosophila species, the correlation between their phylogenetic classification and the classification on the BLSOMs was observed to visualize oligonucleotides diagnostic for species-specific clustering.

  3. CGI: Java software for mapping and visualizing data from array-based comparative genomic hybridization and expression profiling.

    Science.gov (United States)

    Gu, Joyce Xiuweu-Xu; Wei, Michael Yang; Rao, Pulivarthi H; Lau, Ching C; Behl, Sanjiv; Man, Tsz-Kwong

    2007-10-06

    With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator) that matches the BAC clones from array-based comparative genomic hybridization (aCGH) to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specific BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License.

  4. CGI: Java Software for Mapping and Visualizing Data from Array-based Comparative Genomic Hybridization and Expression Profiling

    Directory of Open Access Journals (Sweden)

    Joyce Xiuweu-Xu Gu

    2007-01-01

    Full Text Available With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator that matches the BAC clones from array-based comparative genomic hybridization (aCGH to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specifi c BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License.

  5. The genomic applications in practice and prevention network.

    Science.gov (United States)

    Khoury, Muin J; Feero, W Gregory; Reyes, Michele; Citrin, Toby; Freedman, Andrew; Leonard, Debra; Burke, Wylie; Coates, Ralph; Croyle, Robert T; Edwards, Karen; Kardia, Sharon; McBride, Colleen; Manolio, Teri; Randhawa, Gurvaneet; Rasooly, Rebekah; St Pierre, Jeannette; Terry, Sharon

    2009-07-01

    The authors describe the rationale and initial development of a new collaborative initiative, the Genomic Applications in Practice and Prevention Network. The network convened by the Centers for Disease Control and Prevention and the National Institutes of Health includes multiple stakeholders from academia, government, health care, public health, industry and consumers. The premise of Genomic Applications in Practice and Prevention Network is that there is an unaddressed chasm between gene discoveries and demonstration of their clinical validity and utility. This chasm is due to the lack of readily accessible information about the utility of most genomic applications and the lack of necessary knowledge by consumers and providers to implement what is known. The mission of Genomic Applications in Practice and Prevention Network is to accelerate and streamline the effective integration of validated genomic knowledge into the practice of medicine and public health, by empowering and sponsoring research, evaluating research findings, and disseminating high quality information on candidate genomic applications in practice and prevention. Genomic Applications in Practice and Prevention Network will develop a process that links ongoing collection of information on candidate genomic applications to four crucial domains: (1) knowledge synthesis and dissemination for new and existing technologies, and the identification of knowledge gaps, (2) a robust evidence-based recommendation development process, (3) translation research to evaluate validity, utility and impact in the real world and how to disseminate and implement recommended genomic applications, and (4) programs to enhance practice, education, and surveillance.

  6. Large-scale genomic 2D visualization reveals extensive CG-AT skew correlation in bird genomes

    Directory of Open Access Journals (Sweden)

    Deng Xuemei

    2007-11-01

    Full Text Available Abstract Background Bird genomes have very different compositional structure compared with other warm-blooded animals. The variation in the base skew rules in the vertebrate genomes remains puzzling, but it must relate somehow to large-scale genome evolution. Current research is inclined to relate base skew with mutations and their fixation. Here we wish to explore base skew correlations in bird genomes, to develop methods for displaying and quantifying such correlations at different scales, and to discuss possible explanations for the peculiarities of the bird genomes in skew correlation. Results We have developed a method called Base Skew Double Triangle (BSDT for exhibiting the genome-scale change of AT/CG skew as a two-dimensional square picture, showing base skews at many scales simultaneously in a single image. By this method we found that most chicken chromosomes have high AT/CG skew correlation (symmetry in 2D picture, except for some microchromosomes. No other organisms studied (18 species show such high skew correlations. This visualized high correlation was validated by three kinds of quantitative calculations with overlapping and non-overlapping windows, all indicating that chicken and birds in general have a special genome structure. Similar features were also found in some of the mammal genomes, but clearly much weaker than in chickens. We presume that the skew correlation feature evolved near the time that birds separated from other vertebrate lineages. When we eliminated the repeat sequences from the genomes, the AT and CG skews correlation increased for some mammal genomes, but were still clearly lower than in chickens. Conclusion Our results suggest that BSDT is an expressive visualization method for AT and CG skew and enabled the discovery of the very high skew correlation in bird genomes; this peculiarity is worth further study. Computational analysis indicated that this correlation might be a compositional characteristic

  7. The Genomic Code: Genome Evolution and Potential Applications

    KAUST Repository

    Bernardi, Giorgio

    2016-01-25

    The genome of metazoans is organized according to a genomic code which comprises three laws: 1) Compositional correlations hold between contiguous coding and non-coding sequences, as well as among the three codon positions of protein-coding genes; these correlations are the consequence of the fact that the genomes under consideration consist of fairly homogeneous, long (≥200Kb) sequences, the isochores; 2) Although isochores are defined on the basis of purely compositional properties, GC levels of isochores are correlated with all tested structural and functional properties of the genome; 3) GC levels of isochores are correlated with chromosome architecture from interphase to metaphase; in the case of interphase the correlation concerns isochores and the three-dimensional “topological associated domains” (TADs); in the case of mitotic chromosomes, the correlation concerns isochores and chromosomal bands. Finally, the genomic code is the fourth and last pillar of molecular biology, the first three pillars being 1) the double helix structure of DNA; 2) the regulation of gene expression in prokaryotes; and 3) the genetic code.

  8. Visual Comparison of Multiple Gene Expression Datasets in a Genomic Context

    Directory of Open Access Journals (Sweden)

    Borowski Krzysztof

    2008-06-01

    Full Text Available The need for novel methods of visualizing microarray data is growing. New perspectives are beneficial to finding patterns in expression data. The Bluejay genome browser provides an integrative way of visualizing gene expression datasets in a genomic context. We have now developed the functionality to display multiple microarray datasets simultaneously in Bluejay, in order to provide researchers with a comprehensive view of their datasets linked to a graphical representation of gene function. This will enable biologists to obtain valuable insights on expression patterns, by allowing them to analyze the expression values in relation to the gene locations as well as to compare expression profiles of related genomes or of di erent experiments for the same genome.

  9. CMS: a web-based system for visualization and analysis of genome-wide methylation data of human cancers.

    Science.gov (United States)

    Gu, Fei; Doderer, Mark S; Huang, Yi-Wen; Roa, Juan C; Goodfellow, Paul J; Kizer, E Lynette; Huang, Tim H M; Chen, Yidong

    2013-01-01

    DNA methylation of promoter CpG islands is associated with gene suppression, and its unique genome-wide profiles have been linked to tumor progression. Coupled with high-throughput sequencing technologies, it can now efficiently determine genome-wide methylation profiles in cancer cells. Also, experimental and computational technologies make it possible to find the functional relationship between cancer-specific methylation patterns and their clinicopathological parameters. Cancer methylome system (CMS) is a web-based database application designed for the visualization, comparison and statistical analysis of human cancer-specific DNA methylation. Methylation intensities were obtained from MBDCap-sequencing, pre-processed and stored in the database. 191 patient samples (169 tumor and 22 normal specimen) and 41 breast cancer cell-lines are deposited in the database, comprising about 6.6 billion uniquely mapped sequence reads. This provides comprehensive and genome-wide epigenetic portraits of human breast cancer and endometrial cancer to date. Two views are proposed for users to better understand methylation structure at the genomic level or systemic methylation alteration at the gene level. In addition, a variety of annotation tracks are provided to cover genomic information. CMS includes important analytic functions for interpretation of methylation data, such as the detection of differentially methylated regions, statistical calculation of global methylation intensities, multiple gene sets of biologically significant categories, interactivity with UCSC via custom-track data. We also present examples of discoveries utilizing the framework. CMS provides visualization and analytic functions for cancer methylome datasets. A comprehensive collection of datasets, a variety of embedded analytic functions and extensive applications with biological and translational significance make this system powerful and unique in cancer methylation research. CMS is freely accessible

  10. Current development and application of soybean genomics

    Institute of Scientific and Technical Information of China (English)

    Lingli HE; Jing ZHAO; Man ZHAO; Chaoying HE

    2011-01-01

    Soybean (Glycine max),an important domesticated species originated in China,constitutes a major source of edible oils and high-quality plant proteins worldwide.In spite of its complex genome as a consequence of an ancient tetraploidilization,platforms for map-based genomics,sequence-based genomics,comparative genomics and functional genomics have been well developed in the last decade,thus rich repertoires of genomic tools and resources are available,which have been influencing the soybean genetic improvement.Here we mainly review the progresses of soybean (including its wild relative Glycine soja) genomics and its impetus for soybean breeding,and raise the major biological questions needing to be addressed.Genetic maps,physical maps,QTL and EST mapping have been so well achieved that the marker assisted selection and positional cloning in soybean is feasible and even routine.Whole genome sequencing and transcriptomic analyses provide a large collection of molecular markers and predicted genes,which are instrumental to comparative genomics and functional genomics.Comparative genomics has started to reveal the evolution of soybean genome and the molecular basis of soybean domestication process.Microarrays resources,mutagenesis and efficient transformation systems become essential components of soybean functional genomics.Furthermore,phenotypic functional genomics via both forward and reverse genetic approaches has inferred functions of many genes involved in plant and seed development,in response to abiotic stresses,functioning in plant-pathogenic microbe interactions,and controlling the oil and protein content of seed.These achievements have paved the way for generation of transgenic or genetically modified (GM) soybean crops.

  11. GEnomes Management Application (GEM.app): a new software tool for large-scale collaborative genome analysis.

    Science.gov (United States)

    Gonzalez, Michael A; Lebrigio, Rafael F Acosta; Van Booven, Derek; Ulloa, Rick H; Powell, Eric; Speziani, Fiorella; Tekin, Mustafa; Schüle, Rebecca; Züchner, Stephan

    2013-06-01

    Novel genes are now identified at a rapid pace for many Mendelian disorders, and increasingly, for genetically complex phenotypes. However, new challenges have also become evident: (1) effectively managing larger exome and/or genome datasets, especially for smaller labs; (2) direct hands-on analysis and contextual interpretation of variant data in large genomic datasets; and (3) many small and medium-sized clinical and research-based investigative teams around the world are generating data that, if combined and shared, will significantly increase the opportunities for the entire community to identify new genes. To address these challenges, we have developed GEnomes Management Application (GEM.app), a software tool to annotate, manage, visualize, and analyze large genomic datasets (https://genomics.med.miami.edu/). GEM.app currently contains ∼1,600 whole exomes from 50 different phenotypes studied by 40 principal investigators from 15 different countries. The focus of GEM.app is on user-friendly analysis for nonbioinformaticians to make next-generation sequencing data directly accessible. Yet, GEM.app provides powerful and flexible filter options, including single family filtering, across family/phenotype queries, nested filtering, and evaluation of segregation in families. In addition, the system is fast, obtaining results within 4 sec across ∼1,200 exomes. We believe that this system will further enhance identification of genetic causes of human disease. © 2013 Wiley Periodicals, Inc.

  12. Enhancing Visual Basic GUI Applications using VRML Scenes

    OpenAIRE

    Bala Dhandayuthapani Veerasamy

    2010-01-01

    Rapid Application Development (RAD) enables ever expanding needs for speedy development of computer application programs that are sophisticated, reliable, and full-featured. Visual Basic was the first RAD tool for the Windows operating system, and too many people say still it is the best. To provide very good attraction in visual basic 6 applications, this paper directing to use VRML scenes over the visual basic environment.

  13. Application of Genomic Tools in Plant Breeding

    OpenAIRE

    Pérez-de-Castro, A.M.; Vilanova, S.; Cañizares, J.; Pascual, L.; Blanca, J.M.; Díez, M.J.; Prohens, J.; Picó, B.

    2012-01-01

    Plant breeding has been very successful in developing improved varieties using conventional tools and methodologies. Nowadays, the availability of genomic tools and resources is leading to a new revolution of plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. Next Generation Sequencing (NGS) technologies are allowing the mass sequencing of genomes and transcriptomes, which is producing a vast array of genomic...

  14. A Flexible Framework for Collaborative Visualization Applications using JAVASPACES

    National Research Council Canada - National Science Library

    Butler, Sean

    2001-01-01

    ...(Trademark), a high-level network programming API. This thesis describes a tool for developing collaborative visualization software using JavaSpaces-an application framework and accompanying toolkit...

  15. Oncogenomic portals for the visualization and analysis of genome-wide cancer data.

    Science.gov (United States)

    Klonowska, Katarzyna; Czubak, Karol; Wojciechowska, Marzena; Handschuh, Luiza; Zmienko, Agnieszka; Figlerowicz, Marek; Dams-Kozlowska, Hanna; Kozlowski, Piotr

    2016-01-05

    Somatically acquired genomic alterations that drive oncogenic cellular processes are of great scientific and clinical interest. Since the initiation of large-scale cancer genomic projects (e.g., the Cancer Genome Project, The Cancer Genome Atlas, and the International Cancer Genome Consortium cancer genome projects), a number of web-based portals have been created to facilitate access to multidimensional oncogenomic data and assist with the interpretation of the data. The portals provide the visualization of small-size mutations, copy number variations, methylation, and gene/protein expression data that can be correlated with the available clinical, epidemiological, and molecular features. Additionally, the portals enable to analyze the gathered data with the use of various user-friendly statistical tools. Herein, we present a highly illustrated review of seven portals, i.e., Tumorscape, UCSC Cancer Genomics Browser, ICGC Data Portal, COSMIC, cBioPortal, IntOGen, and BioProfiling.de. All of the selected portals are user-friendly and can be exploited by scientists from different cancer-associated fields, including those without bioinformatics background. It is expected that the use of the portals will contribute to a better understanding of cancer molecular etiology and will ultimately accelerate the translation of genomic knowledge into clinical practice.

  16. IRscope: An online program to visualize the junction sites of chloroplast genomes.

    Science.gov (United States)

    Amiryousefi, Ali; Hyvönen, Jaakko; Poczai, Peter

    2018-04-05

    Genome plotting is performed using a wide range of visualizations tools each with emphasis on a different informative dimension of the genome. These tools can provide a deeper insight into the genomic structure of the organism. Here we announce a new visualization tool that is specifically designed for chloroplast genomes. It allows the users to depict the genetic architecture of up to ten chloroplast genomes in the vicinity of the sites connecting the inverted repeats to the short and long single copy regions. The software and its dependent libraries are fully coded in R and the reflected plot is scaled up to realistic size of nucleotide base pairs in the vicinity of the junction sites. We introduce a website for easier use of the program as well as R source code of the software to be used in case of preferences to be changed and integrated into personal pipelines. The input of the program is an annotation GenBank (.gb) file, the accession or GI number of the sequence or a DOGMA output file. The software was tested using over a hundred embryophyte chloroplast genomes and in all cases a reliable output was obtained. Source codes and the online suit available @ https://irscope.shinyapps.io/irapp/ or @ https://github.com/Limpfrog/irscope. ali.amiryousefi@helsinki.fi.

  17. Application of Andrew's Plots to Visualization of Multidimensional Data

    Science.gov (United States)

    Grinshpun, Vadim

    2016-01-01

    Importance: The article raises a point of visual representation of big data, recently considered to be demanded for many scientific and real-life applications, and analyzes particulars for visualization of multi-dimensional data, giving examples of the visual analytics-related problems. Objectives: The purpose of this paper is to study application…

  18. Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms

    Directory of Open Access Journals (Sweden)

    Meller Jaroslaw

    2007-03-01

    Full Text Available Abstract Background Identifying syntenic regions, i.e., blocks of genes or other markers with evolutionary conserved order, and quantifying evolutionary relatedness between genomes in terms of chromosomal rearrangements is one of the central goals in comparative genomics. However, the analysis of synteny and the resulting assessment of genome rearrangements are sensitive to the choice of a number of arbitrary parameters that affect the detection of synteny blocks. In particular, the choice of a set of markers and the effect of different aggregation strategies, which enable coarse graining of synteny blocks and exclusion of micro-rearrangements, need to be assessed. Therefore, existing tools and resources that facilitate identification, visualization and analysis of synteny need to be further improved to provide a flexible platform for such analysis, especially in the context of multiple genomes. Results We present a new tool, Cinteny, for fast identification and analysis of synteny with different sets of markers and various levels of coarse graining of syntenic blocks. Using Hannenhalli-Pevzner approach and its extensions, Cinteny also enables interactive determination of evolutionary relationships between genomes in terms of the number of rearrangements (the reversal distance. In particular, Cinteny provides: i integration of synteny browsing with assessment of evolutionary distances for multiple genomes; ii flexibility to adjust the parameters and re-compute the results on-the-fly; iii ability to work with user provided data, such as orthologous genes, sequence tags or other conserved markers. In addition, Cinteny provides many annotated mammalian, invertebrate and fungal genomes that are pre-loaded and available for analysis at http://cinteny.cchmc.org. Conclusion Cinteny allows one to automatically compare multiple genomes and perform sensitivity analysis for synteny block detection and for the subsequent computation of reversal distances

  19. [Genomic selection of milk cattle. The practical application over five years].

    Science.gov (United States)

    Smaragdov, M G

    2013-11-01

    Genomic selection is a method based on the use of single nucleotide polymorphisms (SNPs) as markers for detecting animal or plant genotype values. The review describes the genomic selection of milk cattle 5 years after the design of dense SNP chips. References to the application of genomic selection to other animal and plant species are given. The main principles of constructing linear and nonlinear mathematical models that allow one to determine genomic estimates in animals are briefly described. Particular attention is focused on the accuracy and the phenomenon of the additivity ofgenomic estimates, as well as to the prospective use of various genomic selection schemes that consider it over dozens of generations. Information including international organizations that provide the consolidation of genomic information from different countries aimed at designing global reference populations of milk cattle is reported. The results of the practical application of genomic selection to detecting of the breeding value of milk cattle over 5 years are demonstrated in the table, which makes it possible to visually assess the achievements of this highly technological field of cattle breeding.

  20. Genome editing: progress and challenges for medical applications

    Directory of Open Access Journals (Sweden)

    Dana Carroll

    2016-11-01

    Full Text Available Editorial summary The development of the CRISPR-Cas platform for genome editing has greatly simplified the process of making targeted genetic modifications. Applications of genome editing are expected to have a substantial impact on human therapies through the development of better animal models, new target discovery, and direct therapeutic intervention.

  1. Application of genomic tools in plant breeding.

    Science.gov (United States)

    Pérez-de-Castro, A M; Vilanova, S; Cañizares, J; Pascual, L; Blanca, J M; Díez, M J; Prohens, J; Picó, B

    2012-05-01

    Plant breeding has been very successful in developing improved varieties using conventional tools and methodologies. Nowadays, the availability of genomic tools and resources is leading to a new revolution of plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. Next Generation Sequencing (NGS) technologies are allowing the mass sequencing of genomes and transcriptomes, which is producing a vast array of genomic information. The analysis of NGS data by means of bioinformatics developments allows discovering new genes and regulatory sequences and their positions, and makes available large collections of molecular markers. Genome-wide expression studies provide breeders with an understanding of the molecular basis of complex traits. Genomic approaches include TILLING and EcoTILLING, which make possible to screen mutant and germplasm collections for allelic variants in target genes. Re-sequencing of genomes is very useful for the genome-wide discovery of markers amenable for high-throughput genotyping platforms, like SSRs and SNPs, or the construction of high density genetic maps. All these tools and resources facilitate studying the genetic diversity, which is important for germplasm management, enhancement and use. Also, they allow the identification of markers linked to genes and QTLs, using a diversity of techniques like bulked segregant analysis (BSA), fine genetic mapping, or association mapping. These new markers are used for marker assisted selection, including marker assisted backcross selection, 'breeding by design', or new strategies, like genomic selection. In conclusion, advances in genomics are providing breeders with new tools and methodologies that allow a great leap forward in plant breeding, including the 'superdomestication' of crops and the genetic dissection and breeding for complex traits.

  2. Figure 4 from Integrative Genomics Viewer: Visualizing Big Data | Office of Cancer Genomics

    Science.gov (United States)

    Gene-list view of genomic data. The gene-list view allows users to compare data across a set of loci. The data in this figure includes copy number, mutation, and clinical data from 202 glioblastoma samples from TCGA. Adapted from Figure 7; Thorvaldsdottir H et al. 2012

  3. Figure 2 from Integrative Genomics Viewer: Visualizing Big Data | Office of Cancer Genomics

    Science.gov (United States)

    Grouping and sorting genomic data in IGV. The IGV user interface displaying 202 glioblastoma samples from TCGA. Samples are grouped by tumor subtype (second annotation column) and data type (first annotation column) and sorted by copy number of the EGFR locus (middle column). Adapted from Figure 1; Robinson et al. 2011

  4. Figure 5 from Integrative Genomics Viewer: Visualizing Big Data | Office of Cancer Genomics

    Science.gov (United States)

    Split-Screen View. The split-screen view is useful for exploring relationships of genomic features that are independent of chromosomal location. Color is used here to indicate mate pairs that map to different chromosomes, chromosomes 1 and 6, suggesting a translocation event. Adapted from Figure 8; Thorvaldsdottir H et al. 2012

  5. Visual Analytics of Complex Genomics Data to Guide Effective Treatment Decisions

    Directory of Open Access Journals (Sweden)

    Quang Vinh Nguyen

    2016-09-01

    Full Text Available In cancer biology, genomics represents a big data problem that needs accurate visual data processing and analytics. The human genome is very complex with thousands of genes that contain the information about the individual patients and the biological mechanisms of their disease. Therefore, when building a framework for personalised treatment, the complexity of the genome must be captured in meaningful and actionable ways. This paper presents a novel visual analytics framework that enables effective analysis of large and complex genomics data. By providing interactive visualisations from the overview of the entire patient cohort to the detail view of individual genes, our work potentially guides effective treatment decisions for childhood cancer patients. The framework consists of multiple components enabling the complete analytics supporting personalised medicines, including similarity space construction, automated analysis, visualisation, gene-to-gene comparison and user-centric interaction and exploration based on feature selection. In addition to the traditional way to visualise data, we utilise the Unity3D platform for developing a smooth and interactive visual presentation of the information. This aims to provide better rendering, image quality, ergonomics and user experience to non-specialists or young users who are familiar with 3D gaming environments and interfaces. We illustrate the effectiveness of our approach through case studies with datasets from childhood cancers, B-cell Acute Lymphoblastic Leukaemia (ALL and Rhabdomyosarcoma (RMS patients, on how to guide the effective treatment decision in the cohort.

  6. Generating descriptive visual words and visual phrases for large-scale image applications.

    Science.gov (United States)

    Zhang, Shiliang; Tian, Qi; Hua, Gang; Huang, Qingming; Gao, Wen

    2011-09-01

    Bag-of-visual Words (BoWs) representation has been applied for various problems in the fields of multimedia and computer vision. The basic idea is to represent images as visual documents composed of repeatable and distinctive visual elements, which are comparable to the text words. Notwithstanding its great success and wide adoption, visual vocabulary created from single-image local descriptors is often shown to be not as effective as desired. In this paper, descriptive visual words (DVWs) and descriptive visual phrases (DVPs) are proposed as the visual correspondences to text words and phrases, where visual phrases refer to the frequently co-occurring visual word pairs. Since images are the carriers of visual objects and scenes, a descriptive visual element set can be composed by the visual words and their combinations which are effective in representing certain visual objects or scenes. Based on this idea, a general framework is proposed for generating DVWs and DVPs for image applications. In a large-scale image database containing 1506 object and scene categories, the visual words and visual word pairs descriptive to certain objects or scenes are identified and collected as the DVWs and DVPs. Experiments show that the DVWs and DVPs are informative and descriptive and, thus, are more comparable with the text words than the classic visual words. We apply the identified DVWs and DVPs in several applications including large-scale near-duplicated image retrieval, image search re-ranking, and object recognition. The combination of DVW and DVP performs better than the state of the art in large-scale near-duplicated image retrieval in terms of accuracy, efficiency and memory consumption. The proposed image search re-ranking algorithm: DWPRank outperforms the state-of-the-art algorithm by 12.4% in mean average precision and about 11 times faster in efficiency.

  7. VISMASHUP: streamlining the creation of custom visualization applications

    Energy Technology Data Exchange (ETDEWEB)

    Ahrens, James P [Los Alamos National Laboratory; Santos, Emanuele [UNIV OF UTAH; Lins, Lauro [UNIV OF UTAH; Freire, Juliana [UNIV OF UTAH; Silva, Cl' audio T [UNIV OF UTAH

    2010-01-01

    Visualization is essential for understanding the increasing volumes of digital data. However, the process required to create insightful visualizations is involved and time consuming. Although several visualization tools are available, including tools with sophisticated visual interfaces, they are out of reach for users who have little or no knowledge of visualization techniques and/or who do not have programming expertise. In this paper, we propose VISMASHUP, a new framework for streamlining the creation of customized visualization applications. Because these applications can be customized for very specific tasks, they can hide much of the complexity in a visualization specification and make it easier for users to explore visualizations by manipulating a small set of parameters. We describe the framework and how it supports the various tasks a designer needs to carry out to develop an application, from mining and exploring a set of visualization specifications (pipelines), to the creation of simplified views of the pipelines, and the automatic generation of the application and its interface. We also describe the implementation of the system and demonstrate its use in two real application scenarios.

  8. Characterizing Phage Genomes for Therapeutic Applications

    Directory of Open Access Journals (Sweden)

    Casandra W. Philipson

    2018-04-01

    Full Text Available Multi-drug resistance is increasing at alarming rates. The efficacy of phage therapy, treating bacterial infections with bacteriophages alone or in combination with traditional antibiotics, has been demonstrated in emergency cases in the United States and in other countries, however remains to be approved for wide-spread use in the US. One limiting factor is a lack of guidelines for assessing the genomic safety of phage candidates. We present the phage characterization workflow used by our team to generate data for submitting phages to the Federal Drug Administration (FDA for authorized use. Essential analysis checkpoints and warnings are detailed for obtaining high-quality genomes, excluding undesirable candidates, rigorously assessing a phage genome for safety and evaluating sequencing contamination. This workflow has been developed in accordance with community standards for high-throughput sequencing of viral genomes as well as principles for ideal phages used for therapy. The feasibility and utility of the pipeline is demonstrated on two new phage genomes that meet all safety criteria. We propose these guidelines as a minimum standard for phages being submitted to the FDA for review as investigational new drug candidates.

  9. Characterizing Phage Genomes for Therapeutic Applications.

    Science.gov (United States)

    Philipson, Casandra W; Voegtly, Logan J; Lueder, Matthew R; Long, Kyle A; Rice, Gregory K; Frey, Kenneth G; Biswas, Biswajit; Cer, Regina Z; Hamilton, Theron; Bishop-Lilly, Kimberly A

    2018-04-10

    Multi-drug resistance is increasing at alarming rates. The efficacy of phage therapy, treating bacterial infections with bacteriophages alone or in combination with traditional antibiotics, has been demonstrated in emergency cases in the United States and in other countries, however remains to be approved for wide-spread use in the US. One limiting factor is a lack of guidelines for assessing the genomic safety of phage candidates. We present the phage characterization workflow used by our team to generate data for submitting phages to the Federal Drug Administration (FDA) for authorized use. Essential analysis checkpoints and warnings are detailed for obtaining high-quality genomes, excluding undesirable candidates, rigorously assessing a phage genome for safety and evaluating sequencing contamination. This workflow has been developed in accordance with community standards for high-throughput sequencing of viral genomes as well as principles for ideal phages used for therapy. The feasibility and utility of the pipeline is demonstrated on two new phage genomes that meet all safety criteria. We propose these guidelines as a minimum standard for phages being submitted to the FDA for review as investigational new drug candidates.

  10. Development and application of Human Genome Epidemiology

    Science.gov (United States)

    Xu, Jingwen

    2017-12-01

    Epidemiology is a science that studies distribution of diseases and health in population and its influencing factors, it also studies how to prevent and cure disease and promote health strategies and measures. Epidemiology has developed rapidly in recent years and it is an intercross subject with various other disciplines to form a series of branch disciplines such as Genetic epidemiology, molecular epidemiology, drug epidemiology and tumor epidemiology. With the implementation and completion of Human Genome Project (HGP), Human Genome Epidemiology (HuGE) has emerged at this historic moment. In this review, the development of Human Genome Epidemiology, research content, the construction and structure of relevant network, research standards, as well as the existing results and problems are briefly outlined.

  11. Using Interactive Data Visualizations for Exploratory Analysis in Undergraduate Genomics Coursework: Field Study Findings and Guidelines

    Science.gov (United States)

    Kumar, Anuj; Nong, Paige; Su, Gang; Meng, Fan

    2016-01-01

    Life scientists increasingly use visual analytics to explore large data sets and generate hypotheses. Undergraduate biology majors should be learning these same methods. Yet visual analytics is one of the most underdeveloped areas of undergraduate biology education. This study sought to determine the feasibility of undergraduate biology majors conducting exploratory analysis using the same interactive data visualizations as practicing scientists. We examined 22 upper level undergraduates in a genomics course as they engaged in a case-based inquiry with an interactive heat map. We qualitatively and quantitatively analyzed students’ visual analytic behaviors, reasoning and outcomes to identify student performance patterns, commonly shared efficiencies and task completion. We analyzed students’ successes and difficulties in applying knowledge and skills relevant to the visual analytics case and related gaps in knowledge and skill to associated tool designs. Findings show that undergraduate engagement in visual analytics is feasible and could be further strengthened through tool usability improvements. We identify these improvements. We speculate, as well, on instructional considerations that our findings suggested may also enhance visual analytics in case-based modules. PMID:26877625

  12. Rethinking Visual Analytics for Streaming Data Applications

    Energy Technology Data Exchange (ETDEWEB)

    Crouser, R. Jordan; Franklin, Lyndsey; Cook, Kris

    2017-01-01

    In the age of data science, the use of interactive information visualization techniques has become increasingly ubiquitous. From online scientific journals to the New York Times graphics desk, the utility of interactive visualization for both storytelling and analysis has become ever more apparent. As these techniques have become more readily accessible, the appeal of combining interactive visualization with computational analysis continues to grow. Arising out of a need for scalable, human-driven analysis, primary objective of visual analytics systems is to capitalize on the complementary strengths of human and machine analysis, using interactive visualization as a medium for communication between the two. These systems leverage developments from the fields of information visualization, computer graphics, machine learning, and human-computer interaction to support insight generation in areas where purely computational analyses fall short. Over the past decade, visual analytics systems have generated remarkable advances in many historically challenging analytical contexts. These include areas such as modeling political systems [Crouser et al. 2012], detecting financial fraud [Chang et al. 2008], and cybersecurity [Harrison et al. 2012]. In each of these contexts, domain expertise and human intuition is a necessary component of the analysis. This intuition is essential to building trust in the analytical products, as well as supporting the translation of evidence into actionable insight. In addition, each of these examples also highlights the need for scalable analysis. In each case, it is infeasible for a human analyst to manually assess the raw information unaided, and the communication overhead to divide the task between a large number of analysts makes simple parallelism intractable. Regardless of the domain, visual analytics tools strive to optimize the allocation of human analytical resources, and to streamline the sensemaking process on data that is massive

  13. Whole genome amplification - Review of applications and advances

    Energy Technology Data Exchange (ETDEWEB)

    Hawkins, Trevor L.; Detter, J.C.; Richardson, Paul

    2001-11-15

    The concept of Whole Genome Amplification is something that has arisen in the past few years as modifications to the polymerase chain reaction (PCR) have been adapted to replicate regions of genomes which are of biological interest. The applications here are many--forensics, embryonic disease diagnosis, bio terrorism genome detection, ''imoralization'' of clinical samples, microbial diversity, and genotyping. The key question is if DNA can be replicated a genome at a time without bias or non random distribution of the target. Several papers published in the last year and currently in preparation may lead to the conclusion that whole genome amplification may indeed be possible and therefore open up a new avenue to molecular biology.

  14. Applications of Support Vector Machine (SVM) Learning in Cancer Genomics.

    Science.gov (United States)

    Huang, Shujun; Cai, Nianguang; Pacheco, Pedro Penzuti; Narrandes, Shavira; Wang, Yang; Xu, Wayne

    2018-01-01

    Machine learning with maximization (support) of separating margin (vector), called support vector machine (SVM) learning, is a powerful classification tool that has been used for cancer genomic classification or subtyping. Today, as advancements in high-throughput technologies lead to production of large amounts of genomic and epigenomic data, the classification feature of SVMs is expanding its use in cancer genomics, leading to the discovery of new biomarkers, new drug targets, and a better understanding of cancer driver genes. Herein we reviewed the recent progress of SVMs in cancer genomic studies. We intend to comprehend the strength of the SVM learning and its future perspective in cancer genomic applications. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  15. CRISPR Mediated Genome Engineering and its Application in Industry.

    Science.gov (United States)

    Kaboli, Saeed; Babazada, Hasan

    2018-01-01

    The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) method has been dramatically changing the field of genome engineering. It is a rapid, highly efficient and versatile tool for precise modification of genome that uses a guide RNA (gRNA) to target Cas9 to a specific sequence. This novel RNA-guided genome-editing technique has become a revolutionary tool in biomedical science and has many innovative applications in different fields. In this review, we briefly introduce the Cas9-mediated genome-editing tool, summarize the recent advances in CRISPR/Cas9 technology to engineer the genomes of a wide variety of organisms, and discuss their applications to treatment of fungal and viral disease. We also discuss advantageous of CRISPR/Cas9 technology to drug design, creation of animal model, and to food, agricultural and energy sciences. Adoption of the CRISPR/Cas9 technology in biomedical and biotechnological researches would create innovative applications of it not only for breeding of strains exhibiting desired traits for specific industrial and medical applications, but also for investigation of genome function.

  16. Visualizing information across multidimensional post-genomic structured and textual databases.

    Science.gov (United States)

    Tao, Ying; Friedman, Carol; Lussier, Yves A

    2005-04-15

    Visualizing relationships among biological information to facilitate understanding is crucial to biological research during the post-genomic era. Although different systems have been developed to view gene-phenotype relationships for specific databases, very few have been designed specifically as a general flexible tool for visualizing multidimensional genotypic and phenotypic information together. Our goal is to develop a method for visualizing multidimensional genotypic and phenotypic information and a model that unifies different biological databases in order to present the integrated knowledge using a uniform interface. We developed a novel, flexible and generalizable visualization tool, called PhenoGenesviewer (PGviewer), which in this paper was used to display gene-phenotype relationships from a human-curated database (OMIM) and from an automatic method using a Natural Language Processing tool called BioMedLEE. Data obtained from multiple databases were first integrated into a uniform structure and then organized by PGviewer. PGviewer provides a flexible query interface that allows dynamic selection and ordering of any desired dimension in the databases. Based on users' queries, results can be visualized using hierarchical expandable trees that present views specified by users according to their research interests. We believe that this method, which allows users to dynamically organize and visualize multiple dimensions, is a potentially powerful and promising tool that should substantially facilitate biological research. PhenogenesViewer as well as its support and tutorial are available at http://www.dbmi.columbia.edu/pgviewer/ Lussier@dbmi.columbia.edu.

  17. Clinically Applicable Inhibitors Impacting Genome Stability.

    Science.gov (United States)

    Prakash, Anu; Garcia-Moreno, Juan F; Brown, James A L; Bourke, Emer

    2018-05-13

    Advances in technology have facilitated the molecular profiling (genomic and transcriptomic) of tumours, and has led to improved stratification of patients and the individualisation of treatment regimes. To fully realize the potential of truly personalised treatment options, we need targeted therapies that precisely disrupt the compensatory pathways identified by profiling which allow tumours to survive or gain resistance to treatments. Here, we discuss recent advances in novel therapies that impact the genome (chromosomes and chromatin), pathways targeted and the stage of the pathways targeted. The current state of research will be discussed, with a focus on compounds that have advanced into trials (clinical and pre-clinical). We will discuss inhibitors of specific DNA damage responses and other genome stability pathways, including those in development, which are likely to synergistically combine with current therapeutic options. Tumour profiling data, combined with the knowledge of new treatments that affect the regulation of essential tumour signalling pathways, is revealing fundamental insights into cancer progression and resistance mechanisms. This is the forefront of the next evolution of advanced oncology medicine that will ultimately lead to improved survival and may, one day, result in many cancers becoming chronic conditions, rather than fatal diseases.

  18. Genetic parameter estimates for carcass traits and visual scores including or not genomic information.

    Science.gov (United States)

    Gordo, D G M; Espigolan, R; Tonussi, R L; Júnior, G A F; Bresolin, T; Magalhães, A F Braga; Feitosa, F L; Baldi, F; Carvalheiro, R; Tonhati, H; de Oliveira, H N; Chardulo, L A L; de Albuquerque, L G

    2016-05-01

    The objective of this study was to determine whether visual scores used as selection criteria in Nellore breeding programs are effective indicators of carcass traits measured after slaughter. Additionally, this study evaluated the effect of different structures of the relationship matrix ( and ) on the estimation of genetic parameters and on the prediction accuracy of breeding values. There were 13,524 animals for visual scores of conformation (CS), finishing precocity (FP), and muscling (MS) and 1,753, 1,747, and 1,564 for LM area (LMA), backfat thickness (BF), and HCW, respectively. Of these, 1,566 animals were genotyped using a high-density panel containing 777,962 SNP. Six analyses were performed using multitrait animal models, each including the 3 visual scores and 1 carcass trait. For the visual scores, the model included direct additive genetic and residual random effects and the fixed effects of contemporary group (defined by year of birth, management group at yearling, and farm) and the linear effect of age of animal at yearling. The same model was used for the carcass traits, replacing the effect of age of animal at yearling with the linear effect of age of animal at slaughter. The variance and covariance components were estimated by the REML method in analyses using the numerator relationship matrix () or combining the genomic and the numerator relationship matrices (). The heritability estimates for the visual scores obtained with the 2 methods were similar and of moderate magnitude (0.23-0.34), indicating that these traits should response to direct selection. The heritabilities for LMA, BF, and HCW were 0.13, 0.07, and 0.17, respectively, using matrix and 0.29, 0.16, and 0.23, respectively, using matrix . The genetic correlations between the visual scores and carcass traits were positive, and higher correlations were generally obtained when matrix was used. Considering the difficulties and cost of measuring carcass traits postmortem, visual scores of

  19. Application for TJ-II Signals Visualization: User's Guide

    International Nuclear Information System (INIS)

    Sanchez, E.; Portas, A. B.; Cremy, C.; Vega, J.

    2000-01-01

    In this documents are described the functionalities of the application developed by the Data Acquisition Group for TJ-II signal visualization. There are two versions of the application, the On-line version, used for signal visualization during TJ-II operation, and the Off-line version, used for signal visualization without TJ-II operation. Both versions of the application consist in a graphical user interface developed for X/Motif, in which most of the actions can be done using the mouse buttons. The functionalities of both versions of the application are described in this user's guide, beginning at the application start-up and explaining in detail all the options that it provides and the actions that can be done with each graphic control. (Author) 8 refs

  20. CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences

    Science.gov (United States)

    2012-01-01

    Background The complete sequences of chloroplast genomes provide wealthy information regarding the evolutionary history of species. With the advance of next-generation sequencing technology, the number of completely sequenced chloroplast genomes is expected to increase exponentially, powerful computational tools annotating the genome sequences are in urgent need. Results We have developed a web server CPGAVAS. The server accepts a complete chloroplast genome sequence as input. First, it predicts protein-coding and rRNA genes based on the identification and mapping of the most similar, full-length protein, cDNA and rRNA sequences by integrating results from Blastx, Blastn, protein2genome and est2genome programs. Second, tRNA genes and inverted repeats (IR) are identified using tRNAscan, ARAGORN and vmatch respectively. Third, it calculates the summary statistics for the annotated genome. Fourth, it generates a circular map ready for publication. Fifth, it can create a Sequin file for GenBank submission. Last, it allows the extractions of protein and mRNA sequences for given list of genes and species. The annotation results in GFF3 format can be edited using any compatible annotation editing tools. The edited annotations can then be uploaded to CPGAVAS for update and re-analyses repeatedly. Using known chloroplast genome sequences as test set, we show that CPGAVAS performs comparably to another application DOGMA, while having several superior functionalities. Conclusions CPGAVAS allows the semi-automatic and complete annotation of a chloroplast genome sequence, and the visualization, editing and analysis of the annotation results. It will become an indispensible tool for researchers studying chloroplast genomes. The software is freely accessible from http://www.herbalgenomics.org/cpgavas. PMID:23256920

  1. CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences

    Directory of Open Access Journals (Sweden)

    Liu Chang

    2012-12-01

    Full Text Available Abstract Background The complete sequences of chloroplast genomes provide wealthy information regarding the evolutionary history of species. With the advance of next-generation sequencing technology, the number of completely sequenced chloroplast genomes is expected to increase exponentially, powerful computational tools annotating the genome sequences are in urgent need. Results We have developed a web server CPGAVAS. The server accepts a complete chloroplast genome sequence as input. First, it predicts protein-coding and rRNA genes based on the identification and mapping of the most similar, full-length protein, cDNA and rRNA sequences by integrating results from Blastx, Blastn, protein2genome and est2genome programs. Second, tRNA genes and inverted repeats (IR are identified using tRNAscan, ARAGORN and vmatch respectively. Third, it calculates the summary statistics for the annotated genome. Fourth, it generates a circular map ready for publication. Fifth, it can create a Sequin file for GenBank submission. Last, it allows the extractions of protein and mRNA sequences for given list of genes and species. The annotation results in GFF3 format can be edited using any compatible annotation editing tools. The edited annotations can then be uploaded to CPGAVAS for update and re-analyses repeatedly. Using known chloroplast genome sequences as test set, we show that CPGAVAS performs comparably to another application DOGMA, while having several superior functionalities. Conclusions CPGAVAS allows the semi-automatic and complete annotation of a chloroplast genome sequence, and the visualization, editing and analysis of the annotation results. It will become an indispensible tool for researchers studying chloroplast genomes. The software is freely accessible from http://www.herbalgenomics.org/cpgavas.

  2. BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters

    Directory of Open Access Journals (Sweden)

    Gong Cheng

    2017-11-01

    Full Text Available Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists; accordingly, its application in biological research has been limited. In order to popularize this technology in the field of bioinformatics and to promote the use of publicly available bioinformatics tools, such as Dockerfiles and Images from communities, government sources, and private owners in the Docker Hub Registry and other Docker-based resources, we introduce here a complete and accurate bioinformatics workflow based on Docker. The present workflow enables analysis and visualization of pan-genomes and biosynthetic gene clusters of bacteria. This provides a new solution for bioinformatics mining of big data from various publicly available biological databases. The present step-by-step guide creates an integrative workflow through a Dockerfile to allow researchers to build their own Image and run Container easily.

  3. BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters.

    Science.gov (United States)

    Cheng, Gong; Lu, Quan; Ma, Ling; Zhang, Guocai; Xu, Liang; Zhou, Zongshan

    2017-01-01

    Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists; accordingly, its application in biological research has been limited. In order to popularize this technology in the field of bioinformatics and to promote the use of publicly available bioinformatics tools, such as Dockerfiles and Images from communities, government sources, and private owners in the Docker Hub Registry and other Docker-based resources, we introduce here a complete and accurate bioinformatics workflow based on Docker. The present workflow enables analysis and visualization of pan-genomes and biosynthetic gene clusters of bacteria. This provides a new solution for bioinformatics mining of big data from various publicly available biological databases. The present step-by-step guide creates an integrative workflow through a Dockerfile to allow researchers to build their own Image and run Container easily.

  4. Design and visualization of synthetic holograms for security applications

    International Nuclear Information System (INIS)

    Škeren, M; Nývlt, M; Svoboda, J

    2013-01-01

    In this paper we present a software for the design and visualization of holographic elements containing full scale of visual effects. It enables to simulate an observation of the holographic elements under general conditions including different light sources with various spectral and coherence properties and various geometries of reconstruction. Furthermore, recent technologies offer interesting possibilities for the 3D visualization such as the 3D techniques based on shutter or polarization glasses, anaglyphs, etc. The presented software is compatible with the mentioned techniques and enables an application of the 3D hardware tools for visualization. The software package can be used not only for visualization of the existing designs, but also for a fine tuning of the spatial, kinetic, and color properties of the hologram. Moreover, the holograms containing all types of the 3D effects, general color mixing, kinetic behavior, diffractive cryptograms, etc. can be translated using the software directly to a high resolution micro-structure.

  5. Genome editing in pluripotent stem cells: research and therapeutic applications

    Energy Technology Data Exchange (ETDEWEB)

    Deleidi, Michela, E-mail: michela.deleidi@dzne.de [German Center for Neurodegenerative Diseases (DZNE) Tübingen within the Helmholtz Association, Tübingen (Germany); Hertie Institute for Clinical Brain Research, University of Tübingen (Germany); Yu, Cong [Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, New York (United States)

    2016-05-06

    Recent progress in human pluripotent stem cell (hPSC) and genome editing technologies has opened up new avenues for the investigation of human biology in health and disease as well as the development of therapeutic applications. Gene editing approaches with programmable nucleases have been successfully established in hPSCs and applied to study gene function, develop novel animal models and perform genetic and chemical screens. Several studies now show the successful editing of disease-linked alleles in somatic and patient-derived induced pluripotent stem cells (iPSCs) as well as in animal models. Importantly, initial clinical trials have shown the safety of programmable nucleases for ex vivo somatic gene therapy. In this context, the unlimited proliferation potential and the pluripotent properties of iPSCs may offer advantages for gene targeting approaches. However, many technical and safety issues still need to be addressed before genome-edited iPSCs are translated into the clinical setting. Here, we provide an overview of the available genome editing systems and discuss opportunities and perspectives for their application in basic research and clinical practice, with a particular focus on hPSC based research and gene therapy approaches. Finally, we discuss recent research on human germline genome editing and its social and ethical implications. - Highlights: • Programmable nucleases have proven efficient and specific for genome editing in human pluripotent stem cells (hPSCs). • Genome edited hPSCs can be employed to study gene function in health and disease as well as drug and chemical screens. • Genome edited hPSCs hold great promise for ex vivo gene therapy approaches. • Technical and safety issues should be first addressed to advance the clinical use of gene-edited hPSCs.

  6. Genome editing in pluripotent stem cells: research and therapeutic applications

    International Nuclear Information System (INIS)

    Deleidi, Michela; Yu, Cong

    2016-01-01

    Recent progress in human pluripotent stem cell (hPSC) and genome editing technologies has opened up new avenues for the investigation of human biology in health and disease as well as the development of therapeutic applications. Gene editing approaches with programmable nucleases have been successfully established in hPSCs and applied to study gene function, develop novel animal models and perform genetic and chemical screens. Several studies now show the successful editing of disease-linked alleles in somatic and patient-derived induced pluripotent stem cells (iPSCs) as well as in animal models. Importantly, initial clinical trials have shown the safety of programmable nucleases for ex vivo somatic gene therapy. In this context, the unlimited proliferation potential and the pluripotent properties of iPSCs may offer advantages for gene targeting approaches. However, many technical and safety issues still need to be addressed before genome-edited iPSCs are translated into the clinical setting. Here, we provide an overview of the available genome editing systems and discuss opportunities and perspectives for their application in basic research and clinical practice, with a particular focus on hPSC based research and gene therapy approaches. Finally, we discuss recent research on human germline genome editing and its social and ethical implications. - Highlights: • Programmable nucleases have proven efficient and specific for genome editing in human pluripotent stem cells (hPSCs). • Genome edited hPSCs can be employed to study gene function in health and disease as well as drug and chemical screens. • Genome edited hPSCs hold great promise for ex vivo gene therapy approaches. • Technical and safety issues should be first addressed to advance the clinical use of gene-edited hPSCs.

  7. Mojo Hand, a TALEN design tool for genome editing applications

    Directory of Open Access Journals (Sweden)

    Neff Kevin L

    2013-01-01

    Full Text Available Abstract Background Recent studies of transcription activator-like (TAL effector domains fused to nucleases (TALENs demonstrate enormous potential for genome editing. Effective design of TALENs requires a combination of selecting appropriate genetic features, finding pairs of binding sites based on a consensus sequence, and, in some cases, identifying endogenous restriction sites for downstream molecular genetic applications. Results We present the web-based program Mojo Hand for designing TAL and TALEN constructs for genome editing applications (http://www.talendesign.org. We describe the algorithm and its implementation. The features of Mojo Hand include (1 automatic download of genomic data from the National Center for Biotechnology Information, (2 analysis of any DNA sequence to reveal pairs of binding sites based on a user-defined template, (3 selection of restriction-enzyme recognition sites in the spacer between the TAL monomer binding sites including options for the selection of restriction enzyme suppliers, and (4 output files designed for subsequent TALEN construction using the Golden Gate assembly method. Conclusions Mojo Hand enables the rapid identification of TAL binding sites for use in TALEN design. The assembly of TALEN constructs, is also simplified by using the TAL-site prediction program in conjunction with a spreadsheet management aid of reagent concentrations and TALEN formulation. Mojo Hand enables scientists to more rapidly deploy TALENs for genome editing applications.

  8. Mojo Hand, a TALEN design tool for genome editing applications.

    Science.gov (United States)

    Neff, Kevin L; Argue, David P; Ma, Alvin C; Lee, Han B; Clark, Karl J; Ekker, Stephen C

    2013-01-16

    Recent studies of transcription activator-like (TAL) effector domains fused to nucleases (TALENs) demonstrate enormous potential for genome editing. Effective design of TALENs requires a combination of selecting appropriate genetic features, finding pairs of binding sites based on a consensus sequence, and, in some cases, identifying endogenous restriction sites for downstream molecular genetic applications. We present the web-based program Mojo Hand for designing TAL and TALEN constructs for genome editing applications (http://www.talendesign.org). We describe the algorithm and its implementation. The features of Mojo Hand include (1) automatic download of genomic data from the National Center for Biotechnology Information, (2) analysis of any DNA sequence to reveal pairs of binding sites based on a user-defined template, (3) selection of restriction-enzyme recognition sites in the spacer between the TAL monomer binding sites including options for the selection of restriction enzyme suppliers, and (4) output files designed for subsequent TALEN construction using the Golden Gate assembly method. Mojo Hand enables the rapid identification of TAL binding sites for use in TALEN design. The assembly of TALEN constructs, is also simplified by using the TAL-site prediction program in conjunction with a spreadsheet management aid of reagent concentrations and TALEN formulation. Mojo Hand enables scientists to more rapidly deploy TALENs for genome editing applications.

  9. Novel applications of array comparative genomic hybridization in molecular diagnostics.

    Science.gov (United States)

    Cheung, Sau W; Bi, Weimin

    2018-05-31

    In 2004, the implementation of array comparative genomic hybridization (array comparative genome hybridization [CGH]) into clinical practice marked a new milestone for genetic diagnosis. Array CGH and single-nucleotide polymorphism (SNP) arrays enable genome-wide detection of copy number changes in a high resolution, and therefore microarray has been recognized as the first-tier test for patients with intellectual disability or multiple congenital anomalies, and has also been applied prenatally for detection of clinically relevant copy number variations in the fetus. Area covered: In this review, the authors summarize the evolution of array CGH technology from their diagnostic laboratory, highlighting exonic SNP arrays developed in the past decade which detect small intragenic copy number changes as well as large DNA segments for the region of heterozygosity. The applications of array CGH to human diseases with different modes of inheritance with the emphasis on autosomal recessive disorders are discussed. Expert commentary: An exonic array is a powerful and most efficient clinical tool in detecting genome wide small copy number variants in both dominant and recessive disorders. However, whole-genome sequencing may become the single integrated platform for detection of copy number changes, single-nucleotide changes as well as balanced chromosomal rearrangements in the near future.

  10. eXframe: reusable framework for storage, analysis and visualization of genomics experiments

    Directory of Open Access Journals (Sweden)

    Sinha Amit U

    2011-11-01

    Full Text Available Abstract Background Genome-wide experiments are routinely conducted to measure gene expression, DNA-protein interactions and epigenetic status. Structured metadata for these experiments is imperative for a complete understanding of experimental conditions, to enable consistent data processing and to allow retrieval, comparison, and integration of experimental results. Even though several repositories have been developed for genomics data, only a few provide annotation of samples and assays using controlled vocabularies. Moreover, many of them are tailored for a single type of technology or measurement and do not support the integration of multiple data types. Results We have developed eXframe - a reusable web-based framework for genomics experiments that provides 1 the ability to publish structured data compliant with accepted standards 2 support for multiple data types including microarrays and next generation sequencing 3 query, analysis and visualization integration tools (enabled by consistent processing of the raw data and annotation of samples and is available as open-source software. We present two case studies where this software is currently being used to build repositories of genomics experiments - one contains data from hematopoietic stem cells and another from Parkinson's disease patients. Conclusion The web-based framework eXframe offers structured annotation of experiments as well as uniform processing and storage of molecular data from microarray and next generation sequencing platforms. The framework allows users to query and integrate information across species, technologies, measurement types and experimental conditions. Our framework is reusable and freely modifiable - other groups or institutions can deploy their own custom web-based repositories based on this software. It is interoperable with the most important data formats in this domain. We hope that other groups will not only use eXframe, but also contribute their own

  11. XML-Based Visual Specification of Multidisciplinary Applications

    Science.gov (United States)

    Al-Theneyan, Ahmed; Jakatdar, Amol; Mehrotra, Piyush; Zubair, Mohammad

    2001-01-01

    The advancements in the Internet and Web technologies have fueled a growing interest in developing a web-based distributed computing environment. We have designed and developed Arcade, a web-based environment for designing, executing, monitoring, and controlling distributed heterogeneous applications, which is easy to use and access, portable, and provides support through all phases of the application development and execution. A major focus of the environment is the specification of heterogeneous, multidisciplinary applications. In this paper we focus on the visual and script-based specification interface of Arcade. The web/browser-based visual interface is designed to be intuitive to use and can also be used for visual monitoring during execution. The script specification is based on XML to: (1) make it portable across different frameworks, and (2) make the development of our tools easier by using the existing freely available XML parsers and editors. There is a one-to-one correspondence between the visual and script-based interfaces allowing users to go back and forth between the two. To support this we have developed translators that translate a script-based specification to a visual-based specification, and vice-versa. These translators are integrated with our tools and are transparent to users.

  12. Virtual Reality, 3D Stereo Visualization, and Applications in Robotics

    DEFF Research Database (Denmark)

    Livatino, Salvatore

    2006-01-01

    , while little can be found about the advantages of stereoscopic visualization in mobile robot tele-guide applications. This work investigates stereoscopic robot tele-guide under different conditions, including typical navigation scenarios and the use of synthetic and real images. This work also...

  13. Visual Development Environment for Semantically Interoperable Smart Cities Applications

    OpenAIRE

    Roukounaki , Aikaterini; Soldatos , John; Petrolo , Riccardo; Loscri , Valeria; Mitton , Nathalie; Serrano , Martin

    2015-01-01

    International audience; This paper presents an IoT architecture for the semantic interoperability of diverse IoT systems and applications in smart cities. The architecture virtualizes diverse IoT systems and ensures their modelling and representation according to common standards-based IoT ontologies. Furthermore, based on this architecture, the paper introduces a first-of-a-kind visual development environment which eases the development of semantically interoperable applications in smart cit...

  14. Informative genomic microsatellite markers for efficient genotyping applications in sugarcane.

    Science.gov (United States)

    Parida, Swarup K; Kalia, Sanjay K; Kaul, Sunita; Dalal, Vivek; Hemaprabha, G; Selvi, Athiappan; Pandit, Awadhesh; Singh, Archana; Gaikwad, Kishor; Sharma, Tilak R; Srivastava, Prem Shankar; Singh, Nagendra K; Mohapatra, Trilochan

    2009-01-01

    Genomic microsatellite markers are capable of revealing high degree of polymorphism. Sugarcane (Saccharum sp.), having a complex polyploid genome requires more number of such informative markers for various applications in genetics and breeding. With the objective of generating a large set of microsatellite markers designated as Sugarcane Enriched Genomic MicroSatellite (SEGMS), 6,318 clones from genomic libraries of two hybrid sugarcane cultivars enriched with 18 different microsatellite repeat-motifs were sequenced to generate 4.16 Mb high-quality sequences. Microsatellites were identified in 1,261 of the 5,742 non-redundant clones that accounted for 22% enrichment of the libraries. Retro-transposon association was observed for 23.1% of the identified microsatellites. The utility of the microsatellite containing genomic sequences were demonstrated by higher primer designing potential (90%) and PCR amplification efficiency (87.4%). A total of 1,315 markers including 567 class I microsatellite markers were designed and placed in the public domain for unrestricted use. The level of polymorphism detected by these markers among sugarcane species, genera, and varieties was 88.6%, while cross-transferability rate was 93.2% within Saccharum complex and 25% to cereals. Cloning and sequencing of size variant amplicons revealed that the variation in the number of repeat-units was the main source of SEGMS fragment length polymorphism. High level of polymorphism and wide range of genetic diversity (0.16-0.82 with an average of 0.44) assayed with the SEGMS markers suggested their usefulness in various genotyping applications in sugarcane.

  15. Application of neutron radiography to visualization of multiphase flows

    International Nuclear Information System (INIS)

    Takenaka, N.; Fujii, T.; Nishizaki, K.; Asano, H.; Ono, A.; Sonoda, K.; Akagawa, K.

    1990-01-01

    Visualizations by real-time neutron radiography are demonstrated of various flow patterns of nitrogen gas-water two-phase flow in a stainless-steel tube, water inverted annular flow in a stainless-steel tube, flashing flow in an aluminium nozzle and fluidized bed in aluminium tube and vessels. Photographs every 1/60 s are presented by an image processing method to show the dynamic behaviours of the various flow patterns. It is shown that this visualization method can be applied efficiently to multiphase flow researches and will be applicable to multiphase flows in industrial machines. (author)

  16. MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads.

    Science.gov (United States)

    Tyakht, Alexander V; Popenko, Anna S; Belenikin, Maxim S; Altukhov, Ilya A; Pavlenko, Alexander V; Kostryukova, Elena S; Selezneva, Oksana V; Larin, Andrei K; Karpova, Irina Y; Alexeev, Dmitry G

    2012-12-07

    MALINA is a web service for bioinformatic analysis of whole-genome metagenomic data obtained from human gut microbiota sequencing. As input data, it accepts metagenomic reads of various sequencing technologies, including long reads (such as Sanger and 454 sequencing) and next-generation (including SOLiD and Illumina). It is the first metagenomic web service that is capable of processing SOLiD color-space reads, to authors' knowledge. The web service allows phylogenetic and functional profiling of metagenomic samples using coverage depth resulting from the alignment of the reads to the catalogue of reference sequences which are built into the pipeline and contain prevalent microbial genomes and genes of human gut microbiota. The obtained metagenomic composition vectors are processed by the statistical analysis and visualization module containing methods for clustering, dimension reduction and group comparison. Additionally, the MALINA database includes vectors of bacterial and functional composition for human gut microbiota samples from a large number of existing studies allowing their comparative analysis together with user samples, namely datasets from Russian Metagenome project, MetaHIT and Human Microbiome Project (downloaded from http://hmpdacc.org). MALINA is made freely available on the web at http://malina.metagenome.ru. The website is implemented in JavaScript (using Ext JS), Microsoft .NET Framework, MS SQL, Python, with all major browsers supported.

  17. BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications.

    Science.gov (United States)

    Cui, Ya; Chen, Xiaowei; Luo, Huaxia; Fan, Zhen; Luo, Jianjun; He, Shunmin; Yue, Haiyan; Zhang, Peng; Chen, Runsheng

    2016-06-01

    We here present BioCircos.js, an interactive and lightweight JavaScript library especially for biological data interactive visualization. BioCircos.js facilitates the development of web-based applications for circular visualization of various biological data, such as genomic features, genetic variations, gene expression and biomolecular interactions. BioCircos.js and its manual are freely available online at http://bioinfo.ibp.ac.cn/biocircos/ rschen@ibp.ac.cn Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  18. Closing the gap between knowledge and clinical application: challenges for genomic translation.

    Science.gov (United States)

    Burke, Wylie; Korngiebel, Diane M

    2015-01-01

    Despite early predictions and rapid progress in research, the introduction of personal genomics into clinical practice has been slow. Several factors contribute to this translational gap between knowledge and clinical application. The evidence available to support genetic test use is often limited, and implementation of new testing programs can be challenging. In addition, the heterogeneity of genomic risk information points to the need for strategies to select and deliver the information most appropriate for particular clinical needs. Accomplishing these tasks also requires recognition that some expectations for personal genomics are unrealistic, notably expectations concerning the clinical utility of genomic risk assessment for common complex diseases. Efforts are needed to improve the body of evidence addressing clinical outcomes for genomics, apply implementation science to personal genomics, and develop realistic goals for genomic risk assessment. In addition, translational research should emphasize the broader benefits of genomic knowledge, including applications of genomic research that provide clinical benefit outside the context of personal genomic risk.

  19. Future Translational Applications From the Contemporary Genomics Era

    Science.gov (United States)

    Fox, Caroline S.; Hall, Jennifer L.; Arnett, Donna K.; Ashley, Euan A.; Delles, Christian; Engler, Mary B.; Freeman, Mason W.; Johnson, Julie A.; Lanfear, David E.; Liggett, Stephen B.; Lusis, Aldons J.; Loscalzo, Joseph; MacRae, Calum A.; Musunuru, Kiran; Newby, L. Kristin; O’Donnell, Christopher J.; Rich, Stephen S.; Terzic, Andre

    2016-01-01

    The field of genetics and genomics has advanced considerably with the achievement of recent milestones encompassing the identification of many loci for cardiovascular disease and variable drug responses. Despite this achievement, a gap exists in the understanding and advancement to meaningful translation that directly affects disease prevention and clinical care. The purpose of this scientific statement is to address the gap between genetic discoveries and their practical application to cardiovascular clinical care. In brief, this scientific statement assesses the current timeline for effective translation of basic discoveries to clinical advances, highlighting past successes. Current discoveries in the area of genetics and genomics are covered next, followed by future expectations, tools, and competencies for achieving the goal of improving clinical care. PMID:25882488

  20. Applications of Genomic Sequencing in Pediatric CNS Tumors.

    Science.gov (United States)

    Bavle, Abhishek A; Lin, Frank Y; Parsons, D Williams

    2016-05-01

    Recent advances in genome-scale sequencing methods have resulted in a significant increase in our understanding of the biology of human cancers. When applied to pediatric central nervous system (CNS) tumors, these remarkable technological breakthroughs have facilitated the molecular characterization of multiple tumor types, provided new insights into the genetic basis of these cancers, and prompted innovative strategies that are changing the management paradigm in pediatric neuro-oncology. Genomic tests have begun to affect medical decision making in a number of ways, from delineating histopathologically similar tumor types into distinct molecular subgroups that correlate with clinical characteristics, to guiding the addition of novel therapeutic agents for patients with high-risk or poor-prognosis tumors, or alternatively, reducing treatment intensity for those with a favorable prognosis. Genomic sequencing has also had a significant impact on translational research strategies in pediatric CNS tumors, resulting in wide-ranging applications that have the potential to direct the rational preclinical screening of novel therapeutic agents, shed light on tumor heterogeneity and evolution, and highlight differences (or similarities) between pediatric and adult CNS tumors. Finally, in addition to allowing the identification of somatic (tumor-specific) mutations, the analysis of patient-matched constitutional (germline) DNA has facilitated the detection of pathogenic germline alterations in cancer genes in patients with CNS tumors, with critical implications for genetic counseling and tumor surveillance strategies for children with familial predisposition syndromes. As our understanding of the molecular landscape of pediatric CNS tumors continues to advance, innovative applications of genomic sequencing hold significant promise for further improving the care of children with these cancers.

  1. Robust Control for High-Speed Visual Servoing Applications

    DEFF Research Database (Denmark)

    Ellekilde, Lars-Peter; Favrholdt, Peter; Paulin, Mads

    2007-01-01

    This paper presents a new control scheme for visual servoing applications. The approach employs quadratic optimization, and explicitly handles both joint position, velocity and acceleration limits. Contrary to existing techniques, our method does not rely on large safety margins and slow task...... execution to avoid joint limits, and is hence able to exploit the full potential of the robot. Furthermore, our control scheme guarantees a well-defined behavior of the robot even when it is in a singular configuration, and thus handles both internal and external singularities robustly. We demonstrate...... the correctness and efficiency of our approach in a number of visual servoing applications, and compare it to a range of previously proposed techniques....

  2. SCSODC: Integrating Ocean Data for Visualization Sharing and Application

    International Nuclear Information System (INIS)

    Xu, C; Xie, Q; Li, S; Wang, D

    2014-01-01

    The South China Sea Ocean Data Center (SCSODC) was founded in 2010 in order to improve collecting and managing of ocean data of the South China Sea Institute of Oceanology (SCSIO). The mission of SCSODC is to ensure the long term scientific stewardship of ocean data, information and products – collected through research groups, monitoring stations and observation cruises – and to facilitate the efficient use and distribution to possible users. However, data sharing and applications were limited due to the characteristics of distribution and heterogeneity that made it difficult to integrate the data. To surmount those difficulties, the Data Sharing System has been developed by the SCSODC using the most appropriate information management and information technology. The Data Sharing System uses open standards and tools to promote the capability to integrate ocean data and to interact with other data portals or users and includes a full range of processes such as data discovery, evaluation and access combining C/S and B/S mode. It provides a visualized management interface for the data managers and a transparent and seamless data access and application environment for users. Users are allowed to access data using the client software and to access interactive visualization application interface via a web browser. The architecture, key technologies and functionality of the system are discussed briefly in this paper. It is shown that the system of SCSODC is able to implement web visualization sharing and seamless access to ocean data in a distributed and heterogeneous environment

  3. SCSODC: Integrating Ocean Data for Visualization Sharing and Application

    Science.gov (United States)

    Xu, C.; Li, S.; Wang, D.; Xie, Q.

    2014-02-01

    The South China Sea Ocean Data Center (SCSODC) was founded in 2010 in order to improve collecting and managing of ocean data of the South China Sea Institute of Oceanology (SCSIO). The mission of SCSODC is to ensure the long term scientific stewardship of ocean data, information and products - collected through research groups, monitoring stations and observation cruises - and to facilitate the efficient use and distribution to possible users. However, data sharing and applications were limited due to the characteristics of distribution and heterogeneity that made it difficult to integrate the data. To surmount those difficulties, the Data Sharing System has been developed by the SCSODC using the most appropriate information management and information technology. The Data Sharing System uses open standards and tools to promote the capability to integrate ocean data and to interact with other data portals or users and includes a full range of processes such as data discovery, evaluation and access combining C/S and B/S mode. It provides a visualized management interface for the data managers and a transparent and seamless data access and application environment for users. Users are allowed to access data using the client software and to access interactive visualization application interface via a web browser. The architecture, key technologies and functionality of the system are discussed briefly in this paper. It is shown that the system of SCSODC is able to implement web visualization sharing and seamless access to ocean data in a distributed and heterogeneous environment.

  4. Use of application containers and workflows for genomic data analysis

    Directory of Open Access Journals (Sweden)

    Wade L Schulz

    2016-01-01

    Full Text Available Background: The rapid acquisition of biological data and development of computationally intensive analyses has led to a need for novel approaches to software deployment. In particular, the complexity of common analytic tools for genomics makes them difficult to deploy and decreases the reproducibility of computational experiments. Methods: Recent technologies that allow for application virtualization, such as Docker, allow developers and bioinformaticians to isolate these applications and deploy secure, scalable platforms that have the potential to dramatically increase the efficiency of big data processing. Results: While limitations exist, this study demonstrates a successful implementation of a pipeline with several discrete software applications for the analysis of next-generation sequencing (NGS data. Conclusions: With this approach, we significantly reduced the amount of time needed to perform clonal analysis from NGS data in acute myeloid leukemia.

  5. Use of application containers and workflows for genomic data analysis

    Science.gov (United States)

    Schulz, Wade L.; Durant, Thomas J. S.; Siddon, Alexa J.; Torres, Richard

    2016-01-01

    Background: The rapid acquisition of biological data and development of computationally intensive analyses has led to a need for novel approaches to software deployment. In particular, the complexity of common analytic tools for genomics makes them difficult to deploy and decreases the reproducibility of computational experiments. Methods: Recent technologies that allow for application virtualization, such as Docker, allow developers and bioinformaticians to isolate these applications and deploy secure, scalable platforms that have the potential to dramatically increase the efficiency of big data processing. Results: While limitations exist, this study demonstrates a successful implementation of a pipeline with several discrete software applications for the analysis of next-generation sequencing (NGS) data. Conclusions: With this approach, we significantly reduced the amount of time needed to perform clonal analysis from NGS data in acute myeloid leukemia. PMID:28163975

  6. Landscape metrics application in ecological and visual landscape assessment

    Directory of Open Access Journals (Sweden)

    Gavrilović Suzana

    2017-01-01

    Full Text Available The development of landscape-ecological approach application in spatial planning provides exact theoretical and empirical evidence for monitoring ecological consequences of natural and/or anthropogenic factors, particularly changes in spatial structures caused by them. Landscape pattern which feature diverse landscape values is the holder of the unique landscape character at different spatial levels and represents a perceptual domain for its users. Using the landscape metrics, the parameters of landscape composition and configuration are mathematical algorithms that quantify the specific spatial characteristics used for interpretation of landscape features and processes (physical and ecological aspect, as well as forms (visual aspect and the meaning (cognitive aspect of the landscape. Landscape metrics has been applied mostly in the ecological and biodiversity assessments as well as in the determination of the level of structural change of landscape, but more and more applied in the assessment of the visual character of the landscape. Based on a review of relevant literature, the aim of this work is to show the main trends of landscape metrics within the aspect of ecological and visual assessments. The research methodology is based on the analysis, classification and systematization of the research studies published from 2000 to 2016, where the landscape metrics is applied: (1 the analysis of landscape pattern and its changes, (2 the analysis of biodiversity and habitat function and (3 a visual landscape assessment. By selecting representative metric parameters for the landscape composition and configuration, for each category is formed the basis for further landscape metrics research and application for the integrated ecological and visual assessment of the landscape values. Contemporary conceptualization of the landscape is seen holistically, and the future research should be directed towards the development of integrated landscape assessment

  7. Structured Matrix Completion with Applications to Genomic Data Integration.

    Science.gov (United States)

    Cai, Tianxi; Cai, T Tony; Zhang, Anru

    2016-01-01

    Matrix completion has attracted significant recent attention in many fields including statistics, applied mathematics and electrical engineering. Current literature on matrix completion focuses primarily on independent sampling models under which the individual observed entries are sampled independently. Motivated by applications in genomic data integration, we propose a new framework of structured matrix completion (SMC) to treat structured missingness by design. Specifically, our proposed method aims at efficient matrix recovery when a subset of the rows and columns of an approximately low-rank matrix are observed. We provide theoretical justification for the proposed SMC method and derive lower bound for the estimation errors, which together establish the optimal rate of recovery over certain classes of approximately low-rank matrices. Simulation studies show that the method performs well in finite sample under a variety of configurations. The method is applied to integrate several ovarian cancer genomic studies with different extent of genomic measurements, which enables us to construct more accurate prediction rules for ovarian cancer survival.

  8. Applicability of SCAR markers to food genomics: olive oil traceability.

    Science.gov (United States)

    Pafundo, Simona; Agrimonti, Caterina; Maestri, Elena; Marmiroli, Nelson

    2007-07-25

    DNA analysis with molecular markers has opened a shortcut toward a genomic comprehension of complex organisms. The availability of micro-DNA extraction methods, coupled with selective amplification of the smallest extracted fragments with molecular markers, could equally bring a breakthrough in food genomics: the identification of original components in food. Amplified fragment length polymorphisms (AFLPs) have been instrumental in plant genomics because they may allow rapid and reliable analysis of multiple and potentially polymorphic sites. Nevertheless, their direct application to the analysis of DNA extracted from food matrixes is complicated by the low quality of DNA extracted: its high degradation and the presence of inhibitors of enzymatic reactions. The conversion of an AFLP fragment to a robust and specific single-locus PCR-based marker, therefore, could extend the use of molecular markers to large-scale analysis of complex agro-food matrixes. In the present study is reported the development of sequence characterized amplified regions (SCARs) starting from AFLP profiles of monovarietal olive oils analyzed on agarose gel; one of these was used to identify differences among 56 olive cultivars. All the developed markers were purposefully amplified in olive oils to apply them to olive oil traceability.

  9. aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations.

    Directory of Open Access Journals (Sweden)

    Victor Renault

    Full Text Available Copy number variations (CNV include net gains or losses of part or whole chromosomal regions. They differ from copy neutral loss of heterozygosity (cn-LOH events which do not induce any net change in the copy number and are often associated with uniparental disomy. These phenomena have long been reported to be associated with diseases and particularly in cancer. Losses/gains of genomic regions are often correlated with lower/higher gene expression. On the other hand, loss of heterozygosity (LOH and cn-LOH are common events in cancer and may be associated with the loss of a functional tumor suppressor gene. Therefore, identifying recurrent CNV and cn-LOH events can be important as they may highlight common biological components and give insights into the development or mechanisms of a disease. However, no currently available tools allow a comprehensive whole-genome visualization of recurrent CNVs and cn-LOH in groups of samples providing absolute quantification of the aberrations leading to the loss of potentially important information.To overcome these limitations, we developed aCNViewer (Absolute CNV Viewer, a visualization tool for absolute CNVs and cn-LOH across a group of samples. aCNViewer proposes three graphical representations: dendrograms, bi-dimensional heatmaps showing chromosomal regions sharing similar abnormality patterns, and quantitative stacked histograms facilitating the identification of recurrent absolute CNVs and cn-LOH. We illustrated aCNViewer using publically available hepatocellular carcinomas (HCCs Affymetrix SNP Array data (Fig 1A. Regions 1q and 8q present a similar percentage of total gains but significantly different copy number gain categories (p-value of 0.0103 with a Fisher exact test, validated by another cohort of HCCs (p-value of 5.6e-7 (Fig 2B.aCNViewer is implemented in python and R and is available with a GNU GPLv3 license on GitHub https://github.com/FJD-CEPH/aCNViewer and Docker https://hub.docker.com/r/fjdceph/acnviewer/.aCNViewer@cephb.fr.

  10. aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations.

    Science.gov (United States)

    Renault, Victor; Tost, Jörg; Pichon, Fabien; Wang-Renault, Shu-Fang; Letouzé, Eric; Imbeaud, Sandrine; Zucman-Rossi, Jessica; Deleuze, Jean-François; How-Kit, Alexandre

    2017-01-01

    Copy number variations (CNV) include net gains or losses of part or whole chromosomal regions. They differ from copy neutral loss of heterozygosity (cn-LOH) events which do not induce any net change in the copy number and are often associated with uniparental disomy. These phenomena have long been reported to be associated with diseases and particularly in cancer. Losses/gains of genomic regions are often correlated with lower/higher gene expression. On the other hand, loss of heterozygosity (LOH) and cn-LOH are common events in cancer and may be associated with the loss of a functional tumor suppressor gene. Therefore, identifying recurrent CNV and cn-LOH events can be important as they may highlight common biological components and give insights into the development or mechanisms of a disease. However, no currently available tools allow a comprehensive whole-genome visualization of recurrent CNVs and cn-LOH in groups of samples providing absolute quantification of the aberrations leading to the loss of potentially important information. To overcome these limitations, we developed aCNViewer (Absolute CNV Viewer), a visualization tool for absolute CNVs and cn-LOH across a group of samples. aCNViewer proposes three graphical representations: dendrograms, bi-dimensional heatmaps showing chromosomal regions sharing similar abnormality patterns, and quantitative stacked histograms facilitating the identification of recurrent absolute CNVs and cn-LOH. We illustrated aCNViewer using publically available hepatocellular carcinomas (HCCs) Affymetrix SNP Array data (Fig 1A). Regions 1q and 8q present a similar percentage of total gains but significantly different copy number gain categories (p-value of 0.0103 with a Fisher exact test), validated by another cohort of HCCs (p-value of 5.6e-7) (Fig 2B). aCNViewer is implemented in python and R and is available with a GNU GPLv3 license on GitHub https://github.com/FJD-CEPH/aCNViewer and Docker https

  11. Natural Inspired Intelligent Visual Computing and Its Application to Viticulture.

    Science.gov (United States)

    Ang, Li Minn; Seng, Kah Phooi; Ge, Feng Lu

    2017-05-23

    This paper presents an investigation of natural inspired intelligent computing and its corresponding application towards visual information processing systems for viticulture. The paper has three contributions: (1) a review of visual information processing applications for viticulture; (2) the development of natural inspired computing algorithms based on artificial immune system (AIS) techniques for grape berry detection; and (3) the application of the developed algorithms towards real-world grape berry images captured in natural conditions from vineyards in Australia. The AIS algorithms in (2) were developed based on a nature-inspired clonal selection algorithm (CSA) which is able to detect the arcs in the berry images with precision, based on a fitness model. The arcs detected are then extended to perform the multiple arcs and ring detectors information processing for the berry detection application. The performance of the developed algorithms were compared with traditional image processing algorithms like the circular Hough transform (CHT) and other well-known circle detection methods. The proposed AIS approach gave a Fscore of 0.71 compared with Fscores of 0.28 and 0.30 for the CHT and a parameter-free circle detection technique (RPCD) respectively.

  12. 802.11s Wireless Mesh Network Visualization Application

    Science.gov (United States)

    Mauldin, James Alexander

    2014-01-01

    Results of past experimentation at NASA Johnson Space Center showed that the IEEE 802.11s standard has better performance than the widely implemented alternative protocol B.A.T.M.A.N (Better Approach to Mobile Ad hoc Networking). 802.11s is now formally incorporated into the Wi- Fi 802.11-2012 standard, which specifies a hybrid wireless mesh networking protocol (HWMP). In order to quickly analyze changes to the routing algorithm and to support optimizing the mesh network behavior for our intended application a visualization tool was developed by modifying and integrating open source tools.

  13. Application of Genomic Technologies to the Breeding of Trees.

    Science.gov (United States)

    Badenes, Maria L; Fernández I Martí, Angel; Ríos, Gabino; Rubio-Cabetas, María J

    2016-01-01

    The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the

  14. GIANT API: an application programming interface for functional genomics.

    Science.gov (United States)

    Roberts, Andrew M; Wong, Aaron K; Fisk, Ian; Troyanskaya, Olga G

    2016-07-08

    GIANT API provides biomedical researchers programmatic access to tissue-specific and global networks in humans and model organisms, and associated tools, which includes functional re-prioritization of existing genome-wide association study (GWAS) data. Using tissue-specific interaction networks, researchers are able to predict relationships between genes specific to a tissue or cell lineage, identify the changing roles of genes across tissues and uncover disease-gene associations. Additionally, GIANT API enables computational tools like NetWAS, which leverages tissue-specific networks for re-prioritization of GWAS results. The web services covered by the API include 144 tissue-specific functional gene networks in human, global functional networks for human and six common model organisms and the NetWAS method. GIANT API conforms to the REST architecture, which makes it stateless, cacheable and highly scalable. It can be used by a diverse range of clients including web browsers, command terminals, programming languages and standalone apps for data analysis and visualization. The API is freely available for use at http://giant-api.princeton.edu. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Image processing and applications based on visualizing navigation service

    Science.gov (United States)

    Hwang, Chyi-Wen

    2015-07-01

    When facing the "overabundant" of semantic web information, in this paper, the researcher proposes the hierarchical classification and visualizing RIA (Rich Internet Application) navigation system: Concept Map (CM) + Semantic Structure (SS) + the Knowledge on Demand (KOD) service. The aim of the Multimedia processing and empirical applications testing, was to investigating the utility and usability of this visualizing navigation strategy in web communication design, into whether it enables the user to retrieve and construct their personal knowledge or not. Furthermore, based on the segment markets theory in the Marketing model, to propose a User Interface (UI) classification strategy and formulate a set of hypermedia design principles for further UI strategy and e-learning resources in semantic web communication. These research findings: (1) Irrespective of whether the simple declarative knowledge or the complex declarative knowledge model is used, the "CM + SS + KOD navigation system" has a better cognition effect than the "Non CM + SS + KOD navigation system". However, for the" No web design experience user", the navigation system does not have an obvious cognition effect. (2) The essential of classification in semantic web communication design: Different groups of user have a diversity of preference needs and different cognitive styles in the CM + SS + KOD navigation system.

  16. Application of visual cryptography for learning in optics and photonics

    Science.gov (United States)

    Mandal, Avikarsha; Wozniak, Peter; Vauderwange, Oliver; Curticapean, Dan

    2016-09-01

    In the age data digitalization, important applications of optics and photonics based sensors and technology lie in the field of biometrics and image processing. Protecting user data in a safe and secure way is an essential task in this area. However, traditional cryptographic protocols rely heavily on computer aided computation. Secure protocols which rely only on human interactions are usually simpler to understand. In many scenarios development of such protocols are also important for ease of implementation and deployment. Visual cryptography (VC) is an encryption technique on images (or text) in which decryption is done by human visual system. In this technique, an image is encrypted into number of pieces (known as shares). When the printed shares are physically superimposed together, the image can be decrypted with human vision. Modern digital watermarking technologies can be combined with VC for image copyright protection where the shares can be watermarks (small identification) embedded in the image. Similarly, VC can be used for improving security of biometric authentication. This paper presents about design and implementation of a practical laboratory experiment based on the concept of VC for a course in media engineering. Specifically, our contribution deals with integration of VC in different schemes for applications like digital watermarking and biometric authentication in the field of optics and photonics. We describe theoretical concepts and propose our infrastructure for the experiment. Finally, we will evaluate the learning outcome of the experiment, performed by the students.

  17. SpectralNET – an application for spectral graph analysis and visualization

    Directory of Open Access Journals (Sweden)

    Schreiber Stuart L

    2005-10-01

    Full Text Available Abstract Background Graph theory provides a computational framework for modeling a variety of datasets including those emerging from genomics, proteomics, and chemical genetics. Networks of genes, proteins, small molecules, or other objects of study can be represented as graphs of nodes (vertices and interactions (edges that can carry different weights. SpectralNET is a flexible application for analyzing and visualizing these biological and chemical networks. Results Available both as a standalone .NET executable and as an ASP.NET web application, SpectralNET was designed specifically with the analysis of graph-theoretic metrics in mind, a computational task not easily accessible using currently available applications. Users can choose either to upload a network for analysis using a variety of input formats, or to have SpectralNET generate an idealized random network for comparison to a real-world dataset. Whichever graph-generation method is used, SpectralNET displays detailed information about each connected component of the graph, including graphs of degree distribution, clustering coefficient by degree, and average distance by degree. In addition, extensive information about the selected vertex is shown, including degree, clustering coefficient, various distance metrics, and the corresponding components of the adjacency, Laplacian, and normalized Laplacian eigenvectors. SpectralNET also displays several graph visualizations, including a linear dimensionality reduction for uploaded datasets (Principal Components Analysis and a non-linear dimensionality reduction that provides an elegant view of global graph structure (Laplacian eigenvectors. Conclusion SpectralNET provides an easily accessible means of analyzing graph-theoretic metrics for data modeling and dimensionality reduction. SpectralNET is publicly available as both a .NET application and an ASP.NET web application from http://chembank.broad.harvard.edu/resources/. Source code is

  18. Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna.

    Science.gov (United States)

    Nakamura, Yoji; Mori, Kazuki; Saitoh, Kenji; Oshima, Kenshiro; Mekuchi, Miyuki; Sugaya, Takuma; Shigenobu, Yuya; Ojima, Nobuhiko; Muta, Shigeru; Fujiwara, Atushi; Yasuike, Motoshige; Oohara, Ichiro; Hirakawa, Hideki; Chowdhury, Vishwajit Sur; Kobayashi, Takanori; Nakajima, Kazuhiro; Sano, Motohiko; Wada, Tokio; Tashiro, Kosuke; Ikeo, Kazuho; Hattori, Masahira; Kuhara, Satoru; Gojobori, Takashi; Inouye, Kiyoshi

    2013-07-02

    Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values, the open-ocean lifestyle of tuna, in which effective sensing systems such as color vision are required for capture of prey, has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna, we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis), using next-generation sequencing technology. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified five common fish visual pigment genes: red-sensitive (middle/long-wavelength sensitive; M/LWS), UV-sensitive (short-wavelength sensitive 1; SWS1), blue-sensitive (SWS2), rhodopsin (RH1), and green-sensitive (RH2) opsin genes. Sequence comparison revealed that tuna's RH1 gene has an amino acid substitution that causes a short-wave shift in the absorption spectrum (i.e., blue shift). Pacific bluefin tuna has at least five RH2 paralogs, the most among studied fishes; four of the proteins encoded may be tuned to blue light at the amino acid level. Moreover, phylogenetic analysis suggested that gene conversions have occurred in each of the SWS2 and RH2 loci in a short period. Thus, Pacific bluefin tuna has undergone evolutionary changes in three genes (RH1, RH2, and SWS2), which may have contributed to detecting blue-green contrast and measuring the distance to prey in the blue-pelagic ocean. These findings provide basic information on behavioral traits of predatory fish and, thereby, could help to improve the technology to culture such fish in captivity for resource management.

  19. MetReS, an Efficient Database for Genomic Applications.

    Science.gov (United States)

    Vilaplana, Jordi; Alves, Rui; Solsona, Francesc; Mateo, Jordi; Teixidó, Ivan; Pifarré, Marc

    2018-02-01

    MetReS (Metabolic Reconstruction Server) is a genomic database that is shared between two software applications that address important biological problems. Biblio-MetReS is a data-mining tool that enables the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the processes of interest and their function. The main goal of this work was to identify the areas where the performance of the MetReS database performance could be improved and to test whether this improvement would scale to larger datasets and more complex types of analysis. The study was started with a relational database, MySQL, which is the current database server used by the applications. We also tested the performance of an alternative data-handling framework, Apache Hadoop. Hadoop is currently used for large-scale data processing. We found that this data handling framework is likely to greatly improve the efficiency of the MetReS applications as the dataset and the processing needs increase by several orders of magnitude, as expected to happen in the near future.

  20. Be-Breeder - an application for analysis of genomic data in plant breeding

    OpenAIRE

    Matias,Filipe Inácio; Granato,Italo Stefanine Correa; Dequigiovanni,Gabriel; Fritsche-Neto,Roberto

    2017-01-01

    Abstract Be-Breeder is an application directed toward genetic breeding of plants, developed through the Shiny package of the R software, which allows different phenotype and molecular (marker) analysis to be undertaken. The section for analysis of molecular data of the Be-Breeder application makes it possible to achieve quality control of genotyping data, to obtain genomic kinship matrices, and to analyze genome selection, genome association, and genetic diversity in a simple manner on line. ...

  1. Analytical Review of Data Visualization Methods in Application to Big Data

    OpenAIRE

    Gorodov, Evgeniy Yur’evich; Gubarev, Vasiliy Vasil’evich

    2013-01-01

    This paper describes the term Big Data in aspects of data representation and visualization. There are some specific problems in Big Data visualization, so there are definitions for these problems and a set of approaches to avoid them. Also, we make a review of existing methods for data visualization in application to Big Data and taking into account the described problems. Summarizing the result, we have provided a classification of visualization methods in application to Big Data.

  2. Interactive visualization and analysis of multimodal datasets for surgical applications.

    Science.gov (United States)

    Kirmizibayrak, Can; Yim, Yeny; Wakid, Mike; Hahn, James

    2012-12-01

    Surgeons use information from multiple sources when making surgical decisions. These include volumetric datasets (such as CT, PET, MRI, and their variants), 2D datasets (such as endoscopic videos), and vector-valued datasets (such as computer simulations). Presenting all the information to the user in an effective manner is a challenging problem. In this paper, we present a visualization approach that displays the information from various sources in a single coherent view. The system allows the user to explore and manipulate volumetric datasets, display analysis of dataset values in local regions, combine 2D and 3D imaging modalities and display results of vector-based computer simulations. Several interaction methods are discussed: in addition to traditional interfaces including mouse and trackers, gesture-based natural interaction methods are shown to control these visualizations with real-time performance. An example of a medical application (medialization laryngoplasty) is presented to demonstrate how the combination of different modalities can be used in a surgical setting with our approach.

  3. A review of visual MODFLOW applications in groundwater modelling

    Science.gov (United States)

    Hariharan, V.; Shankar, M. Uma

    2017-11-01

    Visual MODLOW is a Graphical User Interface for the USGS MODFLOW. It is a commercial software that is popular among the hydrogeologists for its user-friendly features. The software is mainly used for Groundwater flow and contaminant transport models under different conditions. This article is intended to review the versatility of its applications in groundwater modelling for the last 22 years. Agriculture, airfields, constructed wetlands, climate change, drought studies, Environmental Impact Assessment (EIA), landfills, mining operations, river and flood plain monitoring, salt water intrusion, soil profile surveys, watershed analyses, etc., are the areas where the software has been reportedly used till the current date. The review will provide a clarity on the scope of the software in groundwater modelling and research.

  4. MOST-visualization: software for producing automated textbook-style maps of genome-scale metabolic networks.

    Science.gov (United States)

    Kelley, James J; Maor, Shay; Kim, Min Kyung; Lane, Anatoliy; Lun, Desmond S

    2017-08-15

    Visualization of metabolites, reactions and pathways in genome-scale metabolic networks (GEMs) can assist in understanding cellular metabolism. Three attributes are desirable in software used for visualizing GEMs: (i) automation, since GEMs can be quite large; (ii) production of understandable maps that provide ease in identification of pathways, reactions and metabolites; and (iii) visualization of the entire network to show how pathways are interconnected. No software currently exists for visualizing GEMs that satisfies all three characteristics, but MOST-Visualization, an extension of the software package MOST (Metabolic Optimization and Simulation Tool), satisfies (i), and by using a pre-drawn overview map of metabolism based on the Roche map satisfies (ii) and comes close to satisfying (iii). MOST is distributed for free on the GNU General Public License. The software and full documentation are available at http://most.ccib.rutgers.edu/. dslun@rutgers.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  5. Applications of Support Vector Machine (SVM) Learning in Cancer Genomics

    OpenAIRE

    HUANG, SHUJUN; CAI, NIANGUANG; PACHECO, PEDRO PENZUTI; NARANDES, SHAVIRA; WANG, YANG; XU, WAYNE

    2017-01-01

    Machine learning with maximization (support) of separating margin (vector), called support vector machine (SVM) learning, is a powerful classification tool that has been used for cancer genomic classification or subtyping. Today, as advancements in high-throughput technologies lead to production of large amounts of genomic and epigenomic data, the classification feature of SVMs is expanding its use in cancer genomics, leading to the discovery of new biomarkers, new drug targets, and a better ...

  6. ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.

    Science.gov (United States)

    Sablok, Gaurav; Chen, Ting-Wen; Lee, Chi-Ching; Yang, Chi; Gan, Ruei-Chi; Wegrzyn, Jill L; Porta, Nicola L; Nayak, Kinshuk C; Huang, Po-Jung; Varotto, Claudio; Tang, Petrus

    2017-06-01

    Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes. In light of the importance of codon usage patterns in the development of hyper-expression organelle transgenics, we present ChloroMitoCU, the first-ever curated, web-based reference catalog of the codon usage patterns in organelle genomes. ChloroMitoCU contains the pre-compiled codon usage patterns of 328 chloroplast genomes (29,960 CDS) and 3,502 mitochondrial genomes (49,066 CDS), enabling genome-wide exploration and comparative analysis of codon usage patterns across species. ChloroMitoCU allows the phylogenetic comparison of codon usage patterns across organelle genomes, the prediction of codon usage patterns based on user-submitted transcripts or assembled organelle genes, and comparative analysis with the pre-compiled patterns across species of interest. ChloroMitoCU can increase our understanding of the biased patterns of codon usage in organelle genomes across multiple clades. ChloroMitoCU can be accessed at: http://chloromitocu.cgu.edu.tw/. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  7. GeneDig: a web application for accessing genomic and bioinformatics knowledge.

    Science.gov (United States)

    Suciu, Radu M; Aydin, Emir; Chen, Brian E

    2015-02-28

    With the exponential increase and widespread availability of genomic, transcriptomic, and proteomic data, accessing these '-omics' data is becoming increasingly difficult. The current resources for accessing and analyzing these data have been created to perform highly specific functions intended for specialists, and thus typically emphasize functionality over user experience. We have developed a web-based application, GeneDig.org, that allows any general user access to genomic information with ease and efficiency. GeneDig allows for searching and browsing genes and genomes, while a dynamic navigator displays genomic, RNA, and protein information simultaneously for co-navigation. We demonstrate that our application allows more than five times faster and efficient access to genomic information than any currently available methods. We have developed GeneDig as a platform for bioinformatics integration focused on usability as its central design. This platform will introduce genomic navigation to broader audiences while aiding the bioinformatics analyses performed in everyday biology research.

  8. pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data.

    Science.gov (United States)

    Vanderkam, Dan; Aksoy, B Arman; Hodes, Isaac; Perrone, Jaclyn; Hammerbacher, Jeff

    2016-08-01

    P: ileup.js is a new browser-based genome viewer. It is designed to facilitate the investigation of evidence for genomic variants within larger web applications. It takes advantage of recent developments in the JavaScript ecosystem to provide a modular, reliable and easily embedded library. The code and documentation for pileup.js is publicly available at https://github.com/hammerlab/pileup.js under the Apache 2.0 license. correspondence@hammerlab.org. © The Author 2016. Published by Oxford University Press.

  9. Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis.

    Science.gov (United States)

    Zhu, Huayu; Song, Pengyao; Koo, Dal-Hoe; Guo, Luqin; Li, Yanman; Sun, Shouru; Weng, Yiqun; Yang, Luming

    2016-08-05

    clustered in another group. Furthermore, structure analysis was consistent with the dendrogram indicating the 134 watermelon accessions were classified into two populations. The large number of genome wide SSR markers developed herein from the watermelon genome provides a valuable resource for genetic map construction, QTL exploration, map-based gene cloning and marker-assisted selection in watermelon which has a very narrow genetic base and extremely low polymorphism among cultivated lines. Furthermore, the cross-species transferable SSR markers identified herein should also have practical uses in many applications in species of Cucurbitaceae family whose whole genome sequences are not yet available.

  10. ETHICAL ASPECTS OF APPLICATION THE GENOMIC MEDICINE IN SPORT

    Directory of Open Access Journals (Sweden)

    Biljana Vitošević

    2013-07-01

    Full Text Available Today's level of knowledge of molecular biology and genetics is able to change the established belief that genetic predisposition is a good natural gift. The application of gene therapy in healthy individuals in order to increase sports performance is considered as manipulation and gene doping, which is actually believed that it could be a precursor to a broader notion of human "genetic enhancement" of physical characteristics such as strength, intelligence, social behavior and general improving the quality of life by genetic make-ap. In this sense, gene doping can have a significant and long-term impact on health and society in general and requires a more detailed ethical analysis and the implementation of preventive measures. The paper discusses the manipulation of genomic medicine in sport in terms of basic ethical principles and represents academic contributions to the study of the prevention, detection and control of this type of doping. Sport can and should keep the leading position in the scale of moral values in society through ethical arguments based on the balance of equality, rights and responsibilities. We cannot prevent the evolution of the sport, but we can and must direct this evolution in a better direction.

  11. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  12. The Tools, Approaches and Applications of Visual Literacy in the Visual Arts Department of Cross River University of Technology, Calabar, Nigeria

    Science.gov (United States)

    Ecoma, Victor

    2016-01-01

    The paper reflects upon the tools, approaches and applications of visual literacy in the Visual Arts Department of Cross River University of Technology, Calabar, Nigeria. The objective of the discourse is to examine how the visual arts training and practice equip students with skills in visual literacy through methods of production, materials and…

  13. Toxicogenomics: Applications of new functional genomics technologies in toxicology

    NARCIS (Netherlands)

    Heijne, W.H.M.

    2004-01-01

    Toxicogenomics studies toxic effects of substances on organisms in relation to the composition of the genome. It applies the functional genomics technologies transcriptomics, proteomics and metabolomics that determine expression of the genes, proteins and metabolites in a sample. These methods could

  14. Visual cryptography for image processing and security theory, methods, and applications

    CERN Document Server

    Liu, Feng

    2014-01-01

    This unique book describes the fundamental concepts, theories and practice of visual cryptography. The design, construction, analysis, and application of visual cryptography schemes (VCSs) are discussed in detail. Original, cutting-edge research is presented on probabilistic, size invariant, threshold, concolorous, and cheating immune VCS. Features: provides a thorough introduction to the field; examines various common problems in visual cryptography, including the alignment, flipping, cheating, distortion, and thin line problems; reviews a range of VCSs, including XOR-based visual cryptograph

  15. Be-Breeder – an application for analysis of genomic data in plant breeding

    Directory of Open Access Journals (Sweden)

    Filipe Inácio Matias

    2016-12-01

    Full Text Available Be-Breeder is an application directed toward genetic breeding of plants, developed through the Shiny package of the R software, which allows different phenotype and molecular (marker analysis to be undertaken. The section for analysis of molecular data of the Be-Breeder application makes it possible to achieve quality control of genotyping data, to obtain genomic kinship matrices, and to analyze genomic selection, genome association, and genetic diversity in a simple manner on line. This application is available for use in a network through the site of the Allogamous Plant Breeding Laboratory of ESALQ-USP (http://www.genetica.esalq.usp.br/alogamas/R.html.

  16. Applications of image processing and visualization in the evaluation of murder and assault

    Science.gov (United States)

    Oliver, William R.; Rosenman, Julian G.; Boxwala, Aziz; Stotts, David; Smith, John; Soltys, Mitchell; Symon, James; Cullip, Tim; Wagner, Glenn

    1994-09-01

    Recent advances in image processing and visualization are of increasing use in the investigation of violent crime. The Digital Image Processing Laboratory at the Armed Forces Institute of Pathology in collaboration with groups at the University of North Carolina at Chapel Hill are actively exploring visualization applications including image processing of trauma images, 3D visualization, forensic database management and telemedicine. Examples of recent applications are presented. Future directions of effort include interactive consultation and image manipulation tools for forensic data exploration.

  17. A novel genome signature based on inter-nucleotide distances profiles for visualization of metagenomic data

    Science.gov (United States)

    Xie, Xian-Hua; Yu, Zu-Guo; Ma, Yuan-Lin; Han, Guo-Sheng; Anh, Vo

    2017-09-01

    There has been a growing interest in visualization of metagenomic data. The present study focuses on the visualization of metagenomic data using inter-nucleotide distances profile. We first convert the fragment sequences into inter-nucleotide distances profiles. Then we analyze these profiles by principal component analysis. Finally the principal components are used to obtain the 2-D scattered plot according to their source of species. We name our method as inter-nucleotide distances profiles (INP) method. Our method is evaluated on three benchmark data sets used in previous published papers. Our results demonstrate that the INP method is good, alternative and efficient for visualization of metagenomic data.

  18. Controversy and debate on clinical genomics sequencing-paper 1: genomics is not exceptional: rigorous evaluations are necessary for clinical applications of genomic sequencing.

    Science.gov (United States)

    Wilson, Brenda J; Miller, Fiona Alice; Rousseau, François

    2017-12-01

    Next generation genomic sequencing (NGS) technologies-whole genome and whole exome sequencing-are now cheap enough to be within the grasp of many health care organizations. To many, NGS is symbolic of cutting edge health care, offering the promise of "precision" and "personalized" medicine. Historically, research and clinical application has been a two-way street in clinical genetics: research often driven directly by the desire to understand and try to solve immediate clinical problems affecting real, identifiable patients and families, accompanied by a low threshold of willingness to apply research-driven interventions without resort to formal empirical evaluations. However, NGS technologies are not simple substitutes for older technologies and need careful evaluation for use as screening, diagnostic, or prognostic tools. We have concerns across three areas. First, at the moment, analytic validity is unknown because technical platforms are not yet stable, laboratory quality assurance programs are in their infancy, and data interpretation capabilities are badly underdeveloped. Second, clinical validity of genomic findings for patient populations without pre-existing high genetic risk is doubtful, as most clinical experience with NGS technologies relates to patients with a high prior likelihood of a genetic etiology. Finally, we are concerned that proponents argue not only for clinically driven approaches to assessing a patient's genome, but also for seeking out variants associated with unrelated conditions or susceptibilities-so-called "secondary targets"-this is screening on a genomic scale. We argue that clinical uses of genomic sequencing should remain limited to specialist and research settings, that screening for secondary findings in clinical testing should be limited to the maximum extent possible, and that the benefits, harms, and economic implications of their routine use be systematically evaluated. All stakeholders have a responsibility to ensure that

  19. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases.

    Science.gov (United States)

    Shen, Li; Shao, Ningyi; Liu, Xiaochuan; Nestler, Eric

    2014-04-15

    Understanding the relationship between the millions of functional DNA elements and their protein regulators, and how they work in conjunction to manifest diverse phenotypes, is key to advancing our understanding of the mammalian genome. Next-generation sequencing technology is now used widely to probe these protein-DNA interactions and to profile gene expression at a genome-wide scale. As the cost of DNA sequencing continues to fall, the interpretation of the ever increasing amount of data generated represents a considerable challenge. We have developed ngs.plot - a standalone program to visualize enrichment patterns of DNA-interacting proteins at functionally important regions based on next-generation sequencing data. We demonstrate that ngs.plot is not only efficient but also scalable. We use a few examples to demonstrate that ngs.plot is easy to use and yet very powerful to generate figures that are publication ready. We conclude that ngs.plot is a useful tool to help fill the gap between massive datasets and genomic information in this era of big sequencing data.

  20. Genomics of lactic acid bacteria: Current status and potential applications.

    Science.gov (United States)

    Wu, Chongde; Huang, Jun; Zhou, Rongqing

    2017-08-01

    Lactic acid bacteria (LAB) are widely used for the production of a variety of foods and feed raw materials where they contribute to flavor and texture of the fermented products. In addition, specific LAB strains are considered as probiotic due to their health-promoting effects in consumers. Recently, the genome sequencing of LAB is booming and the increased amount of published genomics data brings unprecedented opportunity for us to reveal the important traits of LAB. This review describes the recent progress on LAB genomics and special emphasis is placed on understanding the industry-related physiological features based on genomics analysis. Moreover, strategies to engineer metabolic capacity and stress tolerance of LAB with improved industrial performance are also discussed.

  1. Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications.

    Science.gov (United States)

    Huang, Lei; Ma, Fei; Chapman, Alec; Lu, Sijia; Xie, Xiaoliang Sunney

    2015-01-01

    We present a survey of single-cell whole-genome amplification (WGA) methods, including degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR), multiple displacement amplification (MDA), and multiple annealing and looping-based amplification cycles (MALBAC). The key parameters to characterize the performance of these methods are defined, including genome coverage, uniformity, reproducibility, unmappable rates, chimera rates, allele dropout rates, false positive rates for calling single-nucleotide variations, and ability to call copy-number variations. Using these parameters, we compare five commercial WGA kits by performing deep sequencing of multiple single cells. We also discuss several major applications of single-cell genomics, including studies of whole-genome de novo mutation rates, the early evolution of cancer genomes, circulating tumor cells (CTCs), meiotic recombination of germ cells, preimplantation genetic diagnosis (PGD), and preimplantation genomic screening (PGS) for in vitro-fertilized embryos.

  2. Using the Visualization Software Evaluation Rubric to explore six freely available visualization applications

    Directory of Open Access Journals (Sweden)

    Thea P. Atwood

    2018-01-01

    Full Text Available Objective: As a variety of visualization tools become available to librarians and researchers, it can be challenging to select a tool that is robust and flexible enough to provide the desired visualization outcomes for work or personal use. In this article, the authors provide guidance on several freely available tools, and offer a rubric for use in evaluating visualization tools. Methods: A rubric was generated to assist the authors in assessing the selected six freely available visualization tools. Each author analyzed three tools, and discussed the differences, similarities, challenges, and successes of each. Results: Of the six visualization tools, two tools emerged with high marks. The authors found that the rubric was a successful evaluation tool, and facilitated discussion on the strengths and weaknesses of the six selected visualization pieces of software. Conclusions: Of the six different visualization tools analyzed, all had different functions and features available to best meet the needs of users. In a situation where there are many options available, and it is difficult at first glance to determine a clear winner, a rubric can be useful in providing a method to quickly assess and communicate the effectiveness of a tool.

  3. Mathematical Formula Program Application Visualization and Exercise Room and Construction Problems Using Interactive Visual Basic 6.0

    OpenAIRE

    Putri Soraya; Yudi Irawan Chandra, SKom, MMSI

    2006-01-01

    In the current era of globalization developments in science, technology and information increasingly fast and sophisticated. Many all fields associated with the computer because with knowledge of various computer performance is sought here. With easy to obtain such knowledge, the authors are interested in creating a collection of mathematical applications using Visual Basic 6.0. This application is made to meet the learning needs of students bagiu because the author saw the students are still...

  4. The application of visual communication design in display design

    Institute of Scientific and Technical Information of China (English)

    仪晓华

    2015-01-01

    Visual communication design is a kind of visual language and the art of communication behavior, it condenses complex and chaos and obscure information can in the shortest possible time to be understanding of the functional information, at the same time, make the design work itself sound art, philosophy and culture, cause the audience’s perception experience and emotional resonance, and eventually approved. Display of visual communication don’t like people use language to convey, but in all kinds of display environment by graphics, text, color elements such as passing information to people, visual communication design as a medium between designer and audience, communicate through planar graphic elements, format design, the combination of the text elements, color elements make exhibition has rhythm beauty so as to build a display space, the space information accurate, vivid and clear function division, comfortable, and the outline of rich imagination space to the person and strong visual impression.

  5. MOVE : A Multi-Level Ontology-Based Visualization and Exploration Framework for Genomic Networks

    NARCIS (Netherlands)

    Bosman, D.W.; Blom, E.J.; Ogao, P.J.; Kuipers, O.P.; Roerdink, J.B.T.M.

    2007-01-01

    Among the various research areas that comprise bioinformatics, systems biology is gaining increasing attention. An important goal of systems biology is the unraveling of dynamic interactions between components of living cells (e.g., proteins, genes). These interactions exist among others on genomic,

  6. Parallel computing in genomic research: advances and applications

    Directory of Open Access Journals (Sweden)

    Ocaña K

    2015-11-01

    Full Text Available Kary Ocaña,1 Daniel de Oliveira2 1National Laboratory of Scientific Computing, Petrópolis, Rio de Janeiro, 2Institute of Computing, Fluminense Federal University, Niterói, Brazil Abstract: Today's genomic experiments have to process the so-called "biological big data" that is now reaching the size of Terabytes and Petabytes. To process this huge amount of data, scientists may require weeks or months if they use their own workstations. Parallelism techniques and high-performance computing (HPC environments can be applied for reducing the total processing time and to ease the management, treatment, and analyses of this data. However, running bioinformatics experiments in HPC environments such as clouds, grids, clusters, and graphics processing unit requires the expertise from scientists to integrate computational, biological, and mathematical techniques and technologies. Several solutions have already been proposed to allow scientists for processing their genomic experiments using HPC capabilities and parallelism techniques. This article brings a systematic review of literature that surveys the most recently published research involving genomics and parallel computing. Our objective is to gather the main characteristics, benefits, and challenges that can be considered by scientists when running their genomic experiments to benefit from parallelism techniques and HPC capabilities. Keywords: high-performance computing, genomic research, cloud computing, grid computing, cluster computing, parallel computing

  7. The efficacy of a novel mobile phone application for goldmann ptosis visual field interpretation.

    Science.gov (United States)

    Maamari, Robi N; D'Ambrosio, Michael V; Joseph, Jeffrey M; Tao, Jeremiah P

    2014-01-01

    To evaluate the efficacy of a novel mobile phone application that calculates superior visual field defects on Goldmann visual field charts. Experimental study in which the mobile phone application and 14 oculoplastic surgeons interpreted the superior visual field defect in 10 Goldmann charts. Percent error of the mobile phone application and the oculoplastic surgeons' estimates were calculated compared with computer software computation of the actual defects. Precision and time efficiency of the application were evaluated by processing the same Goldmann visual field chart 10 repeated times. The mobile phone application was associated with a mean percent error of 1.98% (95% confidence interval[CI], 0.87%-3.10%) in superior visual field defect calculation. The average mean percent error of the oculoplastic surgeons' visual estimates was 19.75% (95% CI, 14.39%-25.11%). Oculoplastic surgeons, on average, underestimated the defect in all 10 Goldmann charts. There was high interobserver variance among oculoplastic surgeons. The percent error of the 10 repeated measurements on a single chart was 0.93% (95% CI, 0.40%-1.46%). The average time to process 1 chart was 12.9 seconds (95% CI, 10.9-15.0 seconds). The mobile phone application was highly accurate, precise, and time-efficient in calculating the percent superior visual field defect using Goldmann charts. Oculoplastic surgeon visual interpretations were highly inaccurate, highly variable, and usually underestimated the field vision loss.

  8. Playing with heart and soul…and genomes: sports implications and applications of personal genomics.

    Science.gov (United States)

    Wagner, Jennifer K

    2013-01-01

    Whether the integration of genetic/omic technologies in sports contexts will facilitate player success, promote player safety, or spur genetic discrimination depends largely upon the game rules established by those currently designing genomic sports medicine programs. The integration has already begun, but there is not yet a playbook for best practices. Thus far discussions have focused largely on whether the integration would occur and how to prevent the integration from occurring, rather than how it could occur in such a way that maximizes benefits, minimizes risks, and avoids the exacerbation of racial disparities. Previous empirical research has identified members of the personal genomics industry offering sports-related DNA tests, and previous legal research has explored the impact of collective bargaining in professional sports as it relates to the employment protections of the Genetic Information Nondiscrimination Act (GINA). Building upon that research and upon participant observations with specific sports-related DNA tests purchased from four direct-to-consumer companies in 2011 and broader personal genomics (PGx) services, this anthropological, legal, and ethical (ALE) discussion highlights fundamental issues that must be addressed by those developing personal genomic sports medicine programs, either independently or through collaborations with commercial providers. For example, the vulnerability of student-athletes creates a number of issues that require careful, deliberate consideration. More broadly, however, this ALE discussion highlights potential sports-related implications (that ultimately might mitigate or, conversely, exacerbate racial disparities among athletes) of whole exome/genome sequencing conducted by biomedical researchers and clinicians for non-sports purposes. For example, the possibility that exome/genome sequencing of individuals who are considered to be non-patients, asymptomatic, normal, etc. will reveal the presence of variants of

  9. Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data.

    Science.gov (United States)

    Duforet-Frebourg, Nicolas; Luu, Keurcien; Laval, Guillaume; Bazin, Eric; Blum, Michael G B

    2016-04-01

    To characterize natural selection, various analytical methods for detecting candidate genomic regions have been developed. We propose to perform genome-wide scans of natural selection using principal component analysis (PCA). We show that the common FST index of genetic differentiation between populations can be viewed as the proportion of variance explained by the principal components. Considering the correlations between genetic variants and each principal component provides a conceptual framework to detect genetic variants involved in local adaptation without any prior definition of populations. To validate the PCA-based approach, we consider the 1000 Genomes data (phase 1) considering 850 individuals coming from Africa, Asia, and Europe. The number of genetic variants is of the order of 36 millions obtained with a low-coverage sequencing depth (3×). The correlations between genetic variation and each principal component provide well-known targets for positive selection (EDAR, SLC24A5, SLC45A2, DARC), and also new candidate genes (APPBPP2, TP1A1, RTTN, KCNMA, MYO5C) and noncoding RNAs. In addition to identifying genes involved in biological adaptation, we identify two biological pathways involved in polygenic adaptation that are related to the innate immune system (beta defensins) and to lipid metabolism (fatty acid omega oxidation). An additional analysis of European data shows that a genome scan based on PCA retrieves classical examples of local adaptation even when there are no well-defined populations. PCA-based statistics, implemented in the PCAdapt R package and the PCAdapt fast open-source software, retrieve well-known signals of human adaptation, which is encouraging for future whole-genome sequencing project, especially when defining populations is difficult. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  10. Recent Advances in Microbial Single Cell Genomics Technology and Applications

    Science.gov (United States)

    Stepanauskas, R.

    2016-02-01

    Single cell genomics is increasingly utilized as a powerful tool to decipher the metabolic potential, evolutionary histories and in situ interactions of environmental microorganisms. This transformative technology recovers extensive information from cultivation-unbiased samples of individual, unicellular organisms. Thus, it does not require data binning into arbitrary phylogenetic or functional groups and therefore is highly compatible with agent-based modeling approaches. I will present several technological advances in this field, which significantly improve genomic data recovery from individual cells and provide direct linkages between cell's genomic and phenotypic properties. I will also demonstrate how these new technical capabilities help understanding the metabolic potential and viral infections of the "microbial dark matter" inhabiting aquatic and subsurface environments.

  11. Post-genomics nanotechnology is gaining momentum: nanoproteomics and applications in life sciences.

    Science.gov (United States)

    Kobeissy, Firas H; Gulbakan, Basri; Alawieh, Ali; Karam, Pierre; Zhang, Zhiqun; Guingab-Cagmat, Joy D; Mondello, Stefania; Tan, Weihong; Anagli, John; Wang, Kevin

    2014-02-01

    The post-genomics era has brought about new Omics biotechnologies, such as proteomics and metabolomics, as well as their novel applications to personal genomics and the quantified self. These advances are now also catalyzing other and newer post-genomics innovations, leading to convergences between Omics and nanotechnology. In this work, we systematically contextualize and exemplify an emerging strand of post-genomics life sciences, namely, nanoproteomics and its applications in health and integrative biological systems. Nanotechnology has been utilized as a complementary component to revolutionize proteomics through different kinds of nanotechnology applications, including nanoporous structures, functionalized nanoparticles, quantum dots, and polymeric nanostructures. Those applications, though still in their infancy, have led to several highly sensitive diagnostics and new methods of drug delivery and targeted therapy for clinical use. The present article differs from previous analyses of nanoproteomics in that it offers an in-depth and comparative evaluation of the attendant biotechnology portfolio and their applications as seen through the lens of post-genomics life sciences and biomedicine. These include: (1) immunosensors for inflammatory, pathogenic, and autoimmune markers for infectious and autoimmune diseases, (2) amplified immunoassays for detection of cancer biomarkers, and (3) methods for targeted therapy and automatically adjusted drug delivery such as in experimental stroke and brain injury studies. As nanoproteomics becomes available both to the clinician at the bedside and the citizens who are increasingly interested in access to novel post-genomics diagnostics through initiatives such as the quantified self, we anticipate further breakthroughs in personalized and targeted medicine.

  12. Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna

    OpenAIRE

    Nakamura, Yoji; Mori, Kazuki; Saitoh, Kenji; Oshima, Kenshiro; Mekuchi, Miyuki; Sugaya, Takuma; Shigenobu, Yuya; Ojima, Nobuhiko; Muta, Shigeru; Fujiwara, Atushi; Yasuike, Motoshige; Oohara, Ichiro; Hirakawa, Hideki; Chowdhury, Vishwajit Sur; Kobayashi, Takanori

    2013-01-01

    Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values, the open-ocean lifestyle of tuna, in which effective sensing systems such as color vision are required for capture of prey, has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna, we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis), using next-generation sequencing tec...

  13. Machine vision automated visual inspection theory, practice and applications

    CERN Document Server

    Beyerer, Jürgen; Frese, Christian

    2016-01-01

    The book offers a thorough introduction to machine vision. It is organized in two parts. The first part covers the image acquisition, which is the crucial component of most automated visual inspection systems. All important methods are described in great detail and are presented with a reasoned structure. The second part deals with the modeling and processing of image signals and pays particular regard to methods, which are relevant for automated visual inspection.

  14. Visual Genome: Connecting language and vision using crowdsourced dense image annotations

    NARCIS (Netherlands)

    R. Krishna (Ranjay); Y. Zhu (Yuke); O. Groth (Oliver); J. Johnson (Justin); K. Hata (Kenji); J. Kravitz (Joshua); S. Chen (Stephanie); Y. Kalantidis (Yannis); L.-J. Li (Li-Jia); D.A. Shamma (David); M.S. Bernstein (Michael); L. Fei-Fei (Li)

    2017-01-01

    textabstractDespite progress in perceptual tasks such as image classification, computers still perform poorly on cognitive tasks such as image description and question answering. Cognition is core to tasks that involve not just recognizing, but reasoning about our visual world. However, models used

  15. Application of CRISPR technology in genome editing in agriculture -swine

    Science.gov (United States)

    Decades of selective breeding in agricultural species has led to the derivation of stronger and fitter animals with improved production traits. However, often co-segregating with beneficial traits are less desirable traits. With the plethora of genome data and annotation, has come the technology t...

  16. Parallel computing in genomic research: advances and applications.

    Science.gov (United States)

    Ocaña, Kary; de Oliveira, Daniel

    2015-01-01

    Today's genomic experiments have to process the so-called "biological big data" that is now reaching the size of Terabytes and Petabytes. To process this huge amount of data, scientists may require weeks or months if they use their own workstations. Parallelism techniques and high-performance computing (HPC) environments can be applied for reducing the total processing time and to ease the management, treatment, and analyses of this data. However, running bioinformatics experiments in HPC environments such as clouds, grids, clusters, and graphics processing unit requires the expertise from scientists to integrate computational, biological, and mathematical techniques and technologies. Several solutions have already been proposed to allow scientists for processing their genomic experiments using HPC capabilities and parallelism techniques. This article brings a systematic review of literature that surveys the most recently published research involving genomics and parallel computing. Our objective is to gather the main characteristics, benefits, and challenges that can be considered by scientists when running their genomic experiments to benefit from parallelism techniques and HPC capabilities.

  17. The Application of Visual Basic Computer Programming Language to Simulate Numerical Iterations

    Directory of Open Access Journals (Sweden)

    Abdulkadir Baba HASSAN

    2006-06-01

    Full Text Available This paper examines the application of Visual Basic Computer Programming Language to Simulate Numerical Iterations, the merit of Visual Basic as a Programming Language and the difficulties faced when solving numerical iterations analytically, this research paper encourage the uses of Computer Programming methods for the execution of numerical iterations and finally fashion out and develop a reliable solution using Visual Basic package to write a program for some selected iteration problems.

  18. Analysis of pan-genome content and its application in microbial identification

    DEFF Research Database (Denmark)

    Lukjancenko, Oksana

    microorganisms and eventually speed up the diagnosis of foodborne illnesses. This genomic data can give biologists many possibilities to improve knowledge of organismal evolution and complex genetic systems. The general interest of this PhD thesis is how to obtain relevant information from growing amounts...... groups or genomic structures; and to use the information of a specific proteome to predict which species it might belong to. Two different algorithms, BLAST and profile Hidden Markov Models (HMMs), are used to determine similarity between sequences and to address the questions in this thesis. The first...... the application of PanFunPro to a set of more than 2000 genomes; this paper aims to define set of protein families, which are conserved among all the genomes. Papers V demonstrates comparative genomics analysis of proteomes, belonging to Vibrio genus. In the last project, described in Chapter 5, both BLAST...

  19. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  20. Interactive Processing and Visualization of Image Data forBiomedical and Life Science Applications

    Energy Technology Data Exchange (ETDEWEB)

    Staadt, Oliver G.; Natarjan, Vijay; Weber, Gunther H.; Wiley,David F.; Hamann, Bernd

    2007-02-01

    Background: Applications in biomedical science and life science produce large data sets using increasingly powerful imaging devices and computer simulations. It is becoming increasingly difficult for scientists to explore and analyze these data using traditional tools. Interactive data processing and visualization tools can support scientists to overcome these limitations. Results: We show that new data processing tools and visualization systems can be used successfully in biomedical and life science applications. We present an adaptive high-resolution display system suitable for biomedical image data, algorithms for analyzing and visualization protein surfaces and retinal optical coherence tomography data, and visualization tools for 3D gene expression data. Conclusion: We demonstrated that interactive processing and visualization methods and systems can support scientists in a variety of biomedical and life science application areas concerned with massive data analysis.

  1. Visual servoing in medical robotics: a survey. Part II: tomographic imaging modalities--techniques and applications.

    Science.gov (United States)

    Azizian, Mahdi; Najmaei, Nima; Khoshnam, Mahta; Patel, Rajni

    2015-03-01

    Intraoperative application of tomographic imaging techniques provides a means of visual servoing for objects beneath the surface of organs. The focus of this survey is on therapeutic and diagnostic medical applications where tomographic imaging is used in visual servoing. To this end, a comprehensive search of the electronic databases was completed for the period 2000-2013. Existing techniques and products are categorized and studied, based on the imaging modality and their medical applications. This part complements Part I of the survey, which covers visual servoing techniques using endoscopic imaging and direct vision. The main challenges in using visual servoing based on tomographic images have been identified. 'Supervised automation of medical robotics' is found to be a major trend in this field and ultrasound is the most commonly used tomographic modality for visual servoing. Copyright © 2014 John Wiley & Sons, Ltd.

  2. Preparing Content-Rich Learning Environments with VPython and Excel, Controlled by Visual Basic for Applications

    Science.gov (United States)

    Prayaga, Chandra

    2008-01-01

    A simple interface between VPython and Microsoft (MS) Office products such as Word and Excel, controlled by Visual Basic for Applications, is described. The interface allows the preparation of content-rich, interactive learning environments by taking advantage of the three-dimensional (3D) visualization capabilities of VPython and the GUI…

  3. Visualization of Flow Field: Application of PLIF Technique

    Directory of Open Access Journals (Sweden)

    Jiang Bo Peng

    2018-01-01

    Full Text Available The objective of this paper is to apply planar laser-induced fluorescence (PLIF technology to flow field visualization. This experiment was carried out in a one-meter wind tunnel to study the wake flow field around a circular cylinder. This experiment studied the method of injecting tracer into the flow field; the frequency of the vortex in the wake field and the vortex speed are quantitatively analyzed. This paper gives the correspondence between the speed of the flow field and the frequency of the laser, which could be used as a rough reference standard for future wind tunnel visualization experiments. The result shows that PLIF diagnostic technology has great potential in visualization of flow field.

  4. Visualization in cryogenic environment: Application to two-phase studies

    Science.gov (United States)

    Rousset, Bernard; Chatain, Denis; Puech, Laurent; Thibault, Pierre; Viargues, François; Wolf, Pierre-Etienne

    2009-10-01

    This paper reviews recent technical developments devoted to the study of cryogenic two-phase fluids. These techniques span from simple flow visualization to quantitative measurements of light scattering. It is shown that simple flow pattern configurations are obtained using classical optical tools (CCD cameras, endoscopes), even in most severe environments (high vacuum, high magnetic field). Quantitative measurements include laser velocimetry, particle sizing, and light scattering analysis. In the case of magnetically compensated gravity boiling oxygen, optical access is used to control the poistioning of a bubble subject to buoyancy forces in an experimental cell. Flow visualization on a two-phase superfluid helium pipe-flow, performed as a support of LHC cooldown studies, leads to flow pattern characterization. Visualization includes stratified and atomized flows. Thanks to the low refractive index contrast between the liquid and its vapor, quantitative results on droplet densities can be obtained even in a multiple scattering regime.

  5. Applications of Java and Vector Graphics to Astrophysical Visualization

    Science.gov (United States)

    Edirisinghe, D.; Budiardja, R.; Chae, K.; Edirisinghe, G.; Lingerfelt, E.; Guidry, M.

    2002-12-01

    We describe a series of projects utilizing the portability of Java programming coupled with the compact nature of vector graphics (SVG and SWF formats) for setup and control of calculations, local and collaborative visualization, and interactive 2D and 3D animation presentations in astrophysics. Through a set of examples, we demonstrate how such an approach can allow efficient and user-friendly control of calculations in compiled languages such as Fortran 90 or C++ through portable graphical interfaces written in Java, and how the output of such calculations can be packaged in vector-based animation having interactive controls and extremely high visual quality, but very low bandwidth requirements.

  6. CRISPR/Cas system for yeast genome engineering: advances and applications

    DEFF Research Database (Denmark)

    Stovicek, Vratislav; Holkenbrink, Carina; Borodina, Irina

    2017-01-01

    The methods based on the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) system have quickly gained popularity for genome editing and transcriptional regulation in many organisms, including yeast. This review aims to provide a comprehensive overview...... of CRISPR application for different yeast species: from basic principles and genetic design to applications....

  7. Application of visualization and simulation program to improve work zone safety and mobility.

    Science.gov (United States)

    2010-01-01

    "A previous study sponsored by the Smart Work Zone Deployment Initiative, Feasibility of Visualization and Simulation Applications to Improve Work Zone Safety and Mobility, demonstrated the feasibility of combining readily available, inexpensiv...

  8. Comparison of Burrows-Wheeler transform-based mapping algorithms used in high-throughput whole-genome sequencing: application to Illumina data for livestock genomes

    Science.gov (United States)

    Ongoing developments and cost decreases in next-generation sequencing (NGS) technologies have led to an increase in their application, which has greatly enhanced the fields of genetics and genomics. Mapping sequence reads onto a reference genome is a fundamental step in the analysis of NGS data. Eff...

  9. A cognitive model for visual attention and its application

    NARCIS (Netherlands)

    Bosse, T.; Maanen, P.P. van; Treur, J.

    2007-01-01

    In this paper a cognitive model for visual attention is introduced. The cognitive model is part of the design of a software agent that supports a naval warfare officer in its task to compile a tactical picture of the situation in the field. An executable formal specification of the cognitive model

  10. A String Search Marketing Application Using Visual Programming

    Science.gov (United States)

    Chin, Jerry M.; Chin, Mary H.; Van Landuyt, Cathryn

    2013-01-01

    This paper demonstrates the use of programing software that provides the student programmer visual cues to construct the code to a student programming assignment. This method does not disregard or minimize the syntax or required logical constructs. The student can concentrate more on the logic and less on the language itself.

  11. Sparse representation, modeling and learning in visual recognition theory, algorithms and applications

    CERN Document Server

    Cheng, Hong

    2015-01-01

    This unique text/reference presents a comprehensive review of the state of the art in sparse representations, modeling and learning. The book examines both the theoretical foundations and details of algorithm implementation, highlighting the practical application of compressed sensing research in visual recognition and computer vision. Topics and features: provides a thorough introduction to the fundamentals of sparse representation, modeling and learning, and the application of these techniques in visual recognition; describes sparse recovery approaches, robust and efficient sparse represen

  12. Applications in Foreign Currency Money Changer Cv.xyz Using Microsoft Visual Basic 6.0

    OpenAIRE

    Fanny Ramadhan; Hariyanto.,SKom., MMSI Hariyanto.,SKom., MMSI

    2010-01-01

    This explains the scientific writing about the design of application programs forforeign currency transactions by using Visual Basic 6.0 programming languagecoupled with the flow diagram (flowchart).In scientific writing database is used also by using Microsoft software Accsess 2003which have been integrated in Visual Basic 6.0 program itself. Consists of four tablesof Currency, Customer, Transaction, Employee.In the end application program for foreign currency transactions will be applied to...

  13. An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes.

    Science.gov (United States)

    Liu, Bingqiang; Zhang, Hanyuan; Zhou, Chuan; Li, Guojun; Fennell, Anne; Wang, Guanghui; Kang, Yu; Liu, Qi; Ma, Qin

    2016-08-09

    Phylogenetic footprinting is an important computational technique for identifying cis-regulatory motifs in orthologous regulatory regions from multiple genomes, as motifs tend to evolve slower than their surrounding non-functional sequences. Its application, however, has several difficulties for optimizing the selection of orthologous data and reducing the false positives in motif prediction. Here we present an integrative phylogenetic footprinting framework for accurate motif predictions in prokaryotic genomes (MP(3)). The framework includes a new orthologous data preparation procedure, an additional promoter scoring and pruning method and an integration of six existing motif finding algorithms as basic motif search engines. Specifically, we collected orthologous genes from available prokaryotic genomes and built the orthologous regulatory regions based on sequence similarity of promoter regions. This procedure made full use of the large-scale genomic data and taxonomy information and filtered out the promoters with limited contribution to produce a high quality orthologous promoter set. The promoter scoring and pruning is implemented through motif voting by a set of complementary predicting tools that mine as many motif candidates as possible and simultaneously eliminate the effect of random noise. We have applied the framework to Escherichia coli k12 genome and evaluated the prediction performance through comparison with seven existing programs. This evaluation was systematically carried out at the nucleotide and binding site level, and the results showed that MP(3) consistently outperformed other popular motif finding tools. We have integrated MP(3) into our motif identification and analysis server DMINDA, allowing users to efficiently identify and analyze motifs in 2,072 completely sequenced prokaryotic genomes. The performance evaluation indicated that MP(3) is effective for predicting regulatory motifs in prokaryotic genomes. Its application may enhance

  14. Automating Geospatial Visualizations with Smart Default Renderers for Data Exploration Web Applications

    Science.gov (United States)

    Ekenes, K.

    2017-12-01

    This presentation will outline the process of creating a web application for exploring large amounts of scientific geospatial data using modern automated cartographic techniques. Traditional cartographic methods, including data classification, may inadvertently hide geospatial and statistical patterns in the underlying data. This presentation demonstrates how to use smart web APIs that quickly analyze the data when it loads, and provides suggestions for the most appropriate visualizations based on the statistics of the data. Since there are just a few ways to visualize any given dataset well, it is imperative to provide smart default color schemes tailored to the dataset as opposed to static defaults. Since many users don't go beyond default values, it is imperative that they are provided with smart default visualizations. Multiple functions for automating visualizations are available in the Smart APIs, along with UI elements allowing users to create more than one visualization for a dataset since there isn't a single best way to visualize a given dataset. Since bivariate and multivariate visualizations are particularly difficult to create effectively, this automated approach removes the guesswork out of the process and provides a number of ways to generate multivariate visualizations for the same variables. This allows the user to choose which visualization is most appropriate for their presentation. The methods used in these APIs and the renderers generated by them are not available elsewhere. The presentation will show how statistics can be used as the basis for automating default visualizations of data along continuous ramps, creating more refined visualizations while revealing the spread and outliers of the data. Adding interactive components to instantaneously alter visualizations allows users to unearth spatial patterns previously unknown among one or more variables. These applications may focus on a single dataset that is frequently updated, or configurable

  15. Development and application of streakline visualization in hypervelocity flows

    Energy Technology Data Exchange (ETDEWEB)

    Lemieux, P.; Hornung, H.G. [Graduate Aeronautical Laboratories, California Institute of Technology, Pasadena, CA 91125 (United States)

    2002-07-01

    A method for visualizing streaklines in hypervelocity flows has been developed. The method uses the high temperatures produced in hypervelocity flows to ablate small amounts of sodium deposited onto a wire stretched across the flow and to broaden the lines in the sodium spectrum. By using a dye laser, tuned to a wavelength close to one of the sodium D-lines, as the light source in shadowgraph or Schlieren visualization, streaklines seeded with sodium become visible through absorption and/or enhanced refractivity. The technique has been used to investigate the stability of the shear layer produced by the curved bow shock on a cylindrically blunted wedge. The results suggest that the shear layer is unstable, exhibiting structures with a wavelength that is comparable to half the nose radius of the body. (orig.)

  16. A Visual Galaxy Classification Interface and its Classroom Application

    Science.gov (United States)

    Kautsch, Stefan J.; Phung, Chau; VanHilst, Michael; Castro, Victor H

    2014-06-01

    Galaxy morphology is an important topic in modern astronomy to understand questions concerning the evolution and formation of galaxies and their dark matter content. In order to engage students in exploring galaxy morphology, we developed a web-based, graphical interface that allows students to visually classify galaxy images according to various morphological types. The website is designed with HTML5, JavaScript, PHP, and a MySQL database. The classification interface provides hands-on research experience and training for students and interested clients, and allows them to contribute to studies of galaxy morphology. We present the first results of a pilot study and compare the visually classified types using our interface with that from automated classification routines.

  17. Neural attractor network for application in visual field data classification

    International Nuclear Information System (INIS)

    Fink, Wolfgang

    2004-01-01

    The purpose was to introduce a novel method for computer-based classification of visual field data derived from perimetric examination, that may act as a ' counsellor', providing an independent 'second opinion' to the diagnosing physician. The classification system consists of a Hopfield-type neural attractor network that obtains its input data from perimetric examination results. An iterative relaxation process determines the states of the neurons dynamically. Therefore, even 'noisy' perimetric output, e.g., early stages of a disease, may eventually be classified correctly according to the predefined idealized visual field defect (scotoma) patterns, stored as attractors of the network, that are found with diseases of the eye, optic nerve and the central nervous system. Preliminary tests of the classification system on real visual field data derived from perimetric examinations have shown a classification success of over 80%. Some of the main advantages of the Hopfield-attractor-network-based approach over feed-forward type neural networks are: (1) network architecture is defined by the classification problem; (2) no training is required to determine the neural coupling strengths; (3) assignment of an auto-diagnosis confidence level is possible by means of an overlap parameter and the Hamming distance. In conclusion, the novel method for computer-based classification of visual field data, presented here, furnishes a valuable first overview and an independent 'second opinion' in judging perimetric examination results, pointing towards a final diagnosis by a physician. It should not be considered a substitute for the diagnosing physician. Thanks to the worldwide accessibility of the Internet, the classification system offers a promising perspective towards modern computer-assisted diagnosis in both medicine and tele-medicine, for example and in particular, with respect to non-ophthalmic clinics or in communities where perimetric expertise is not readily available

  18. Visualizing Time-Varying Distribution Data in EOS Application

    Science.gov (United States)

    Shen, Han-Wei

    2004-01-01

    In this research, we have developed several novel visualization methods for spatial probability density function data. Our focus has been on 2D spatial datasets, where each pixel is a random variable, and has multiple samples which are the results of experiments on that random variable. We developed novel clustering algorithms as a means to reduce the information contained in these datasets; and investigated different ways of interpreting and clustering the data.

  19. Modular Sensor Environment : Audio Visual Industry Monitoring Applications

    OpenAIRE

    Guillot, Calvin

    2017-01-01

    This work was made for Electro Waves Oy. The company specializes in Audio-visual services and interactive systems. The purpose of this work is to design and implement a modular sensor environment for the company, which will be used for developing automated systems. This thesis begins with an introduction to sensor systems and their different topologies. It is followed by an introduction to the technologies used in this project. The system is divided in three parts. The client, tha...

  20. Visual application of the American Board of Orthodontics Grading System.

    Science.gov (United States)

    Scott, Steven A; Freer, Terry J

    2005-05-01

    Assessment of treatment outcomes has traditionally been accomplished using the subjective opinion of experienced clinicians. Reduced subjectivity in the assessment of orthodontic treatment can be achieved with the use of an occlusal index. To implement an index for quality assurance purposes is time-consuming and subject to the inherent error of the index. Quality assessment of orthodontic treatment on a routine basis has been difficult to implement in private practice. To investigate whether a clinician can accurately apply the American Board of Orthodontics Objective Grading System by direct visual inspection instead of measuring individual traits. A random sample of 30 cases was selected, including pretreatment and post-treatment upper and lower study casts and panoramic radiographs. The cases were examined and scored with the standardized measuring gauge according to the protocol provided by the American Board of Orthodontics (ABO). The records were re-examined 6 weeks later and the individual traits scored by visual inspection (VI). There were no significant differences between the pre- and post-treatment ABO gauge and VI scores. This study suggests that occlusal traits defined by the ABO Objective Grading System can be accurately assessed by visual inspection. The VI score provides a simple and convenient method for critical evaluation of treatment outcome by a clinician.

  1. Visualization and measurement of ATP levels in living cells replicating hepatitis C virus genome RNA.

    Directory of Open Access Journals (Sweden)

    Tomomi Ando

    Full Text Available Adenosine 5'-triphosphate (ATP is the primary energy currency of all living organisms and participates in a variety of cellular processes. Although ATP requirements during viral lifecycles have been examined in a number of studies, a method by which ATP production can be monitored in real-time, and by which ATP can be quantified in individual cells and subcellular compartments, is lacking, thereby hindering studies aimed at elucidating the precise mechanisms by which viral replication energized by ATP is controlled. In this study, we investigated the fluctuation and distribution of ATP in cells during RNA replication of the hepatitis C virus (HCV, a member of the Flaviviridae family. We demonstrated that cells involved in viral RNA replication actively consumed ATP, thereby reducing cytoplasmic ATP levels. Subsequently, a method to measure ATP levels at putative subcellular sites of HCV RNA replication in living cells was developed by introducing a recently-established Förster resonance energy transfer (FRET-based ATP indicator, called ATeam, into the NS5A coding region of the HCV replicon. Using this method, we were able to observe the formation of ATP-enriched dot-like structures, which co-localize with non-structural viral proteins, within the cytoplasm of HCV-replicating cells but not in non-replicating cells. The obtained FRET signals allowed us to estimate ATP concentrations within HCV replicating cells as ∼5 mM at possible replicating sites and ∼1 mM at peripheral sites that did not appear to be involved in HCV replication. In contrast, cytoplasmic ATP levels in non-replicating Huh-7 cells were estimated as ∼2 mM. To our knowledge, this is the first study to demonstrate changes in ATP concentration within cells during replication of the HCV genome and increased ATP levels at distinct sites within replicating cells. ATeam may be a powerful tool for the study of energy metabolism during replication of the viral genome.

  2. Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes

    DEFF Research Database (Denmark)

    Bohlin, J; Skjerve, E; Ussery, David

    2008-01-01

    with here are mainly used to examine similarities between archaeal and bacterial DNA from different genomes. These methods compare observed genomic frequencies of fixed-sized oligonucleotides with expected values, which can be determined by genomic nucleotide content, smaller oligonucleotide frequencies......, or be based on specific statistical distributions. Advantages with these statistical methods include measurements of phylogenetic relationship with relatively small pieces of DNA sampled from almost anywhere within genomes, detection of foreign/conserved DNA, and homology searches. Our aim was to explore...... the reliability and best suited applications for some popular methods, which include relative oligonucleotide frequencies (ROF), di- to hexanucleotide zero'th order Markov methods (ZOM) and 2.order Markov chain Method (MCM). Tests were performed on distant homology searches with large DNA sequences, detection...

  3. CRISPR/Cas9-mediated genome engineering of CHO cell factories: application and perspectives

    DEFF Research Database (Denmark)

    Lee, Jae Seong; Grav, Lise Marie; Lewis, Nathan E.

    2015-01-01

    repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system enables rapid,easy and efficient engineering of mammalian genomes. It has a wide range of applications frommodification of individual genes to genome-wide screening or regulation of genes. Facile genomeediting using CRISPR/Cas9 empowers...... researchers in the CHO community to elucidate the mechanisticbasis behind high level production of proteins and product quality attributes of interest. Inthis review, we describe the basis of CRISPR/Cas9-mediated genome editing and its applicationfor development of next generation CHO cell factories while...... highlighting both future perspectivesand challenges. As one of the main drivers for the CHO systems biology era, genome engineeringwith CRISPR/Cas9 will pave the way for rational design of CHO cell factories....

  4. Application of Microarray-Based Comparative Genomic Hybridization in Prenatal and Postnatal Settings: Three Case Reports

    Directory of Open Access Journals (Sweden)

    Jing Liu

    2011-01-01

    Full Text Available Microarray-based comparative genomic hybridization (array CGH is a newly emerged molecular cytogenetic technique for rapid evaluation of the entire genome with sub-megabase resolution. It allows for the comprehensive investigation of thousands and millions of genomic loci at once and therefore enables the efficient detection of DNA copy number variations (a.k.a, cryptic genomic imbalances. The development and the clinical application of array CGH have revolutionized the diagnostic process in patients and has provided a clue to many unidentified or unexplained diseases which are suspected to have a genetic cause. In this paper, we present three clinical cases in both prenatal and postnatal settings. Among all, array CGH played a major discovery role to reveal the cryptic and/or complex nature of chromosome arrangements. By identifying the genetic causes responsible for the clinical observation in patients, array CGH has provided accurate diagnosis and appropriate clinical management in a timely and efficient manner.

  5. CRISPR-cas System as a Genome Engineering Platform: Applications in Biomedicine and Biotechnology.

    Science.gov (United States)

    Hashemi, Atieh

    2018-01-01

    Genome editing mediated by Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and its associated proteins (Cas) has recently been considered to be used as efficient, rapid and site-specific tool in the modification of endogenous genes in biomedically important cell types and whole organisms. It has become a predictable and precise method of choice for genome engineering by specifying a 20-nt targeting sequence within its guide RNA. Firstly, this review aims to describe the biology of CRISPR system. Next, the applications of CRISPR-Cas9 in various ways, such as efficient generation of a wide variety of biomedically important cellular models as well as those of animals, modifying epigenomes, conducting genome-wide screens, gene therapy, labelling specific genomic loci in living cells, metabolic engineering of yeast and bacteria and endogenous gene expression regulation by an altered version of this system were reviewed. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  6. Perception, Cognition, and Effectiveness of Visualizations with Applications in Science and Engineering

    Science.gov (United States)

    Borkin, Michelle A.

    Visualization is a powerful tool for data exploration and analysis. With data ever-increasing in quantity and becoming integrated into our daily lives, having effective visualizations is necessary. But how does one design an effective visualization? To answer this question we need to understand how humans perceive, process, and understand visualizations. Through visualization evaluation studies we can gain deeper insight into the basic perception and cognition theory of visualizations, both through domain-specific case studies as well as generalized laboratory experiments. This dissertation presents the results of four evaluation studies, each of which contributes new knowledge to the theory of perception and cognition of visualizations. The results of these studies include a deeper clearer understanding of how color, data representation dimensionality, spatial layout, and visual complexity affect a visualization's effectiveness, as well as how visualization types and visual attributes affect the memorability of a visualization. We first present the results of two domain-specific case study evaluations. The first study is in the field of biomedicine in which we developed a new heart disease diagnostic tool, and conducted a study to evaluate the effectiveness of 2D versus 3D data representations as well as color maps. In the second study, we developed a new visualization tool for filesystem provenance data with applications in computer science and the sciences more broadly. We additionally developed a new time-based hierarchical node grouping method. We then conducted a study to evaluate the effectiveness of the new tool with its radial layout versus the conventional node-link diagram, and the new node grouping method. Finally, we discuss the results of two generalized studies designed to understand what makes a visualization memorable. In the first evaluation we focused on visualization memorability and conducted an online study using Amazon's Mechanical Turk with

  7. An object-based visual attention model for robotic applications.

    Science.gov (United States)

    Yu, Yuanlong; Mann, George K I; Gosine, Raymond G

    2010-10-01

    By extending integrated competition hypothesis, this paper presents an object-based visual attention model, which selects one object of interest using low-dimensional features, resulting that visual perception starts from a fast attentional selection procedure. The proposed attention model involves seven modules: learning of object representations stored in a long-term memory (LTM), preattentive processing, top-down biasing, bottom-up competition, mediation between top-down and bottom-up ways, generation of saliency maps, and perceptual completion processing. It works in two phases: learning phase and attending phase. In the learning phase, the corresponding object representation is trained statistically when one object is attended. A dual-coding object representation consisting of local and global codings is proposed. Intensity, color, and orientation features are used to build the local coding, and a contour feature is employed to constitute the global coding. In the attending phase, the model preattentively segments the visual field into discrete proto-objects using Gestalt rules at first. If a task-specific object is given, the model recalls the corresponding representation from LTM and deduces the task-relevant feature(s) to evaluate top-down biases. The mediation between automatic bottom-up competition and conscious top-down biasing is then performed to yield a location-based saliency map. By combination of location-based saliency within each proto-object, the proto-object-based saliency is evaluated. The most salient proto-object is selected for attention, and it is finally put into the perceptual completion processing module to yield a complete object region. This model has been applied into distinct tasks of robots: detection of task-specific stationary and moving objects. Experimental results under different conditions are shown to validate this model.

  8. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications

    Directory of Open Access Journals (Sweden)

    Blake Robert

    2008-12-01

    Full Text Available Abstract Background Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining. It is a chemolithoautrophic, γ-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1–2 and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism. Results The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation, stress responses, DNA repair, and metal and toxic compound fluxes. Conclusion Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.

  9. Visualization of uncorrelated, tandem symmetry mismatches in the internal genome packaging apparatus of bacteriophage T7.

    Science.gov (United States)

    Guo, Fei; Liu, Zheng; Vago, Frank; Ren, Yue; Wu, Weimin; Wright, Elena T; Serwer, Philip; Jiang, Wen

    2013-04-23

    Motor-driven packaging of a dsDNA genome into a preformed protein capsid through a unique portal vertex is essential in the life cycle of a large number of dsDNA viruses. We have used single-particle electron cryomicroscopy to study the multilayer structure of the portal vertex of the bacteriophage T7 procapsid, the recipient of T7 DNA in packaging. A focused asymmetric reconstruction method was developed and applied to selectively resolve neighboring pairs of symmetry-mismatched layers of the portal vertex. However, structural features in all layers of the multilayer portal vertex could not be resolved simultaneously. Our results imply that layers with mismatched symmetries can join together in several different relative orientations, and that orientations at different interfaces assort independently to produce structural isomers, a process that we call combinatorial assembly isomerism. This isomerism explains rotational smearing in previously reported asymmetric reconstructions of the portal vertex of T7 and other bacteriophages. Combinatorial assembly isomerism may represent a new regime of structural biology in which globally varying structures assemble from a common set of components. Our reconstructions collectively validate previously proposed symmetries, compositions, and sequential order of T7 portal vertex layers, resolving in tandem the 5-fold gene product 10 (gp10) shell, 12-fold gp8 portal ring, and an internal core stack consisting of 12-fold gp14 adaptor ring, 8-fold bowl-shaped gp15, and 4-fold gp16 tip. We also found a small tilt of the core stack relative to the icosahedral fivefold axis and propose that this tilt assists DNA spooling without tangling during packaging.

  10. Optimal brain network synchrony visualization: application in an alcoholism paradigm.

    Science.gov (United States)

    Sakkalis, Vangelis; Tsiaras, Vassilis; Zervakis, Michalis; Tollis, Ioannis

    2007-01-01

    Although Electroencephalographic (EEG) signal synchronization studies have been a topic of increasing interest lately, there is no similar effort in the visualization of such measures. In this direction a graph-theoretic approach devised to study and stress the coupling dynamics of task-performing dynamical networks is proposed. Both linear and nonlinear interdependence measures are investigated in an alcoholism paradigm during mental rehearsal of pictures, which is known to reflect synchronization impairment. More specifically, the widely used magnitude squared coherence; phase synchronization and a robust nonlinear state-space generalized synchronization assessment method are investigated. This paper mostly focuses on a signal-based technique of selecting the optimal visualization threshold using surrogate datasets to correctly identify the most significant correlation patterns. Furthermore, a graph statistical parameter attempts to capture and quantify collective motifs present in the functional brain network. The results are in accordance with previous psychophysiology studies suggesting that an alcoholic subject has impaired synchronization of brain activity and loss of lateralization during the rehearsal process, most prominently in alpha (8-12 Hz) band, as compared to a control subject. Lower beta (13-30 Hz) synchronization was also evident in the alcoholic subject.

  11. Deep data: discovery and visualization Application to hyperspectral ALMA imagery

    Science.gov (United States)

    Merényi, Erzsébet; Taylor, Joshua; Isella, Andrea

    2017-06-01

    Leading-edge telescopes such as the Atacama Large Millimeter and sub-millimeter Array (ALMA), and near-future ones, are capable of imaging the same sky area at hundreds-to-thousands of frequencies with both high spectral and spatial resolution. This provides unprecedented opportunities for discovery about the spatial, kinematical and compositional structure of sources such as molecular clouds or protoplanetary disks, and more. However, in addition to enormous volume, the data also exhibit unprecedented complexity, mandating new approaches for extracting and summarizing relevant information. Traditional techniques such as examining images at selected frequencies become intractable while tools that integrate data across frequencies or pixels (like moment maps) can no longer fully exploit and visualize the rich information. We present a neural map-based machine learning approach that can handle all spectral channels simultaneously, utilizing the full depth of these data for discovery and visualization of spectrally homogeneous spatial regions (spectral clusters) that characterize distinct kinematic behaviors. We demonstrate the effectiveness on an ALMA image cube of the protoplanetary disk HD142527. The tools we collectively name ``NeuroScope'' are efficient for ``Big Data'' due to intelligent data summarization that results in significant sparsity and noise reduction. We also demonstrate a new approach to automate our clustering for fast distillation of large data cubes.

  12. Development of genomic based diagnostics in various application domains

    DEFF Research Database (Denmark)

    Szallasi, Zoltan Imre

    2017-01-01

    We will review the revolution brought about by low cost next generation sequencing in a wide array of diagnostic and industrial applications with a special emphasis on computational requirements and big data challenges.......We will review the revolution brought about by low cost next generation sequencing in a wide array of diagnostic and industrial applications with a special emphasis on computational requirements and big data challenges....

  13. Genetic recombination pathways and their application for genome modification of human embryonic stem cells.

    Science.gov (United States)

    Nieminen, Mikko; Tuuri, Timo; Savilahti, Harri

    2010-10-01

    Human embryonic stem cells are pluripotent cells derived from early human embryo and retain a potential to differentiate into all adult cell types. They provide vast opportunities in cell replacement therapies and are expected to become significant tools in drug discovery as well as in the studies of cellular and developmental functions of human genes. The progress in applying different types of DNA recombination reactions for genome modification in a variety of eukaryotic cell types has provided means to utilize recombination-based strategies also in human embryonic stem cells. Homologous recombination-based methods, particularly those utilizing extended homologous regions and those employing zinc finger nucleases to boost genomic integration, have shown their usefulness in efficient genome modification. Site-specific recombination systems are potent genome modifiers, and they can be used to integrate DNA into loci that contain an appropriate recombination signal sequence, either naturally occurring or suitably pre-engineered. Non-homologous recombination can be used to generate random integrations in genomes relatively effortlessly, albeit with a moderate efficiency and precision. DNA transposition-based strategies offer substantially more efficient random strategies and provide means to generate single-copy insertions, thus potentiating the generation of genome-wide insertion libraries applicable in genetic screens. 2010 Elsevier Inc. All rights reserved.

  14. SeiVis: An interactive visual subsurface modeling application

    KAUST Repository

    Hollt, Thomas

    2012-12-01

    The most important resources to fulfill today’s energy demands are fossil fuels, such as oil and natural gas. When exploiting hydrocarbon reservoirs, a detailed and credible model of the subsurface structures is crucial in order to minimize economic and ecological risks. Creating such a model is an inverse problem: reconstructing structures from measured reflection seismics. The major challenge here is twofold: First, the structures in highly ambiguous seismic data are interpreted in the time domain. Second, a velocity model has to be built from this interpretation to match the model to depth measurements from wells. If it is not possible to obtain a match at all positions, the interpretation has to be updated, going back to the first step. This results in a lengthy back and forth between the different steps, or in an unphysical velocity model in many cases. This paper presents a novel, integrated approach to interactively creating subsurface models from reflection seismics. It integrates the interpretation of the seismic data using an interactive horizon extraction technique based on piecewise global optimization with velocity modeling. Computing and visualizing the effects of changes to the interpretation and velocity model on the depth-converted model on the fly enables an integrated feedback loop that enables a completely new connection of the seismic data in time domain and well data in depth domain. Using a novel joint time/depth visualization, depicting side-by-side views of the original and the resulting depth-converted data, domain experts can directly fit their interpretation in time domain to spatial ground truth data. We have conducted a domain expert evaluation, which illustrates that the presented workflow enables the creation of exact subsurface models much more rapidly than previous approaches. © 2012 IEEE.

  15. SeiVis: An interactive visual subsurface modeling application

    KAUST Repository

    Hollt, Thomas; Freiler, Wolfgang; Gschwantner, Fritz M.; Doleisch, Helmut; Heinemann, Gabor F.; Hadwiger, Markus

    2012-01-01

    The most important resources to fulfill today’s energy demands are fossil fuels, such as oil and natural gas. When exploiting hydrocarbon reservoirs, a detailed and credible model of the subsurface structures is crucial in order to minimize economic and ecological risks. Creating such a model is an inverse problem: reconstructing structures from measured reflection seismics. The major challenge here is twofold: First, the structures in highly ambiguous seismic data are interpreted in the time domain. Second, a velocity model has to be built from this interpretation to match the model to depth measurements from wells. If it is not possible to obtain a match at all positions, the interpretation has to be updated, going back to the first step. This results in a lengthy back and forth between the different steps, or in an unphysical velocity model in many cases. This paper presents a novel, integrated approach to interactively creating subsurface models from reflection seismics. It integrates the interpretation of the seismic data using an interactive horizon extraction technique based on piecewise global optimization with velocity modeling. Computing and visualizing the effects of changes to the interpretation and velocity model on the depth-converted model on the fly enables an integrated feedback loop that enables a completely new connection of the seismic data in time domain and well data in depth domain. Using a novel joint time/depth visualization, depicting side-by-side views of the original and the resulting depth-converted data, domain experts can directly fit their interpretation in time domain to spatial ground truth data. We have conducted a domain expert evaluation, which illustrates that the presented workflow enables the creation of exact subsurface models much more rapidly than previous approaches. © 2012 IEEE.

  16. SeiVis: An Interactive Visual Subsurface Modeling Application.

    Science.gov (United States)

    Hollt, T; Freiler, W; Gschwantner, F; Doleisch, H; Heinemann, G; Hadwiger, M

    2012-12-01

    The most important resources to fulfill today's energy demands are fossil fuels, such as oil and natural gas. When exploiting hydrocarbon reservoirs, a detailed and credible model of the subsurface structures is crucial in order to minimize economic and ecological risks. Creating such a model is an inverse problem: reconstructing structures from measured reflection seismics. The major challenge here is twofold: First, the structures in highly ambiguous seismic data are interpreted in the time domain. Second, a velocity model has to be built from this interpretation to match the model to depth measurements from wells. If it is not possible to obtain a match at all positions, the interpretation has to be updated, going back to the first step. This results in a lengthy back and forth between the different steps, or in an unphysical velocity model in many cases. This paper presents a novel, integrated approach to interactively creating subsurface models from reflection seismics. It integrates the interpretation of the seismic data using an interactive horizon extraction technique based on piecewise global optimization with velocity modeling. Computing and visualizing the effects of changes to the interpretation and velocity model on the depth-converted model on the fly enables an integrated feedback loop that enables a completely new connection of the seismic data in time domain and well data in depth domain. Using a novel joint time/depth visualization, depicting side-by-side views of the original and the resulting depth-converted data, domain experts can directly fit their interpretation in time domain to spatial ground truth data. We have conducted a domain expert evaluation, which illustrates that the presented workflow enables the creation of exact subsurface models much more rapidly than previous approaches.

  17. Multivariate nonparametric regression and visualization with R and applications to finance

    CERN Document Server

    Klemelä, Jussi

    2014-01-01

    A modern approach to statistical learning and its applications through visualization methods With a unique and innovative presentation, Multivariate Nonparametric Regression and Visualization provides readers with the core statistical concepts to obtain complete and accurate predictions when given a set of data. Focusing on nonparametric methods to adapt to the multiple types of data generatingmechanisms, the book begins with an overview of classification and regression. The book then introduces and examines various tested and proven visualization techniques for learning samples and functio

  18. Parallel real-time visualization system for large-scale simulation. Application to WSPEEDI

    International Nuclear Information System (INIS)

    Muramatsu, Kazuhiro; Otani, Takayuki; Kitabata, Hideyuki; Matsumoto, Hideki; Takei, Toshifumi; Doi, Shun

    2000-01-01

    The real-time visualization system, PATRAS (PArallel TRAcking Steering system) has been developed on parallel computing servers. The system performs almost all of the visualization tasks on a parallel computing server, and uses image data compression technique for efficient communication between the server and the client terminal. Therefore, the system realizes high performance concurrent visualization in an internet computing environment. The experience in applying PATRAS to WSPEEDI (Worldwide version of System for Prediction Environmental Emergency Dose Information) is reported. The application of PATRAS to WSPEEDI enables users to understand behaviours of radioactive tracers from different release points easily and quickly. (author)

  19. State of the art of parallel scientific visualization applications on PC clusters

    International Nuclear Information System (INIS)

    Juliachs, M.

    2004-01-01

    In this state of the art on parallel scientific visualization applications on PC clusters, we deal with both surface and volume rendering approaches. We first analyze available PC cluster configurations and existing parallel rendering software components for parallel graphics rendering. CEA/DIF has been studying cluster visualization since 2001. This report is part of a study to set up a new visualization research platform. This platform consisting of an eight-node PC cluster under Linux and a tiled display was installed in collaboration with Versailles-Saint-Quentin University in August 2003. (author)

  20. Efficient Server-Aided Secure Two-Party Function Evaluation with Applications to Genomic Computation

    Directory of Open Access Journals (Sweden)

    Blanton Marina

    2016-10-01

    Full Text Available Computation based on genomic data is becoming increasingly popular today, be it for medical or other purposes. Non-medical uses of genomic data in a computation often take place in a server-mediated setting where the server offers the ability for joint genomic testing between the users. Undeniably, genomic data is highly sensitive, which in contrast to other biometry types, discloses a plethora of information not only about the data owner, but also about his or her relatives. Thus, there is an urgent need to protect genomic data. This is particularly true when the data is used in computation for what we call recreational non-health-related purposes. Towards this goal, in this work we put forward a framework for server-aided secure two-party computation with the security model motivated by genomic applications. One particular security setting that we treat in this work provides stronger security guarantees with respect to malicious users than the traditional malicious model. In particular, we incorporate certified inputs into secure computation based on garbled circuit evaluation to guarantee that a malicious user is unable to modify her inputs in order to learn unauthorized information about the other user’s data. Our solutions are general in the sense that they can be used to securely evaluate arbitrary functions and offer attractive performance compared to the state of the art. We apply the general constructions to three specific types of genomic tests: paternity, genetic compatibility, and ancestry testing and implement the constructions. The results show that all such private tests can be executed within a matter of seconds or less despite the large size of one’s genomic data.

  1. Breast Cancer in Africa: Limitations and Opportunities for Application of Genomic Medicine

    Directory of Open Access Journals (Sweden)

    Allison Silverstein

    2016-01-01

    Full Text Available As genomic medicine gains clinical applicability across a spectrum of diseases, insufficient application in low-income settings stands to increase health disparity. Breast cancer screening, diagnosis, and treatment have benefited greatly from genomic medicine in high-income settings. As breast cancer is a leading cause of both cancer incidence and mortality in Africa, attention and resources must be applied to research and clinical initiatives to integrate genomic medicine into breast cancer care. In terms of research, there is a paucity of investigations into genetic determinants of breast cancer specific to African populations, despite consensus in the literature that predisposition and susceptibility genes vary between populations. Therefore, we need targeted strengthening of existing research efforts and support of new initiatives. Results will improve clinical care through screening and diagnosis with genetic testing specific to breast cancer in African populations. Clinically, genomic medicine can provide information capable of improving resource allocation to the population which most stands to benefit from increased screening or tailored treatment modalities. In situations where mammography or chemotherapy options are limited, this information will allow for the greatest impact. Implementation of genomic medicine will face numerous systemic barriers but is essential to improve breast cancer outcomes and survival.

  2. Genome Editing with Crispr-Cas9 Systems: Basic Research and Clinical Applications

    Directory of Open Access Journals (Sweden)

    Anna Meiliana

    2017-04-01

    Full Text Available BACKGROUND: Recently established genome editing technologies will open new avenues for biological research and development. Human genome editing is a powerful tool which offers great scientific and therapeutic potential. CONTENT: Genome editing using the clustered regularly interspaced short palindromic repeats (CRISPR/CRISPRassociated protein 9 (Cas9 technology is revolutionizing the gene function studies and possibly will give rise to an entirely new degree of therapeutics for a large range of diseases. Prompt advances in the CRISPR/Cas9 technology, as well as delivery modalities for gene therapy applications, are dismissing the barriers to the clinical translation of this technology. Many studies conducted showed promising results, but as current available technologies for evaluating off-target gene modification, several elements must be addressed to validate the safety of the CRISPR/Cas9 platform for clinical application, as the ethical implication as well. SUMMARY: The CRISPR/Cas9 system is a powerful genome editing technology with the potential to create a variety of novel therapeutics for a range of diseases, many of which are currently untreatable. KEYWORDS: genome editing, CRISPR-Cas, guideRNA, DSB, ZFNs, TALEN

  3. Development and clinical application of a color pediatric visual acuity chart

    Directory of Open Access Journals (Sweden)

    Shu-Guo Yin

    2014-12-01

    Full Text Available AIM: To introduce a new color pediatric visual acuity chart and its clinical application.METHODS:The color pediatric visual acuity chart was designed based on principle of visual angle. The optotype on the color chart had graphics. The progression rate of optotype size between 2 lines was 10(101/2 and 1.2589. A regular geometric progression of optotype sizes and distribution was employed to arrange 8 lines with 11 optotype on the color chart. The testing distance was 3m. The visual acuity score could be recorded as logarithm of the minimum angle of resolution notation or decimal notation. The reliability of naked distant measurements with this new chart was tested in one eye of 100 children(4 ~6 years oldtaking the Chinese national standard logarithm visual acuity chart standard. RESULTS: The color pediatric visual acuity chart and logarithmic chart controls, visual acuity test results that in the two groups had no significant difference(t=1.2671, P>0.05. Two sets of vision data existed positive correlation(r=0.924, PCONCLUSION:Children are easier to accept used new color pediatric visual acuity chart to inspect vision. New chart is reliability and apply to children's vision screening.

  4. Visapult: A Prototype Remote and Distributed Visualization Application and Framework

    International Nuclear Information System (INIS)

    Bethel, Wes

    2000-01-01

    We describe an approach used for implementing a highly efficient and scalable method for direct volume rendering. Our approach uses a pipelined-parallel decomposition composed of parallel computers and commodity desktop hardware. With our approach, desktop interactivity is divorced from the latency inherent in network-based applications

  5. Ontology-Based Information Visualization: Toward Semantic Web Applications

    NARCIS (Netherlands)

    Fluit, Christiaan; Sabou, Marta; Harmelen, Frank van

    2006-01-01

    The Semantic Web is an extension of the current World Wide Web, based on the idea of exchanging information with explicit, formal, and machine-accessible descriptions of meaning. Providing information with such semantics will enable the construction of applications that have an increased awareness

  6. Application Of Expert System Techniques To A Visual Tracker

    Science.gov (United States)

    Myler, Harley R.; Thompson, Wiley E.; Flachs, Gerald M.

    1985-04-01

    A structure for visual tracking system is presented which relies on information developed from previous tracking scenarios stored in a knowledge base to enhance tracking performance. The system is comprised of a centroid tracker front end which supplies segmented image features to a data reduction algorithm which holds the reduced data in a temporary data base relation. This relation is then classified vio two separate modes, learn and track. Under learn mode, an external teacher-irector operator provides identification and weighting cues for membership in a long-term storage relation within a knowledge base. Track mode operates autonomously from the learn mode where the system determines feature validity by applying fuzzy set membership criteria to previously stored track information in the database. Results determined from the classification generate tracker directives which either enhance or permit current tracking to continue or cause the tracker to search for alternate targets based upon analysis of a global target tracking list. The classification algorithm is based on correlative analysis of the tracker's segmented output presentation after low pass filtering derives lower order harmonics of the feature. The fuzzy set membership criteria is based on size, rotation, Irame location, and past history of the feature. The first three factors are lin-ear operations on the spectra, while the last is generated as a context relation in the knowledge base. The context relation interlinks data between features to facilitate tracker operation during feature occlusion or presence of countermeasures.

  7. Development and potential applications of CRISPR-Cas9 genome editing technology in sarcoma.

    Science.gov (United States)

    Liu, Tang; Shen, Jacson K; Li, Zhihong; Choy, Edwin; Hornicek, Francis J; Duan, Zhenfeng

    2016-04-01

    Sarcomas include some of the most aggressive tumors and typically respond poorly to chemotherapy. In recent years, specific gene fusion/mutations and gene over-expression/activation have been shown to drive sarcoma pathogenesis and development. These emerging genomic alterations may provide targets for novel therapeutic strategies and have the potential to transform sarcoma patient care. The RNA-guided nuclease CRISPR-Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated protein-9 nuclease) is a convenient and versatile platform for site-specific genome editing and epigenome targeted modulation. Given that sarcoma is believed to develop as a result of genetic alterations in mesenchymal progenitor/stem cells, CRISPR-Cas9 genome editing technologies hold extensive application potentials in sarcoma models and therapies. We review the development and mechanisms of the CRISPR-Cas9 system in genome editing and introduce its application in sarcoma research and potential therapy in clinic. Additionally, we propose future directions and discuss the challenges faced with these applications, providing concise and enlightening information for readers interested in this area. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  8. Building online genomics applications using BioPyramid.

    Science.gov (United States)

    Stephenson, Liam; Wakeham, Yoshua; Seidenman, Nick; Choi, Jarny

    2018-03-29

    BioPyramid is a python package, which serves as a scaffold for building an online application for the exploration of gene expression data. It is designed for bioinformaticians wishing to quickly share transformed data and interactive analyses with collaborators. Current R-based tools similarly address the need to quickly share "omics"-data in an exploratory format, but these are generally small-scale, single-dataset solutions. Biopyramid is written in python pyramid framework and scalable to address longer-term or more complex projects. It contains a number of components designed to reduce the time and effort in building such an application from scratch, including gene annotation, dataset models and visualisation tools. Freely available at http://github.com/jarny/biopyramid. Implemented in python and javascript. jarnyc@unimelb.edu.au.

  9. Fat polygonal partitions with applications to visualization and embeddings

    Directory of Open Access Journals (Sweden)

    Mark de Berg

    2013-12-01

    Full Text Available Let T be a rooted and weighted tree, where the weight of any node is equal to the sum of the weights of its children. The popular Treemap algorithm visualizes such a tree as a hierarchical partition of a square into rectangles, where the area of the rectangle corresponding to any node in T is equal to the weight of that node. The aspect ratio of the rectangles in such a rectangular partition necessarily depends on the weights and can become arbitrarily high.We introduce a new hierarchical partition scheme, called a polygonal partition, which uses convex polygons rather than just rectangles. We present two methods for constructing polygonal partitions, both having guarantees on the worst-case aspect ratio of the constructed polygons; in particular, both methods guarantee a bound on the aspect ratio that is independent of the weights of the nodes.We also consider rectangular partitions with slack, where the areas of the rectangles may differ slightly from the weights of the corresponding nodes. We show that this makes it possible to obtain partitions with constant aspect ratio. This result generalizes to hyper-rectangular partitions in ℝd. We use these partitions with slack for embedding ultrametrics into d-dimensional Euclidean space:  we give a polylog(Δ-approximation algorithm for embedding n-point ultrametrics into ℝd with minimum distortion, where Δ denotes the spread of the metric. The previously best-known approximation ratio for this problem was polynomial in n. This is the first algorithm for embedding a non-trivial family of weighted-graph metrics into a space of constant dimension that achieves polylogarithmic approximation ratio.

  10. Adaptive Monocular Visual-Inertial SLAM for Real-Time Augmented Reality Applications in Mobile Devices.

    Science.gov (United States)

    Piao, Jin-Chun; Kim, Shin-Dug

    2017-11-07

    Simultaneous localization and mapping (SLAM) is emerging as a prominent issue in computer vision and next-generation core technology for robots, autonomous navigation and augmented reality. In augmented reality applications, fast camera pose estimation and true scale are important. In this paper, we present an adaptive monocular visual-inertial SLAM method for real-time augmented reality applications in mobile devices. First, the SLAM system is implemented based on the visual-inertial odometry method that combines data from a mobile device camera and inertial measurement unit sensor. Second, we present an optical-flow-based fast visual odometry method for real-time camera pose estimation. Finally, an adaptive monocular visual-inertial SLAM is implemented by presenting an adaptive execution module that dynamically selects visual-inertial odometry or optical-flow-based fast visual odometry. Experimental results show that the average translation root-mean-square error of keyframe trajectory is approximately 0.0617 m with the EuRoC dataset. The average tracking time is reduced by 7.8%, 12.9%, and 18.8% when different level-set adaptive policies are applied. Moreover, we conducted experiments with real mobile device sensors, and the results demonstrate the effectiveness of performance improvement using the proposed method.

  11. Tile-based parallel coordinates and its application in financial visualization

    Science.gov (United States)

    Alsakran, Jamal; Zhao, Ye; Zhao, Xinlei

    2010-01-01

    Parallel coordinates technique has been widely used in information visualization applications and it has achieved great success in visualizing multivariate data and perceiving their trends. Nevertheless, visual clutter usually weakens or even diminishes its ability when the data size increases. In this paper, we first propose a tile-based parallel coordinates, where the plotting area is divided into rectangular tiles. Each tile stores an intersection density that counts the total number of polylines intersecting with that tile. Consequently, the intersection density is mapped to optical attributes, such as color and opacity, by interactive transfer functions. The method visualizes the polylines efficiently and informatively in accordance with the density distribution, and thus, reduces visual cluttering and promotes knowledge discovery. The interactivity of our method allows the user to instantaneously manipulate the tiles distribution and the transfer functions. Specifically, the classic parallel coordinates rendering is a special case of our method when each tile represents only one pixel. A case study on a real world data set, U.S. stock mutual fund data of year 2006, is presented to show the capability of our method in visually analyzing financial data. The presented visual analysis is conducted by an expert in the domain of finance. Our method gains the support from professionals in the finance field, they embrace it as a potential investment analysis tool for mutual fund managers, financial planners, and investors.

  12. Current Knowledge in lentil genomics and its application for crop improvement

    Directory of Open Access Journals (Sweden)

    Shiv eKumar

    2015-02-01

    Full Text Available Most of the lentil growing countries face a certain set of abiotic and biotic stresses causing substantial reduction in crop growth, yield, and production. Until-to date, lentil breeders have used conventional plant breeding techniques of selection-recombination-selection cycle to develop improved cultivars. These techniques have been successful in mainstreaming some of the easy-to-manage monogenic traits. However in case of complex quantitative traits, these conventional techniques are less precise. As most of the economic traits are complex, quantitative and often influenced by environments and genotype-environment (GE interaction, the genetic improvement of these traits becomes difficult. Genomics assisted breeding is relatively powerful and fast approach to develop high yielding varieties more suitable to adverse environmental conditions. New tools such as molecular markers and bioinformatics are expected to generate new knowledge and improve our understanding on the genetics of complex traits. In the past, the limited availability of genomic resources in lentil could not allow breeders to employ these tools in mainstream breeding program. The recent application of the Next Generation Sequencing (NGS and Genotyping by sequencing (GBS technologies has facilitated to speed up the lentil genome sequencing project and large discovery of genome-wide SNP markers. Recently, several linkage maps have been developed in lentil through the use of Expressed Sequenced Tag (EST-derived Simple Sequence Repeat (SSR and Single Nucleotide Polymorphism (SNP markers. These maps have emerged as useful genomic resources to identify QTL imparting tolerance to biotic and abiotic stresses in lentil. In this review, the current knowledge on available genomic resources and its application in lentil breeding program are discussed.

  13. The CRISPR/Cas genome-editing tool: application in improvement of crops

    Directory of Open Access Journals (Sweden)

    SURENDER eKHATODIA

    2016-04-01

    Full Text Available The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR associated Cas9/sgRNA system is a novel fledgling targeted genome-editing technique from bacterial immune system, which is a cheap, easy and most rapidly adopted genome editing tool transforming to revolutionary paradigm. Cas9 protein is an RNA guided endonuclease utilized for creating targeted double stranded breaks with only a short RNA sequence to confer recognition of the target in animals and plants. Development of genetically edited (GE crops similar to those developed by conventional or mutation breeding using this potential technique makes it a promising and extremely versatile tool for providing sustainable productive agriculture for better feeding of rapidly growing population in changing climate. The emerging areas of research for the genome editing in plants are like, interrogating gene function, rewiring the regulatory signaling networks, sgRNA library for high-throughput loss-of-function screening. In this review, we will discuss the broad applicability of the Cas9 nuclease mediated targeted plant genome editing for development of designer crops. The regulatory uncertainty and social acceptance of plant breeding by Cas9 genome editing have also been discussed. The non-GM designer genetically edited plants could prospect climate resilient and sustainable energy agriculture in coming future for maximizing the yield by combating abiotic and biotic stresses with this new innovative plant breeding technique.

  14. Corridor One: An Integrated Distance Visualization Environment for SSI and ASCI Applications

    Energy Technology Data Exchange (ETDEWEB)

    Stevens, Rick [ANL, PI; Leigh, Jason [UIC, PI

    2002-07-14

    Scenarios describe realistic uses of DVC/Distance technologies in several years. Four scenarios are described: Distributed Decision Making; Remote Interactive Computing; Remote Visualization: (a) Remote Immersive Visualization and (b) Remote Scientific Visualization; Remote Virtual Prototyping. Scenarios serve as drivers for the road maps and enable us to check that the functionality and technology in the road maps match application needs. There are four major DVC/Distance technology areas we cover: Networking and QoS; Remote Computing; Remote Visualization; Remote Data. Each road ma consists of two parts, a functionality matrix (what can be done) and a technology matrix (underlying technology). That is, functionality matrices show the desired operational characteristics, while technology matrices show the underlying technology needed. In practice, there isn't always a clean break between functionality and technology, but it still seems useful to try and separate things this way.

  15. Robotic Label Applicator: Design, Development and Visual Servoing Based Control

    Directory of Open Access Journals (Sweden)

    Lin Chyi-Yeu

    2016-01-01

    Full Text Available Use of robotic arms and computer vision in manufacture, and assembly process are getting more interest as flexible customization is becoming priority over mass production as frontier industry practice. In this paper an innovative label applicator as end of arm tooling (EOAT capable of dispensing and applying label stickers of various dimensions to a product is designed, fabricated and tested. The system incorporates a label dispenserapplicator and had eye-in-hand camera system, attached to 6-dof robot arm can autonomously apply a label sticker to the target position on a randomly placed product. Employing multiple advantages from different knowledge basis, mechanism design and vision based automatic control, offers this system distinctive efficiency as well as flexibility to change in manufacturing and assembly process with time and cost saving.

  16. Application of visual basic in high-throughput mass spectrometry-directed purification of combinatorial libraries.

    Science.gov (United States)

    Li, B; Chan, E C Y

    2003-01-01

    We present an approach to customize the sample submission process for high-throughput purification (HTP) of combinatorial parallel libraries using preparative liquid chromatography electrospray ionization mass spectrometry. In this study, Visual Basic and Visual Basic for Applications programs were developed using Microsoft Visual Basic 6 and Microsoft Excel 2000, respectively. These programs are subsequently applied for the seamless electronic submission and handling of data for HTP. Functions were incorporated into these programs where medicinal chemists can perform on-line verification of the purification status and on-line retrieval of postpurification data. The application of these user friendly and cost effective programs in our HTP technology has greatly increased our work efficiency by reducing paper work and manual manipulation of data.

  17. Learning Programming Technique through Visual Programming Application as Learning Media with Fuzzy Rating

    Science.gov (United States)

    Buditjahjanto, I. G. P. Asto; Nurlaela, Luthfiyah; Ekohariadi; Riduwan, Mochamad

    2017-01-01

    Programming technique is one of the subjects at Vocational High School in Indonesia. This subject contains theory and application of programming utilizing Visual Programming. Students experience some difficulties to learn textual learning. Therefore, it is necessary to develop media as a tool to transfer learning materials. The objectives of this…

  18. Learning Science in a Virtual Reality Application: The Impacts of Animated-Virtual Actors' Visual Complexity

    Science.gov (United States)

    Kartiko, Iwan; Kavakli, Manolya; Cheng, Ken

    2010-01-01

    As the technology in computer graphics advances, Animated-Virtual Actors (AVAs) in Virtual Reality (VR) applications become increasingly rich and complex. Cognitive Theory of Multimedia Learning (CTML) suggests that complex visual materials could hinder novice learners from attending to the lesson properly. On the other hand, previous studies have…

  19. Programming Education with a Blocks-Based Visual Language for Mobile Application Development

    Science.gov (United States)

    Mihci, Can; Ozdener, Nesrin

    2014-01-01

    The aim of this study is to assess the impact upon academic success of the use of a reference block-based visual programming tool, namely the MIT App Inventor for Android, as an educational instrument for teaching object-oriented GUI-application development (CS2) concepts to students; who have previously completed a fundamental programming course…

  20. Visual Recognition and Its Application to Robot Arm Control

    Directory of Open Access Journals (Sweden)

    Jih-Gau Juang

    2015-10-01

    Full Text Available This paper presents an application of optical word recognition and fuzzy control to a smartphone automatic test system. The system consists of a robot arm and two webcams. After the words from the control panel that represent commands are recognized by the robot system, the robot arm performs the corresponding actions to test the smartphone. One of the webcams is utilized to capture commands on the screen of the control panel, the other to recognize the words on the screen of the tested smartphone. The method of image processing is based on the Red-Green-Blue (RGB and Hue-Saturation-Luminance (HSL color spaces to reduce the influence of light. Fuzzy theory is used in the robot arm’s position control. The Optical Character Recognition (OCR technique is applied to the word recognition, and the recognition results are then checked by a dictionary process to increase the recognition accuracy. The camera which is used to recognize the tested smartphone also provides object coordinates to the fuzzy controller, then the robot arm moves to the desired positions and presses the desired buttons. The proposed control scheme allows the robot arm to perform different assigned test functions successfully.

  1. Actuated polymer based dielectric mirror for visual spectral range applications

    Science.gov (United States)

    Vergara, Pedro P.; Lunardi, Leda

    2017-08-01

    Miniature dielectric mirrors are useful components for lasers, thin film beam splitters and high quality mirrors in optics. These mirrors usually made from rigid inorganic materials can achieve a reflectance of almost one hundred percent. Being structural components, as soon as fabricated their reflectance and/or bandwidth remains constant. Here it is presented a novel fabrication process of a dielectric mirror based on free standing polymer layers. By applying an electrostatic force between the top and the bottom layers the reflectance can be changed. The large difference between the polymers refractive index and the air allows to achieve a reflectance of more than 85% using only six pairs of nanolayers. Preliminary simulations indicate an actuation speed of less than 1ms. Experimental optical characterization of fabricated structures agrees well with simulation results. Furthermore, structures can be designed to reflect a particular set of colors and/or isolated by using color filters, so a color pixel is fabricated, where the reflectance for each isolated color can be voltage controlled. Potential applications include an active component in a reflective screen display.

  2. Industrial application trends and market perspectives for virtual reality and visual simulation

    Directory of Open Access Journals (Sweden)

    Antonio Valerio Netto

    2004-06-01

    Full Text Available This paper attempts to provide an overview of current market trends in industrial applications of VR (Virtual Reality and VisSim (visual simulation for the next few years. Several market studies recently undertaken are presented and commented. A profile of some companies that are starting to work with these technologies is provided, in an attempt to motivate Brazilian companies into the use of these new technologies by describing successful example applications undertaken by foreign companies.

  3. Application of Saying, Synonyms, Antonyms, and Indonesian Dictionary Using Microsoft Visual Basic 6.0

    OpenAIRE

    Agus Budi Setyawan; Yudi Irawan Chandra, SKom, MMSI

    2005-01-01

    This writing describes the application of the proverb, synonym, antonym, and dictionaries Indonesian. Basically, this application to find out about the meaning of the proverb, synonym, antonym and meaning of the word in Indonesian. For that the author wanted to show them in computerized form using Microsoft Visual Basic 6.0. by presenting it in the form of computerized data that the authors hope that we get a more accurate or the possibility of error becomes smaller. Also expected this appli...

  4. Genome-editing technologies and their potential application in horticultural crop breeding

    Science.gov (United States)

    Xiong, Jin-Song; Ding, Jing; Li, Yi

    2015-01-01

    Plant breeding, one of the oldest agricultural activities, parallels human civilization. Many crops have been domesticated to satisfy human's food and aesthetical needs, including numerous specialty horticultural crops such as fruits, vegetables, ornamental flowers, shrubs, and trees. Crop varieties originated through selection during early human civilization. Other technologies, such as various forms of hybridization, mutation, and transgenics, have also been invented and applied to crop breeding over the past centuries. The progress made in these breeding technologies, especially the modern biotechnology-based breeding technologies, has had a great impact on crop breeding as well as on our lives. Here, we first review the developmental process and applications of these technologies in horticultural crop breeding. Then, we mainly describe the principles of the latest genome-editing technologies and discuss their potential applications in the genetic improvement of horticultural crops. The advantages and challenges of genome-editing technologies in horticultural crop breeding are also discussed. PMID:26504570

  5. Accessibility of dynamic web applications with emphasis on visually impaired users

    Directory of Open Access Journals (Sweden)

    Kingsley Okoye

    2014-09-01

    Full Text Available As the internet is fast migrating from static web pages to dynamic web pages, the users with visual impairment find it confusing and challenging when accessing the contents on the web. There is evidence that dynamic web applications pose accessibility challenges for the visually impaired users. This study shows that a difference can be made through the basic understanding of the technical requirement of users with visual impairment and addresses a number of issues pertinent to the accessibility needs for such users. We propose that only by designing a framework that is structurally flexible, by removing unnecessary extras and thereby making every bit useful (fit-for-purpose, will visually impaired users be given an increased capacity to intuitively access e-contents. This theory is implemented in a dynamic website for the visually impaired designed in this study. Designers should be aware of how the screen reading software works to enable them make reasonable adjustments or provide alternative content that still corresponds to the objective content to increase the possibility of offering faultless service to such users. The result of our research reveals that materials can be added to a content repository or re-used from existing ones by identifying the content types and then transforming them into a flexible and accessible one that fits the requirements of the visually impaired through our method (no-frill + agile methodology rather than computing in advance or designing according to a given specification.

  6. Future Translational Applications From the Contemporary Genomics Era: A Scientific Statement From the American Heart Association

    OpenAIRE

    Fox, Caroline S.; Hall, Jennifer L.; Arnett, Donna K.; Ashley, Euan A.; Delles, Christian; Engler, Mary B.; Freeman, Mason W.; Johnson, Julie A.; Lanfear, David E.; Liggett, Stephen B.; Lusis, Aldons J.; Loscalzo, Joseph; MacRae, Calum A.; Musunuru, Kiran; Newby, L. Kristin

    2015-01-01

    The field of genetics and genomics has advanced considerably with the achievement of recent milestones encompassing the identification of many loci for cardiovascular disease and variable drug responses. Despite this achievement, a gap exists in the understanding and advancement to meaningful translation that directly affects disease prevention and clinical care. The purpose of this scientific statement is to address the gap between genetic discoveries and their practical application to cardi...

  7. Integrating the Visual Arts Back into the Classroom with Mobile Applications: Teaching beyond the "Click and View" Approach

    Science.gov (United States)

    Katz-Buonincontro, Jen; Foster, Aroutis

    2013-01-01

    Teachers can use mobile applications to integrate the visual arts back into the classroom, but how? This article generates recommendations for selecting and using well-designed mobile applications in the visual arts beyond a "click and view " approach. Using quantitative content analysis, the results show the extent to which a sample of…

  8. The main pump motor remote visual check in the application of the domestic nuclear power plants

    International Nuclear Information System (INIS)

    Ge Lianwei; Yu Tao; Fang Jiang; Zhang Ting; Zhang Xingtian; Ding Youyuan

    2014-01-01

    In this paper, the Qinshan nuclear power station the first main pump motor to the successful implementation of remote visual inspection the main pump motor remote visual inspection applications. Qinshan Nuclear Power Plant Units 1 and 2 of the main pump motor inspection results show that the key components of the Qinshan Nuclear Power Plant Units 1 and 2 of the main pump rotor, stator end coils good condition, its problems for 10 years in the motor does not affect the normal use of the motor state disintegration overhaul problems tracking disintegration overhaul in 10 years. (authors)

  9. Visual Monte Carlo and its application to internal and external dosimetry

    International Nuclear Information System (INIS)

    Hunt, J.G.; Silva, F.C. da; Souza-Santos, D. de; Dantas, B.M.; Azeredo, A.; Malatova, I.; Foltanova, S.; Isakson, M.

    2001-01-01

    The program visual Monte Carlo (VMC), combined with voxel phantoms, and its application to three areas of radiation protection: calibration of in vivo measurement systems, dose calculations due to external sources of radiation, and the calculation of Specific Effective Energies is described in this paper. The simulation of photon transport through a voxel phantom requires a Monte Carlo program adapted to voxel geometries. VMC is written in Visual Basic trademark, a Microsoft Windows based program, which is easy to use and has an extensive graphic output. (orig.)

  10. The vertebrate ancestral repertoire of visual opsins, transducin alpha subunits and oxytocin/vasopressin receptors was established by duplication of their shared genomic region in the two rounds of early vertebrate genome duplications.

    Science.gov (United States)

    Lagman, David; Ocampo Daza, Daniel; Widmark, Jenny; Abalo, Xesús M; Sundström, Görel; Larhammar, Dan

    2013-11-02

    Vertebrate color vision is dependent on four major color opsin subtypes: RH2 (green opsin), SWS1 (ultraviolet opsin), SWS2 (blue opsin), and LWS (red opsin). Together with the dim-light receptor rhodopsin (RH1), these form the family of vertebrate visual opsins. Vertebrate genomes contain many multi-membered gene families that can largely be explained by the two rounds of whole genome duplication (WGD) in the vertebrate ancestor (2R) followed by a third round in the teleost ancestor (3R). Related chromosome regions resulting from WGD or block duplications are said to form a paralogon. We describe here a paralogon containing the genes for visual opsins, the G-protein alpha subunit families for transducin (GNAT) and adenylyl cyclase inhibition (GNAI), the oxytocin and vasopressin receptors (OT/VP-R), and the L-type voltage-gated calcium channels (CACNA1-L). Sequence-based phylogenies and analyses of conserved synteny show that the above-mentioned gene families, and many neighboring gene families, expanded in the early vertebrate WGDs. This allows us to deduce the following evolutionary scenario: The vertebrate ancestor had a chromosome containing the genes for two visual opsins, one GNAT, one GNAI, two OT/VP-Rs and one CACNA1-L gene. This chromosome was quadrupled in 2R. Subsequent gene losses resulted in a set of five visual opsin genes, three GNAT and GNAI genes, six OT/VP-R genes and four CACNA1-L genes. These regions were duplicated again in 3R resulting in additional teleost genes for some of the families. Major chromosomal rearrangements have taken place in the teleost genomes. By comparison with the corresponding chromosomal regions in the spotted gar, which diverged prior to 3R, we could time these rearrangements to post-3R. We present an extensive analysis of the paralogon housing the visual opsin, GNAT and GNAI, OT/VP-R, and CACNA1-L gene families. The combined data imply that the early vertebrate WGD events contributed to the evolution of vision and the

  11. Modern Methods of Multidimensional Data Visualization: Analysis, Classification, Implementation, and Applications in Technical Systems

    Directory of Open Access Journals (Sweden)

    I. K. Romanova

    2016-01-01

    Full Text Available The article deals with theoretical and practical aspects of solving the problem of visualization of multidimensional data as an effective means of multivariate analysis of systems. Several classifications are proposed for visualization techniques, according to data types, visualization objects, the method of transformation of coordinates and data. To represent classification are used charts with links to the relevant work. The article also proposes two classifications of modern trends in display technology, including integration of visualization techniques as one of the modern trends of development, along with the introduction of interactive technologies and the dynamics of development processes. It describes some approaches to the visualization problem, which are concerned with fulfilling the needs. The needs are generated by the relevant tasks such as information retrieval in global networks, development of bioinformatics, study and control of business processes, development of regions, etc. The article highlights modern visualization tools, which are capable of improving the efficiency of the multivariate analysis and searching for solutions in multi-objective optimization of technical systems, but are not very actively used for such studies. These are horizontal graphs, graphics "quantile-quantile", etc. The paper proposes to use Choropleth cards traditionally used in cartography for simultaneous presentation of the distribution parameters of several criteria in the space. It notes that visualizations of graphs in network applications can be more actively used to describe the control system. The article suggests using the heat maps to provide graphical representation of the sensitivity of the system quality criteria under variations of options (multivariate analysis of technical systems. It also mentions that it is useful to extend the supervising heat maps to the task of estimating quality of identify in constructing system models. A

  12. Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications.

    Science.gov (United States)

    Christen, Matthias; Del Medico, Luca; Christen, Heinz; Christen, Beat

    2017-01-01

    Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner.

  13. Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications.

    Directory of Open Access Journals (Sweden)

    Matthias Christen

    Full Text Available Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner.

  14. Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

    Science.gov (United States)

    Faith, Jeremiah J; Olson, Andrew J; Gardner, Timothy S; Sachidanandam, Ravi

    2007-09-18

    Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standard flat-file formats and bypassing the database needs of most visualization tools. Visualization as an aide to discovery requires display of novel data in conjunction with static annotations in their chromosomal context. With database-based systems, displaying dynamic results requires temporary tables that need to be tracked for removal. lwgv simplifies the visualization of user-generated results on a local computer. The dynamic results of these analyses are written to transient files, which can import static content from a more permanent file. lwgv is currently used in many different applications, from whole genome browsers to single-gene RNAi design visualization, demonstrating its applicability in a large variety of contexts and scales. lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses in their chromosomal context. It is particularly suited for applications ranging from short sequences to medium-sized genomes when the creation and maintenance of a large software and database infrastructure is not necessary or desired.

  15. Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context

    Directory of Open Access Journals (Sweden)

    Gardner Timothy S

    2007-09-01

    Full Text Available Abstract Background Lightweight genome viewer (lwgv is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standard flat-file formats and bypassing the database needs of most visualization tools. Visualization as an aide to discovery requires display of novel data in conjunction with static annotations in their chromosomal context. With database-based systems, displaying dynamic results requires temporary tables that need to be tracked for removal. Results lwgv simplifies the visualization of user-generated results on a local computer. The dynamic results of these analyses are written to transient files, which can import static content from a more permanent file. lwgv is currently used in many different applications, from whole genome browsers to single-gene RNAi design visualization, demonstrating its applicability in a large variety of contexts and scales. Conclusion lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses in their chromosomal context. It is particularly suited for applications ranging from short sequences to medium-sized genomes when the creation and maintenance of a large software and database infrastructure is not necessary or desired.

  16. APFEL Web a web-based application for the graphical visualization of parton distribution functions

    CERN Document Server

    Carrazza, Stefano; Palazzo, Daniele; Rojo, Juan

    2015-01-01

    We present APFEL Web, a web-based application designed to provide a flexible user-friendly tool for the graphical visualization of parton distribution functions (PDFs). In this note we describe the technical design of the APFEL Web application, motivating the choices and the framework used for the development of this project. We document the basic usage of APFEL Web and show how it can be used to provide useful input for a variety of collider phenomenological studies. Finally we provide some examples showing the output generated by the application.

  17. APFEL Web: a web-based application for the graphical visualization of parton distribution functions

    International Nuclear Information System (INIS)

    Carrazza, Stefano; Ferrara, Alfio; Palazzo, Daniele; Rojo, Juan

    2015-01-01

    We present APFEL Web, a Web-based application designed to provide a flexible user-friendly tool for the graphical visualization of parton distribution functions. In this note we describe the technical design of the APFEL Web application, motivating the choices and the framework used for the development of this project. We document the basic usage of APFEL Web and show how it can be used to provide useful input for a variety of collider phenomenological studies. Finally we provide some examples showing the output generated by the application. (note)

  18. A Fuzzy-Based Approach for Sensing, Coding and Transmission Configuration of Visual Sensors in Smart City Applications.

    Science.gov (United States)

    Costa, Daniel G; Collotta, Mario; Pau, Giovanni; Duran-Faundez, Cristian

    2017-01-05

    The advance of technologies in several areas has allowed the development of smart city applications, which can improve the way of life in modern cities. When employing visual sensors in that scenario, still images and video streams may be retrieved from monitored areas, potentially providing valuable data for many applications. Actually, visual sensor networks may need to be highly dynamic, reflecting the changing of parameters in smart cities. In this context, characteristics of visual sensors and conditions of the monitored environment, as well as the status of other concurrent monitoring systems, may affect how visual sensors collect, encode and transmit information. This paper proposes a fuzzy-based approach to dynamically configure the way visual sensors will operate concerning sensing, coding and transmission patterns, exploiting different types of reference parameters. This innovative approach can be considered as the basis for multi-systems smart city applications based on visual monitoring, potentially bringing significant results for this research field.

  19. Transcription Activator-Like Effectors (TALEs) Hybrid Nucleases for Genome Engineering Application

    KAUST Repository

    Wibowo, Anjar

    2011-06-06

    Gene targeting is a powerful genome engineering tool that can be used for a variety of biotechnological applications. Genomic double-strand DNA breaks generated by engineered site-specific nucleases can stimulate gene targeting. Hybrid nucleases are composed of DNA binding module and DNA cleavage module. Zinc Finger Nucleases were used to generate double-strand DNA breaks but it suffers from failures and lack of reproducibility. The transcription activator–like effectors (TALEs) from plant pathogenic Xanthomonas contain a unique type of DNA-binding domain that bind specific DNA targets. The purpose of this study is to generate novel sequence specific nucleases by fusing a de novo engineered Hax3 TALE-based DNA binding domain to a FokI cleavage domain. Our data show that the de novo engineered TALE nuclease can bind to its target sequence and create double-strand DNA breaks in vitro. We also show that the de novo engineered TALE nuclease is capable of generating double-strand DNA breaks in its target sequence in vivo, when transiently expressed in Nicotiana benthamiana leaves. In conclusion, our data demonstrate that TALE-based hybrid nucleases can be tailored to bind a user-selected DNA sequence and generate site-specific genomic double-strand DNA breaks. TALE-based hybrid nucleases hold much promise as powerful molecular tools for gene targeting applications.

  20. VISUALIZATION METHODS OF VORTICAL FLOWS IN COMPUTATIONAL FLUID DYNAMICS AND THEIR APPLICATIONS

    Directory of Open Access Journals (Sweden)

    K. N. Volkov

    2014-05-01

    Full Text Available The paper deals with conceptions and methods for visual representation of research numerical results in the problems of fluid mechanics and gas. The three-dimensional nature of unsteady flow being simulated creates significant difficulties for the visual representation of results. It complicates control and understanding of numerical data, and exchange and processing of obtained information about the flow field. Approaches to vortical flows visualization with the usage of gradients of primary and secondary scalar and vector fields are discussed. An overview of visualization techniques for vortical flows using different definitions of the vortex and its identification criteria is given. Visualization examples for some solutions of gas dynamics problems related to calculations of jets and cavity flows are presented. Ideas of the vortical structure of the free non-isothermal jet and the formation of coherent vortex structures in the mixing layer are developed. Analysis of formation patterns for spatial flows inside large-scale vortical structures within the enclosed space of the cubic lid-driven cavity is performed. The singular points of the vortex flow in a cubic lid-driven cavity are found based on the results of numerical simulation; their type and location are identified depending on the Reynolds number. Calculations are performed with fine meshes and modern approaches to the simulation of vortical flows (direct numerical simulation and large-eddy simulation. Paradigm of graphical programming and COVISE virtual environment are used for the visual representation of computational results. Application that implements the visualization of the problem is represented as a network which links are modules and each of them is designed to solve a case-specific problem. Interaction between modules is carried out by the input and output ports (data receipt and data transfer giving the possibility to use various input and output devices.

  1. The Inter-Disciplinary Impact of Computerized Application of Spatial Visualization on Motor and Concentration Skills

    Directory of Open Access Journals (Sweden)

    Esther Zaretsky

    2016-02-01

    Full Text Available The present inter-disciplinary research is aimed at investigating the impact of computerized application of spatial visualization on motor and concentration skills. An experiment composed of experimental and control groups for checking the central hypothesis among subjects of the same age group was carried out by physical education MA students. Virtual simulations offer MA students and teachers the unique opportunity to observe and manipulate normally inaccessible objects, variables and processes in real time. The research design focused on a qualitative research comparing the pupils' percents of success in spatial visualization and motor skills between pre- and post- training. The findings showed that just as the students realized the experimental group pupils' achievements, the computer's inter-disciplinary impact on motor performance and concentration skills became clear to the MA students. The virtual computerized training based on spatial visualization mostly contributed to the inter-disciplinary research, physical education and communication. All the findings lead to the conclusion that computerized application of spatial visualization seem to mediate between virtual reality and developing motor skills in real time involving penalty kick, basketball, jumping, etc.

  2. Genome-scale modeling of yeast: chronology, applications and critical perspectives.

    Science.gov (United States)

    Lopes, Helder; Rocha, Isabel

    2017-08-01

    Over the last 15 years, several genome-scale metabolic models (GSMMs) were developed for different yeast species, aiding both the elucidation of new biological processes and the shift toward a bio-based economy, through the design of in silico inspired cell factories. Here, an historical perspective of the GSMMs built over time for several yeast species is presented and the main inheritance patterns among the metabolic reconstructions are highlighted. We additionally provide a critical perspective on the overall genome-scale modeling procedure, underlining incomplete model validation and evaluation approaches and the quest for the integration of regulatory and kinetic information into yeast GSMMs. A summary of experimentally validated model-based metabolic engineering applications of yeast species is further emphasized, while the main challenges and future perspectives for the field are finally addressed. © FEMS 2017.

  3. Future translational applications from the contemporary genomics era: a scientific statement from the American Heart Association.

    Science.gov (United States)

    Fox, Caroline S; Hall, Jennifer L; Arnett, Donna K; Ashley, Euan A; Delles, Christian; Engler, Mary B; Freeman, Mason W; Johnson, Julie A; Lanfear, David E; Liggett, Stephen B; Lusis, Aldons J; Loscalzo, Joseph; MacRae, Calum A; Musunuru, Kiran; Newby, L Kristin; O'Donnell, Christopher J; Rich, Stephen S; Terzic, Andre

    2015-05-12

    The field of genetics and genomics has advanced considerably with the achievement of recent milestones encompassing the identification of many loci for cardiovascular disease and variable drug responses. Despite this achievement, a gap exists in the understanding and advancement to meaningful translation that directly affects disease prevention and clinical care. The purpose of this scientific statement is to address the gap between genetic discoveries and their practical application to cardiovascular clinical care. In brief, this scientific statement assesses the current timeline for effective translation of basic discoveries to clinical advances, highlighting past successes. Current discoveries in the area of genetics and genomics are covered next, followed by future expectations, tools, and competencies for achieving the goal of improving clinical care. © 2015 American Heart Association, Inc.

  4. Visual Display of 5p-arm and 3p-arm miRNA Expression with a Mobile Application.

    Science.gov (United States)

    Pan, Chao-Yu; Kuo, Wei-Ting; Chiu, Chien-Yuan; Lin, Wen-Chang

    2017-01-01

    MicroRNAs (miRNAs) play important roles in human cancers. In previous studies, we have demonstrated that both 5p-arm and 3p-arm of mature miRNAs could be expressed from the same precursor and we further interrogated the 5p-arm and 3p-arm miRNA expression with a comprehensive arm feature annotation list. To assist biologists to visualize the differential 5p-arm and 3p-arm miRNA expression patterns, we utilized a user-friendly mobile App to display. The Cancer Genome Atlas (TCGA) miRNA-Seq expression information. We have collected over 4,500 miRNA-Seq datasets from 15 TCGA cancer types and further processed them with the 5p-arm and 3p-arm annotation analysis pipeline. In order to be displayed with the RNA-Seq Viewer App, annotated 5p-arm and 3p-arm miRNA expression information and miRNA gene loci information were converted into SQLite tables. In this distinct application, for any given miRNA gene, 5p-arm miRNA is illustrated on the top of chromosome ideogram and 3p-arm miRNA is illustrated on the bottom of chromosome ideogram. Users can then easily interrogate the differentially 5p-arm/3p-arm expressed miRNAs with their mobile devices. This study demonstrates the feasibility and utility of RNA-Seq Viewer App in addition to mRNA-Seq data visualization.

  5. Visual Display of 5p-arm and 3p-arm miRNA Expression with a Mobile Application

    Directory of Open Access Journals (Sweden)

    Chao-Yu Pan

    2017-01-01

    Full Text Available MicroRNAs (miRNAs play important roles in human cancers. In previous studies, we have demonstrated that both 5p-arm and 3p-arm of mature miRNAs could be expressed from the same precursor and we further interrogated the 5p-arm and 3p-arm miRNA expression with a comprehensive arm feature annotation list. To assist biologists to visualize the differential 5p-arm and 3p-arm miRNA expression patterns, we utilized a user-friendly mobile App to display. The Cancer Genome Atlas (TCGA miRNA-Seq expression information. We have collected over 4,500 miRNA-Seq datasets from 15 TCGA cancer types and further processed them with the 5p-arm and 3p-arm annotation analysis pipeline. In order to be displayed with the RNA-Seq Viewer App, annotated 5p-arm and 3p-arm miRNA expression information and miRNA gene loci information were converted into SQLite tables. In this distinct application, for any given miRNA gene, 5p-arm miRNA is illustrated on the top of chromosome ideogram and 3p-arm miRNA is illustrated on the bottom of chromosome ideogram. Users can then easily interrogate the differentially 5p-arm/3p-arm expressed miRNAs with their mobile devices. This study demonstrates the feasibility and utility of RNA-Seq Viewer App in addition to mRNA-Seq data visualization.

  6. Linking Automated Data Analysis and Visualization with Applications in Developmental Biology and High-Energy Physics

    Energy Technology Data Exchange (ETDEWEB)

    Ruebel, Oliver [Technical Univ. of Darmstadt (Germany)

    2009-11-20

    Knowledge discovery from large and complex collections of today's scientific datasets is a challenging task. With the ability to measure and simulate more processes at increasingly finer spatial and temporal scales, the increasing number of data dimensions and data objects is presenting tremendous challenges for data analysis and effective data exploration methods and tools. Researchers are overwhelmed with data and standard tools are often insufficient to enable effective data analysis and knowledge discovery. The main objective of this thesis is to provide important new capabilities to accelerate scientific knowledge discovery form large, complex, and multivariate scientific data. The research covered in this thesis addresses these scientific challenges using a combination of scientific visualization, information visualization, automated data analysis, and other enabling technologies, such as efficient data management. The effectiveness of the proposed analysis methods is demonstrated via applications in two distinct scientific research fields, namely developmental biology and high-energy physics.Advances in microscopy, image analysis, and embryo registration enable for the first time measurement of gene expression at cellular resolution for entire organisms. Analysis of high-dimensional spatial gene expression datasets is a challenging task. By integrating data clustering and visualization, analysis of complex, time-varying, spatial gene expression patterns and their formation becomes possible. The analysis framework MATLAB and the visualization have been integrated, making advanced analysis tools accessible to biologist and enabling bioinformatic researchers to directly integrate their analysis with the visualization. Laser wakefield particle accelerators (LWFAs) promise to be a new compact source of high-energy particles and radiation, with wide applications ranging from medicine to physics. To gain insight into the complex physical processes of particle

  7. Linking Automated Data Analysis and Visualization with Applications in Developmental Biology and High-Energy Physics

    International Nuclear Information System (INIS)

    Ruebel, Oliver

    2009-01-01

    Knowledge discovery from large and complex collections of today's scientific datasets is a challenging task. With the ability to measure and simulate more processes at increasingly finer spatial and temporal scales, the increasing number of data dimensions and data objects is presenting tremendous challenges for data analysis and effective data exploration methods and tools. Researchers are overwhelmed with data and standard tools are often insufficient to enable effective data analysis and knowledge discovery. The main objective of this thesis is to provide important new capabilities to accelerate scientific knowledge discovery form large, complex, and multivariate scientific data. The research covered in this thesis addresses these scientific challenges using a combination of scientific visualization, information visualization, automated data analysis, and other enabling technologies, such as efficient data management. The effectiveness of the proposed analysis methods is demonstrated via applications in two distinct scientific research fields, namely developmental biology and high-energy physics.Advances in microscopy, image analysis, and embryo registration enable for the first time measurement of gene expression at cellular resolution for entire organisms. Analysis of high-dimensional spatial gene expression datasets is a challenging task. By integrating data clustering and visualization, analysis of complex, time-varying, spatial gene expression patterns and their formation becomes possible. The analysis framework MATLAB and the visualization have been integrated, making advanced analysis tools accessible to biologist and enabling bioinformatic researchers to directly integrate their analysis with the visualization. Laser wakefield particle accelerators (LWFAs) promise to be a new compact source of high-energy particles and radiation, with wide applications ranging from medicine to physics. To gain insight into the complex physical processes of particle

  8. Anterior esthetics and the visual arts: beauty, elements of composition, and their clinical application to dentistry.

    Science.gov (United States)

    Valo, T S

    1995-01-01

    The challenge of developing a pleasing smile is an artistic venture. A study of how the visual arts have explored the nature of beauty and the elements of artistic composition will enhance our artistic abilities in cosmetic dentistry. This review discusses the perception of beauty and important features of that which we call beautiful. The discussion uses important works of art to demonstrate elements of composition, which are then made relevant in a dental application.

  9. An Application of Mosaic Diagrams to the Visualization of Set Relationships

    OpenAIRE

    Luz, Saturnino; Masoodian, Masood

    2017-01-01

    We present an application of mosaic diagrams to the visualisation of set relations. Venn and Euler diagrams are the best known visual representations of sets and their relationships (intersections, containment or subsets, exclusion or disjointness). In recent years, alternative forms of visualisation have been proposed. Among them, linear diagrams have been shown to compare favourably to Venn and Euler diagrams, in supporting non-interactive assessment of set relationships. Recent studies tha...

  10. Applications Payroll Smk Bina Putra Jakarta Teacher Using Microsoft Visual Basic 6.0

    OpenAIRE

    Damayanti Damayanti; Susi Wagiyati P, SKom, MMSI

    2003-01-01

    At current developments in computer technology is increasing, technology is able to provide information so precise and accurate that no doubt. SMK BINA PUTRA eg JAKARTA in teacher salaries to handle manually. So that work on the calculation of teachers' salaries will spend a long completion. Then the writer tries to make the application on the teacher salary calculation SMK BINA PUTRA JAKARTA using Visual Basic 6.0. The purpose of the calculation of salaries of teachers at SMK BINA PUTRA JAK...

  11. Shop for Mobile Phone Applications Using Microsoft Visual Basic 6.0

    OpenAIRE

    Muhammad Syahroji; Sutarno, Skom., MMSI Sutarno, Skom., MMSI

    2007-01-01

    Scientific writing is about cellular phone information, equipment and also card mobile phone users by using Microsoft Visual Basic 6.0. The making of this application is intended to facilitate notification of everything on your mobile phone which is still classified as manual. Therefore, this writing is made to computerize work that is in a mobile phone store that can provide services more easily to the buyers.

  12. Development of an Android-based Learning Media Application for Visually Impaired Students

    Directory of Open Access Journals (Sweden)

    Nurul Azmi

    2017-06-01

    Full Text Available This research aims to develop the English for Disability (EFORD application, on Android-based learning english media for Visually Impaired students and determine its based this on assessment of matter expert, media expert, special needs teacher and students. The research method adopted in this research is Research and Development (R&D. The development of this application through five phases: (1 Analysis of problems, through observation and interviews. (2 Collecting information as product planning / analysis of the needs of the media as required of blind children. (3 The design phase of products such as the manufacture of flow and storyboard navigation map.(4 Design validation phase form of an expert assessment of the media is developed. (5 testing products phase, such as assessment of the application by blind students. The results of this research is EFORD application which is feasible to be used as English learning media for visual impairment application based on assessment: 1Media expert it's obtained a percentage scored 95%, include for very worthy category, 2Subject matter, expert its obtained percentage scored 75% include for worthy category and 3 Special needs teacher it's obtained a percentage scored 83% include for very worthy category. Upon demonstration, students indicated the positive response of ≥ 70% in each indicator. Therefore English learning media with Android based application English for Disability (EFORD is very feasible to be used as an English learning media especially grammar and speaking English content for students of visual impairment for a number of reasons. This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

  13. Fine-grained visual marine vessel classification for coastal surveillance and defense applications

    Science.gov (United States)

    Solmaz, Berkan; Gundogdu, Erhan; Karaman, Kaan; Yücesoy, Veysel; Koç, Aykut

    2017-10-01

    The need for capabilities of automated visual content analysis has substantially increased due to presence of large number of images captured by surveillance cameras. With a focus on development of practical methods for extracting effective visual data representations, deep neural network based representations have received great attention due to their success in visual categorization of generic images. For fine-grained image categorization, a closely related yet a more challenging research problem compared to generic image categorization due to high visual similarities within subgroups, diverse applications were developed such as classifying images of vehicles, birds, food and plants. Here, we propose the use of deep neural network based representations for categorizing and identifying marine vessels for defense and security applications. First, we gather a large number of marine vessel images via online sources grouping them into four coarse categories; naval, civil, commercial and service vessels. Next, we subgroup naval vessels into fine categories such as corvettes, frigates and submarines. For distinguishing images, we extract state-of-the-art deep visual representations and train support-vector-machines. Furthermore, we fine tune deep representations for marine vessel images. Experiments address two scenarios, classification and verification of naval marine vessels. Classification experiment aims coarse categorization, as well as learning models of fine categories. Verification experiment embroils identification of specific naval vessels by revealing if a pair of images belongs to identical marine vessels by the help of learnt deep representations. Obtaining promising performance, we believe these presented capabilities would be essential components of future coastal and on-board surveillance systems.

  14. MEVA--An Interactive Visualization Application for Validation of Multifaceted Meteorological Data with Multiple 3D Devices.

    Directory of Open Access Journals (Sweden)

    Carolin Helbig

    Full Text Available To achieve more realistic simulations, meteorologists develop and use models with increasing spatial and temporal resolution. The analyzing, comparing, and visualizing of resulting simulations becomes more and more challenging due to the growing amounts and multifaceted character of the data. Various data sources, numerous variables and multiple simulations lead to a complex database. Although a variety of software exists suited for the visualization of meteorological data, none of them fulfills all of the typical domain-specific requirements: support for quasi-standard data formats and different grid types, standard visualization techniques for scalar and vector data, visualization of the context (e.g., topography and other static data, support for multiple presentation devices used in modern sciences (e.g., virtual reality, a user-friendly interface, and suitability for cooperative work.Instead of attempting to develop yet another new visualization system to fulfill all possible needs in this application domain, our approach is to provide a flexible workflow that combines different existing state-of-the-art visualization software components in order to hide the complexity of 3D data visualization tools from the end user. To complete the workflow and to enable the domain scientists to interactively visualize their data without advanced skills in 3D visualization systems, we developed a lightweight custom visualization application (MEVA - multifaceted environmental data visualization application that supports the most relevant visualization and interaction techniques and can be easily deployed. Specifically, our workflow combines a variety of different data abstraction methods provided by a state-of-the-art 3D visualization application with the interaction and presentation features of a computer-games engine. Our customized application includes solutions for the analysis of multirun data, specifically with respect to data uncertainty and

  15. Developing Cancer Informatics Applications and Tools Using the NCI Genomic Data Commons API.

    Science.gov (United States)

    Wilson, Shane; Fitzsimons, Michael; Ferguson, Martin; Heath, Allison; Jensen, Mark; Miller, Josh; Murphy, Mark W; Porter, James; Sahni, Himanso; Staudt, Louis; Tang, Yajing; Wang, Zhining; Yu, Christine; Zhang, Junjun; Ferretti, Vincent; Grossman, Robert L

    2017-11-01

    The NCI Genomic Data Commons (GDC) was launched in 2016 and makes available over 4 petabytes (PB) of cancer genomic and associated clinical data to the research community. This dataset continues to grow and currently includes over 14,500 patients. The GDC is an example of a biomedical data commons, which collocates biomedical data with storage and computing infrastructure and commonly used web services, software applications, and tools to create a secure, interoperable, and extensible resource for researchers. The GDC is (i) a data repository for downloading data that have been submitted to it, and also a system that (ii) applies a common set of bioinformatics pipelines to submitted data; (iii) reanalyzes existing data when new pipelines are developed; and (iv) allows users to build their own applications and systems that interoperate with the GDC using the GDC Application Programming Interface (API). We describe the GDC API and how it has been used both by the GDC itself and by third parties. Cancer Res; 77(21); e15-18. ©2017 AACR . ©2017 American Association for Cancer Research.

  16. Applications of population genetics to animal breeding, from wright, fisher and lush to genomic prediction.

    Science.gov (United States)

    Hill, William G

    2014-01-01

    Although animal breeding was practiced long before the science of genetics and the relevant disciplines of population and quantitative genetics were known, breeding programs have mainly relied on simply selecting and mating the best individuals on their own or relatives' performance. This is based on sound quantitative genetic principles, developed and expounded by Lush, who attributed much of his understanding to Wright, and formalized in Fisher's infinitesimal model. Analysis at the level of individual loci and gene frequency distributions has had relatively little impact. Now with access to genomic data, a revolution in which molecular information is being used to enhance response with "genomic selection" is occurring. The predictions of breeding value still utilize multiple loci throughout the genome and, indeed, are largely compatible with additive and specifically infinitesimal model assumptions. I discuss some of the history and genetic issues as applied to the science of livestock improvement, which has had and continues to have major spin-offs into ideas and applications in other areas.

  17. An Application of Multivariate Statistical Analysis for Query-Driven Visualization

    Energy Technology Data Exchange (ETDEWEB)

    Gosink, Luke J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Garth, Christoph [Univ. of California, Davis, CA (United States); Anderson, John C. [Univ. of California, Davis, CA (United States); Bethel, E. Wes [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joy, Kenneth I. [Univ. of California, Davis, CA (United States)

    2011-03-01

    Driven by the ability to generate ever-larger, increasingly complex data, there is an urgent need in the scientific community for scalable analysis methods that can rapidly identify salient trends in scientific data. Query-Driven Visualization (QDV) strategies are among the small subset of techniques that can address both large and highly complex datasets. This paper extends the utility of QDV strategies with a statistics-based framework that integrates non-parametric distribution estimation techniques with a new segmentation strategy to visually identify statistically significant trends and features within the solution space of a query. In this framework, query distribution estimates help users to interactively explore their query's solution and visually identify the regions where the combined behavior of constrained variables is most important, statistically, to their inquiry. Our new segmentation strategy extends the distribution estimation analysis by visually conveying the individual importance of each variable to these regions of high statistical significance. We demonstrate the analysis benefits these two strategies provide and show how they may be used to facilitate the refinement of constraints over variables expressed in a user's query. We apply our method to datasets from two different scientific domains to demonstrate its broad applicability.

  18. Genome sequence of three Psychrobacter sp. strains with potential applications in bioremediation

    Directory of Open Access Journals (Sweden)

    Aide Lasa

    2017-06-01

    Full Text Available To date, the genus Psychrobacter consists of 37 recognized species isolated from different sources, however they are more frequently found in cold and other non-polar environments of low water activity. Some strains belonging to the genus have shown different enzymatic activities with potential applications in bioremediation or food industry. In the present study, the whole genome sequences of three Psychrobacter-like strains (C 20.9, Cmf 22.2 and Rd 27.2 isolated from reared clams in Galicia (Spain are described. The sequenced genomes resulted in an assembly size of 3,143,782 bp for C 20.9 isolate, 3,168,467 bp for Cmf 22.2 isolate and 3,028,386 bp for Rd 27.2 isolate. Among the identified coding sequences of the genomes, mercury detoxification and biogeochemistry genes were found, as well as genes related to heavy metals and antibiotic resistance. Also virulence-related features were identified such as the siderophore vibrioferrin or an aerobactin-like siderophore. The phylogenetic analysis of the 16S rRNA gene suggested that these strains may represent novel species of the Psychrobacter genus. The genome sequences of the Psychrobacter sp. strains have been deposited at DDBJ/EMBL/GenBank under the accession numbers MRYA00000000 (Cmf 22.2, MRYB00000000 (Rd 27.2 and MRYC00000000 (C 20.9, and the sequences could be found at the site https://www.ncbi.nlm.nih.gov/bioproject/PRJNA353858.

  19. Multi-scale image segmentation method with visual saliency constraints and its application

    Science.gov (United States)

    Chen, Yan; Yu, Jie; Sun, Kaimin

    2018-03-01

    Object-based image analysis method has many advantages over pixel-based methods, so it is one of the current research hotspots. It is very important to get the image objects by multi-scale image segmentation in order to carry out object-based image analysis. The current popular image segmentation methods mainly share the bottom-up segmentation principle, which is simple to realize and the object boundaries obtained are accurate. However, the macro statistical characteristics of the image areas are difficult to be taken into account, and fragmented segmentation (or over-segmentation) results are difficult to avoid. In addition, when it comes to information extraction, target recognition and other applications, image targets are not equally important, i.e., some specific targets or target groups with particular features worth more attention than the others. To avoid the problem of over-segmentation and highlight the targets of interest, this paper proposes a multi-scale image segmentation method with visually saliency graph constraints. Visual saliency theory and the typical feature extraction method are adopted to obtain the visual saliency information, especially the macroscopic information to be analyzed. The visual saliency information is used as a distribution map of homogeneity weight, where each pixel is given a weight. This weight acts as one of the merging constraints in the multi- scale image segmentation. As a result, pixels that macroscopically belong to the same object but are locally different can be more likely assigned to one same object. In addition, due to the constraint of visual saliency model, the constraint ability over local-macroscopic characteristics can be well controlled during the segmentation process based on different objects. These controls will improve the completeness of visually saliency areas in the segmentation results while diluting the controlling effect for non- saliency background areas. Experiments show that this method works

  20. GenColors-based comparative genome databases for small eukaryotic genomes.

    Science.gov (United States)

    Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Sühnel, Jürgen; Glöckner, Gernot

    2013-01-01

    Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources.

  1. Software applications to three-dimensional visualization of forest landscapes -- A case study demontrating the use of visual nature studio (VNS) in visualizing fire spread in forest landscapes

    Science.gov (United States)

    Brian J. Williams; Bo Song; Chou Chiao-Ying; Thomas M. Williams; John Hom

    2010-01-01

    Three-dimensional (3D) visualization is a useful tool that depicts virtual forest landscapes on computer. Previous studies in visualization have required high end computer hardware and specialized technical skills. A virtual forest landscape can be used to show different effects of disturbances and management scenarios on a computer, which allows observation of forest...

  2. Genomic Testing

    Science.gov (United States)

    ... this database. Top of Page Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) In 2004, the Centers for Disease Control and Prevention launched the EGAPP initiative to establish and test a ... and other applications of genomic technology that are in transition from ...

  3. A Brain Computer Interface for Robust Wheelchair Control Application Based on Pseudorandom Code Modulated Visual Evoked Potential

    DEFF Research Database (Denmark)

    Mohebbi, Ali; Engelsholm, Signe K.D.; Puthusserypady, Sadasivan

    2015-01-01

    In this pilot study, a novel and minimalistic Brain Computer Interface (BCI) based wheelchair control application was developed. The system was based on pseudorandom code modulated Visual Evoked Potentials (c-VEPs). The visual stimuli in the scheme were generated based on the Gold code...

  4. Application of a visualization method of image data base in nuclear cardiology

    International Nuclear Information System (INIS)

    Damien, J.; Bruyant, Ph.; Moreno, L.; Gabain, M.; Sayegh, Y.; Bontemps, L.; Itti, R.

    1997-01-01

    Medical imaging is undoubtedly one of the medical branches which benefited at most by the offsprings of computer science development. We present here a visualization software of image data base, making use of the last innovations in the field of multimedia application. The objective of such a software is to provide a reference tool for a given medical specialty offering at the same time, a high quality iconography, a rigorous content of the comments and the matching of graphical interfaces. Applied to nuclear cardiology and implanted on CD ROM, it contains a given number of clinical cases (around 150) which sweep quasi-exhaustively the subject. Each case centered around scintigraphic examination (myocardial tomographs, ventriculographs, SPECT, etc) makes available 'static' pictures (series of cross sections, planispheric images, ECG), animated cartoons (synchronized series, 3D visualization, etc) and also the clinical history of the patient and the records of complementary examinations (coronary-graphic, for instance). Being independent of the image data base which it visualizes, our software is easily applicable to other nuclear medicine specialties (neurology, renal exploration) and also to other modalities. It is multilingual already (French and English) and soon will be supplemented by a code dedicated to knowledge assessment intended to be an efficient tool in education and continuous formation. A Macintosh version will be soon obtainable and a demonstration diskette is free available on request

  5. The Saccharomyces Genome Database Variant Viewer.

    Science.gov (United States)

    Sheppard, Travis K; Hitz, Benjamin C; Engel, Stacia R; Song, Giltae; Balakrishnan, Rama; Binkley, Gail; Costanzo, Maria C; Dalusag, Kyla S; Demeter, Janos; Hellerstedt, Sage T; Karra, Kalpana; Nash, Robert S; Paskov, Kelley M; Skrzypek, Marek S; Weng, Shuai; Wong, Edith D; Cherry, J Michael

    2016-01-04

    The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. In recent years, we have moved toward increased representation of sequence variation and allelic differences within S. cerevisiae. The publication of numerous additional genomes has motivated the creation of new tools for their annotation and analysis. Here we present the Variant Viewer: a dynamic open-source web application for the visualization of genomic and proteomic differences. Multiple sequence alignments have been constructed across high quality genome sequences from 11 different S. cerevisiae strains and stored in the SGD. The alignments and summaries are encoded in JSON and used to create a two-tiered dynamic view of the budding yeast pan-genome, available at http://www.yeastgenome.org/variant-viewer. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Text Stream Trend Analysis using Multiscale Visual Analytics with Applications to Social Media Systems

    Energy Technology Data Exchange (ETDEWEB)

    Steed, Chad A [ORNL; Beaver, Justin M [ORNL; BogenII, Paul L. [Google Inc.; Drouhard, Margaret MEG G [ORNL; Pyle, Joshua M [ORNL

    2015-01-01

    In this paper, we introduce a new visual analytics system, called Matisse, that allows exploration of global trends in textual information streams with specific application to social media platforms. Despite the potential for real-time situational awareness using these services, interactive analysis of such semi-structured textual information is a challenge due to the high-throughput and high-velocity properties. Matisse addresses these challenges through the following contributions: (1) robust stream data management, (2) automated sen- timent/emotion analytics, (3) inferential temporal, geospatial, and term-frequency visualizations, and (4) a flexible drill-down interaction scheme that progresses from macroscale to microscale views. In addition to describing these contributions, our work-in-progress paper concludes with a practical case study focused on the analysis of Twitter 1% sample stream information captured during the week of the Boston Marathon bombings.

  7. Applications of flow visualization to the development of an innovative boom system

    International Nuclear Information System (INIS)

    Wong, K.F.V.; Wolek, A.

    1996-01-01

    A new oil retention boom system design was developed using a flow visualization technique. Hydrogen bubbles were generated on a fine wire cathode and placed in a stream of moving water with a strong light source to visualize the flow. Observations were made of the flow patterns around some basic shapes and booms modelled as cylinders with and without a skirt. The most effective system design had two booms with skirts in parallel with a submerged airfoil designed to cause the oil to separate and recirculate. Oil was allowed to flow above the airfoil into the recirculation region between the two floating booms. The new system is expected to outperform the conventional boom system only when flow velocity is high. Its most successful application would be in situations where flow is perpendicular to the length of the boom. 1 ref., 6 figs

  8. Visualization, analysis, and design of COMBO-FISH probes in the grid-based GLOBE 3D genome platform

    NARCIS (Netherlands)

    F.N. Kepper (Nick); E. Schmitt (Eberhard); M. Lesnussa (Michael); Y. Weiland (Yanina); H.J.F.M.M. Eussen (Bert); F.G. Grosveld (Frank); M. Hausmann (Michael); T.A. Knoch (Tobias)

    2010-01-01

    textabstractThe genome architecture in cell nuclei plays an important role in modern microscopy for the monitoring of medical diagnosis and therapy since changes of function and dynamics of genes are interlinked with changing geometrical parameters. The planning of corresponding diagnostic

  9. Genome engineering in ophthalmology: Application of CRISPR/Cas to the treatment of eye disease.

    Science.gov (United States)

    Hung, Sandy S C; McCaughey, Tristan; Swann, Olivia; Pébay, Alice; Hewitt, Alex W

    2016-07-01

    The Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) and CRISPR-associated protein (Cas) system has enabled an accurate and efficient means to edit the human genome. Rapid advances in this technology could results in imminent clinical application, and with favourable anatomical and immunological profiles, ophthalmic disease will be at the forefront of such work. There have been a number of breakthroughs improving the specificity and efficacy of CRISPR/Cas-mediated genome editing. Similarly, better methods to identify off-target cleavage sites have also been developed. With the impending clinical utility of CRISPR/Cas technology, complex ethical issues related to the regulation and management of the precise applications of human gene editing must be considered. This review discusses the current progress and recent breakthroughs in CRISPR/Cas-based gene engineering, and outlines some of the technical issues that must be addressed before gene correction, be it in vivo or in vitro, is integrated into ophthalmic care. We outline a clinical pipeline for CRISPR-based treatments of inherited eye diseases and provide an overview of the important ethical implications of gene editing and how these may influence the future of this technology. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Resolution of habitat-associated ecogenomic signatures in bacteriophage genomes and application to microbial source tracking.

    Science.gov (United States)

    Ogilvie, Lesley A; Nzakizwanayo, Jonathan; Guppy, Fergus M; Dedi, Cinzia; Diston, David; Taylor, Huw; Ebdon, James; Jones, Brian V

    2018-04-01

    Just as the expansion in genome sequencing has revealed and permitted the exploitation of phylogenetic signals embedded in bacterial genomes, the application of metagenomics has begun to provide similar insights at the ecosystem level for microbial communities. However, little is known regarding this aspect of bacteriophage associated with microbial ecosystems, and if phage encode discernible habitat-associated signals diagnostic of underlying microbiomes. Here we demonstrate that individual phage can encode clear habitat-related 'ecogenomic signatures', based on relative representation of phage-encoded gene homologues in metagenomic data sets. Furthermore, we show the ecogenomic signature encoded by the gut-associated ɸB124-14 can be used to segregate metagenomes according to environmental origin, and distinguish 'contaminated' environmental metagenomes (subject to simulated in silico human faecal pollution) from uncontaminated data sets. This indicates phage-encoded ecological signals likely possess sufficient discriminatory power for use in biotechnological applications, such as development of microbial source tracking tools for monitoring water quality.

  11. Visual-vestibular cue integration for heading perception: applications of optimal cue integration theory.

    Science.gov (United States)

    Fetsch, Christopher R; Deangelis, Gregory C; Angelaki, Dora E

    2010-05-01

    The perception of self-motion is crucial for navigation, spatial orientation and motor control. In particular, estimation of one's direction of translation, or heading, relies heavily on multisensory integration in most natural situations. Visual and nonvisual (e.g., vestibular) information can be used to judge heading, but each modality alone is often insufficient for accurate performance. It is not surprising, then, that visual and vestibular signals converge frequently in the nervous system, and that these signals interact in powerful ways at the level of behavior and perception. Early behavioral studies of visual-vestibular interactions consisted mainly of descriptive accounts of perceptual illusions and qualitative estimation tasks, often with conflicting results. In contrast, cue integration research in other modalities has benefited from the application of rigorous psychophysical techniques, guided by normative models that rest on the foundation of ideal-observer analysis and Bayesian decision theory. Here we review recent experiments that have attempted to harness these so-called optimal cue integration models for the study of self-motion perception. Some of these studies used nonhuman primate subjects, enabling direct comparisons between behavioral performance and simultaneously recorded neuronal activity. The results indicate that humans and monkeys can integrate visual and vestibular heading cues in a manner consistent with optimal integration theory, and that single neurons in the dorsal medial superior temporal area show striking correlates of the behavioral effects. This line of research and other applications of normative cue combination models should continue to shed light on mechanisms of self-motion perception and the neuronal basis of multisensory integration.

  12. Genomic prediction using different estimation methodology, blending and cross-validation techniques for growth traits and visual scores in Hereford and Braford cattle.

    Science.gov (United States)

    Campos, G S; Reimann, F A; Cardoso, L L; Ferreira, C E R; Junqueira, V S; Schmidt, P I; Braccini Neto, J; Yokoo, M J I; Sollero, B P; Boligon, A A; Cardoso, F F

    2018-05-07

    The objective of the present study was to evaluate the accuracy and bias of direct and blended genomic predictions using different methods and cross-validation techniques for growth traits (weight and weight gains) and visual scores (conformation, precocity, muscling and size) obtained at weaning and at yearling in Hereford and Braford breeds. Phenotypic data contained 126,290 animals belonging to the Delta G Connection genetic improvement program, and a set of 3,545 animals genotyped with the 50K chip and 131 sires with the 777K. After quality control, 41,045 markers remained for all animals. An animal model was used to estimate (co)variances components and to predict breeding values, which were later used to calculate the deregressed estimated breeding values (DEBV). Animals with genotype and phenotype for the traits studied were divided into four or five groups by random and k-means clustering cross-validation strategies. The values of accuracy of the direct genomic values (DGV) were moderate to high magnitude for at weaning and at yearling traits, ranging from 0.19 to 0.45 for the k-means and 0.23 to 0.78 for random clustering among all traits. The greatest gain in relation to the pedigree BLUP (PBLUP) was 9.5% with the BayesB method with both the k-means and the random clustering. Blended genomic value accuracies ranged from 0.19 to 0.56 for k-means and from 0.21 to 0.82 for random clustering. The analyzes using the historical pedigree and phenotypes contributed additional information to calculate the GEBV and in general, the largest gains were for the single-step (ssGBLUP) method in bivariate analyses with a mean increase of 43.00% among all traits measured at weaning and of 46.27% for those evaluated at yearling. The accuracy values for the marker effects estimation methods were lower for k-means clustering, indicating that the training set relationship to the selection candidates is a major factor affecting accuracy of genomic predictions. The gains in

  13. Optimal Design of Low-Density SNP Arrays for Genomic Prediction: Algorithm and Applications.

    Directory of Open Access Journals (Sweden)

    Xiao-Lin Wu

    population. The utility of this MOLO algorithm was also demonstrated in a real application, in which a 6K SNP panel was optimized conditional on 5,260 obligatory SNP selected based on SNP-trait association in U.S. Holstein animals. With this MOLO algorithm, both imputation error rate and genomic prediction error rate were minimal.

  14. Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database.

    Science.gov (United States)

    Winsor, Geoffrey L; Griffiths, Emma J; Lo, Raymond; Dhillon, Bhavjinder K; Shay, Julie A; Brinkman, Fiona S L

    2016-01-04

    The Pseudomonas Genome Database (http://www.pseudomonas.com) is well known for the application of community-based annotation approaches for producing a high-quality Pseudomonas aeruginosa PAO1 genome annotation, and facilitating whole-genome comparative analyses with other Pseudomonas strains. To aid analysis of potentially thousands of complete and draft genome assemblies, this database and analysis platform was upgraded to integrate curated genome annotations and isolate metadata with enhanced tools for larger scale comparative analysis and visualization. Manually curated gene annotations are supplemented with improved computational analyses that help identify putative drug targets and vaccine candidates or assist with evolutionary studies by identifying orthologs, pathogen-associated genes and genomic islands. The database schema has been updated to integrate isolate metadata that will facilitate more powerful analysis of genomes across datasets in the future. We continue to place an emphasis on providing high-quality updates to gene annotations through regular review of the scientific literature and using community-based approaches including a major new Pseudomonas community initiative for the assignment of high-quality gene ontology terms to genes. As we further expand from thousands of genomes, we plan to provide enhancements that will aid data visualization and analysis arising from whole-genome comparative studies including more pan-genome and population-based approaches. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Integrating Visualization Applications, such as ParaView, into HEP Software Frameworks for In-situ Event Displays

    Science.gov (United States)

    Lyon, A. L.; Kowalkowski, J. B.; Jones, C. D.

    2017-10-01

    ParaView is a high performance visualization application not widely used in High Energy Physics (HEP). It is a long standing open source project led by Kitware and involves several Department of Energy (DOE) and Department of Defense (DOD) laboratories. Futhermore, it has been adopted by many DOE supercomputing centers and other sites. ParaView is unique in speed and efficiency by using state-of-the-art techniques developed by the academic visualization community that are often not found in applications written by the HEP community. In-situ visualization of events, where event details are visualized during processing/analysis, is a common task for experiment software frameworks. Kitware supplies Catalyst, a library that enables scientific software to serve visualization objects to client ParaView viewers yielding a real-time event display. Connecting ParaView to the Fermilab art framework will be described and the capabilities it brings discussed.

  16. Integrating Visualization Applications, such as ParaView, into HEP Software Frameworks for In-situ Event Displays

    Energy Technology Data Exchange (ETDEWEB)

    Lyon, A. L. [Fermilab; Kowalkowski, J. B. [Fermilab; Jones, C. D. [Fermilab

    2017-11-22

    ParaView is a high performance visualization application not widely used in High Energy Physics (HEP). It is a long standing open source project led by Kitware and involves several Department of Energy (DOE) and Department of Defense (DOD) laboratories. Futhermore, it has been adopted by many DOE supercomputing centers and other sites. ParaView is unique in speed and efficiency by using state-of-the-art techniques developed by the academic visualization community that are often not found in applications written by the HEP community. In-situ visualization of events, where event details are visualized during processing/analysis, is a common task for experiment software frameworks. Kitware supplies Catalyst, a library that enables scientific software to serve visualization objects to client ParaView viewers yielding a real-time event display. Connecting ParaView to the Fermilab art framework will be described and the capabilities it brings discussed.

  17. Features of photo-visual technologies application in the study of attitude to discriminatory behavior in situations of ethnic interaction

    Directory of Open Access Journals (Sweden)

    Bzezyan Anastasia Ambarcumovna

    2017-10-01

    Full Text Available The article focuses on the application of social psychology, and visual technologies, such as photography. It stresses that this type of visual technology is used in research aimed at the study of communication, interpersonal knowledge, and inter-ethnic relations. Within these areas of research we apply photos of human appearance with the status of the criterion of categorization, identification, classification, the mechanism of recognition of certain social and ethnic groups, and attitudes. So far visual technology was insufficiently applied in studying relationships in various discriminatory practices including discrimination, which is designated as ethnic-lookism. The work discusses researches that studied identification and assessment of the man's face of different races through the application of visual technologies. The authors come to the conclusion, that the visual experience in the mainstreaming of discriminatory practices including ethnic-lookism becomes a promising direction in studying the attitudes to discriminatory behaviour in various situations of interaction.

  18. Design of a Braille Learning Application for Visually Impaired Students in Bangladesh.

    Science.gov (United States)

    Nahar, Lutfun; Jaafar, Azizah; Ahamed, Eistiak; Kaish, A B M A

    2015-01-01

    Visually impaired students (VIS) are unable to get visual information, which has made their learning process complicated. This paper discusses the overall situation of VIS in Bangladesh and identifies major challenges that they are facing in getting education. The Braille system is followed to educate blind students in Bangladesh. However, lack of Braille based educational resources and technological solutions have made the learning process lengthy and complicated for VIS. As a developing country, Bangladesh cannot afford for the costly Braille related technological tools for VIS. Therefore, a mobile phone based Braille application, "mBRAILLE", for Android platform is designed to provide an easy Braille learning technology for VIS in Bangladesh. The proposed design is evaluated by experts in assistive technology for students with disabilities, and advanced learners of Braille. The application aims to provide a Bangla and English Braille learning platform for VIS. In this paper, we depict iterative (participatory) design of the application along with a preliminary evaluation with 5 blind subjects, and 1 sighted and 2 blind experts. The results show that the design scored an overall satisfaction level of 4.53 out of 5 by all respondents, indicating that our design is ready for the next step of development.

  19. ELATE: an open-source online application for analysis and visualization of elastic tensors

    International Nuclear Information System (INIS)

    Gaillac, Romain; Coudert, François-Xavier; Pullumbi, Pluton

    2016-01-01

    We report on the implementation of a tool for the analysis of second-order elastic stiffness tensors, provided with both an open-source Python module and a standalone online application allowing the visualization of anisotropic mechanical properties. After describing the software features, how we compute the conventional elastic constants and how we represent them graphically, we explain our technical choices for the implementation. In particular, we focus on why a Python module is used to generate the HTML web page with embedded Javascript for dynamical plots. (paper)

  20. A Mobile Phone Application Enabling Visually Impaired Users to Find and Read Product Barcodes.

    Science.gov (United States)

    Tekin, Ender; Coughlan, James M

    2010-07-01

    While there are many barcode readers available for identifying products in a supermarket or at home on mobile phones (e.g., Red Laser iPhone app), such readers are inaccessible to blind or visually impaired persons because of their reliance on visual feedback from the user to center the barcode in the camera's field of view. We describe a mobile phone application that guides a visually impaired user to the barcode on a package in real-time using the phone's built-in video camera. Once the barcode is located by the system, the user is prompted with audio signals to bring the camera closer to the barcode until it can be resolved by the camera, which is then decoded and the corresponding product information read aloud using text-to-speech. Experiments with a blind volunteer demonstrate proof of concept of our system, which allowed the volunteer to locate barcodes which were then translated to product information that was announced to the user. We successfully tested a series of common products, as well as user-generated barcodes labeling household items that may not come with barcodes.

  1. Quantitative Evaluation of Stereo Visual Odometry for Autonomous Vessel Localisation in Inland Waterway Sensing Applications

    Directory of Open Access Journals (Sweden)

    Thomas Kriechbaumer

    2015-12-01

    Full Text Available Autonomous survey vessels can increase the efficiency and availability of wide-area river environment surveying as a tool for environment protection and conservation. A key challenge is the accurate localisation of the vessel, where bank-side vegetation or urban settlement preclude the conventional use of line-of-sight global navigation satellite systems (GNSS. In this paper, we evaluate unaided visual odometry, via an on-board stereo camera rig attached to the survey vessel, as a novel, low-cost localisation strategy. Feature-based and appearance-based visual odometry algorithms are implemented on a six degrees of freedom platform operating under guided motion, but stochastic variation in yaw, pitch and roll. Evaluation is based on a 663 m-long trajectory (>15,000 image frames and statistical error analysis against ground truth position from a target tracking tachymeter integrating electronic distance and angular measurements. The position error of the feature-based technique (mean of ±0.067 m is three times smaller than that of the appearance-based algorithm. From multi-variable statistical regression, we are able to attribute this error to the depth of tracked features from the camera in the scene and variations in platform yaw. Our findings inform effective strategies to enhance stereo visual localisation for the specific application of river monitoring.

  2. Bringing Legacy Visualization Software to Modern Computing Devices via Application Streaming

    Science.gov (United States)

    Fisher, Ward

    2014-05-01

    Planning software compatibility across forthcoming generations of computing platforms is a problem commonly encountered in software engineering and development. While this problem can affect any class of software, data analysis and visualization programs are particularly vulnerable. This is due in part to their inherent dependency on specialized hardware and computing environments. A number of strategies and tools have been designed to aid software engineers with this task. While generally embraced by developers at 'traditional' software companies, these methodologies are often dismissed by the scientific software community as unwieldy, inefficient and unnecessary. As a result, many important and storied scientific software packages can struggle to adapt to a new computing environment; for example, one in which much work is carried out on sub-laptop devices (such as tablets and smartphones). Rewriting these packages for a new platform often requires significant investment in terms of development time and developer expertise. In many cases, porting older software to modern devices is neither practical nor possible. As a result, replacement software must be developed from scratch, wasting resources better spent on other projects. Enabled largely by the rapid rise and adoption of cloud computing platforms, 'Application Streaming' technologies allow legacy visualization and analysis software to be operated wholly from a client device (be it laptop, tablet or smartphone) while retaining full functionality and interactivity. It mitigates much of the developer effort required by other more traditional methods while simultaneously reducing the time it takes to bring the software to a new platform. This work will provide an overview of Application Streaming and how it compares against other technologies which allow scientific visualization software to be executed from a remote computer. We will discuss the functionality and limitations of existing application streaming

  3. A new study on diffusion tensor imaging of the whole visual pathway fiber bundle and clinical application

    Institute of Scientific and Technical Information of China (English)

    TAO Xiao-feng; WANG Zhong-qiu; GONG Wan-qing; JIANG Qing-jun; SHI Zeng-ru

    2009-01-01

    Background With conventional imaging methods only the morphous of the visual nerve fiber bundles can be demonstrated, while the earlier period functional changes can not be demonstrated. We hypothesized that diffusion tensor imaging (DTI) would demonstrated the whole optic never fiber bundle and visual pathway and the earlier period functional changes. The purpose of the present study was to evaluate the application of DTI technique in the demonstration of the whole optic never fiber bundle and visual pathway, and the influence of orbital tumors on them. Methods GE 1.5T signa HD MR System, and the software package DTV2 were adopted. The total 45 subjects were enrolled, including 15 volunteers and 30 patients. All patients had ocular proptosis from minor to major. Seven patients had visual acuity decrescence. Results The nerve fiber bundles, e.g. optic chiasma, optic tract and optic radiation in posterior visual pathway were well demonstrated in all cases. Wherein, the intact whole visual pathway fiber bundles were clearly revealed in 10 volunteers and 17 patients, and optic nerve was not wholly revealed in the rest of the subjects. Shift of optic nerve caused by compression and partial deformation were seen in 7 patients with orbital tumor. In 6 of 7 patients, DTI displayed significant abscise and deformation of visual nerve. Chi-square test indicated significant correlation between visual acuity decrescence and DTI visual nerve non-display. Conclusions Visual nerve fiber bundles and the whole visual pathway were visualized in most of patients with DTI. It might be an effective method of providing imaging evidence for visual nerve fiber earlier period functional changes, and laid a foundation for the study in other cranial nerves.

  4. Genome editing and genetic engineering in livestock for advancing agricultural and biomedical applications.

    Science.gov (United States)

    Telugu, Bhanu P; Park, Ki-Eun; Park, Chi-Hun

    2017-08-01

    Genetic modification of livestock has a longstanding and successful history, starting with domestication several thousand years ago. Modern animal breeding strategies predominantly based on marker-assisted and genomic selection, artificial insemination, and embryo transfer have led to significant improvement in the performance of domestic animals, and are the basis for regular supply of high quality animal derived food. However, the current strategy of breeding animals over multiple generations to introduce novel traits is not realistic in responding to the unprecedented challenges such as changing climate, pandemic diseases, and feeding an anticipated 3 billion increase in global population in the next three decades. Consequently, sophisticated genetic modifications that allow for seamless introgression of novel alleles or traits and introduction of precise modifications without affecting the overall genetic merit of the animal are required for addressing these pressing challenges. The requirement for precise modifications is especially important in the context of modeling human diseases for the development of therapeutic interventions. The animal science community envisions the genome editors as essential tools in addressing these critical priorities in agriculture and biomedicine, and for advancing livestock genetic engineering for agriculture, biomedical as well as "dual purpose" applications.

  5. PRED-CLASS: cascading neural networks for generalized protein classification and genome-wide applications.

    Science.gov (United States)

    Pasquier, C; Promponas, V J; Hamodrakas, S J

    2001-08-15

    A cascading system of hierarchical, artificial neural networks (named PRED-CLASS) is presented for the generalized classification of proteins into four distinct classes-transmembrane, fibrous, globular, and mixed-from information solely encoded in their amino acid sequences. The architecture of the individual component networks is kept very simple, reducing the number of free parameters (network synaptic weights) for faster training, improved generalization, and the avoidance of data overfitting. Capturing information from as few as 50 protein sequences spread among the four target classes (6 transmembrane, 10 fibrous, 13 globular, and 17 mixed), PRED-CLASS was able to obtain 371 correct predictions out of a set of 387 proteins (success rate approximately 96%) unambiguously assigned into one of the target classes. The application of PRED-CLASS to several test sets and complete proteomes of several organisms demonstrates that such a method could serve as a valuable tool in the annotation of genomic open reading frames with no functional assignment or as a preliminary step in fold recognition and ab initio structure prediction methods. Detailed results obtained for various data sets and completed genomes, along with a web sever running the PRED-CLASS algorithm, can be accessed over the World Wide Web at http://o2.biol.uoa.gr/PRED-CLASS.

  6. Feature Usage Explorer: Usage Monitoring and Visualization Tool in HTML5 Based Applications

    Directory of Open Access Journals (Sweden)

    Sarunas Marciuska

    2013-10-01

    Full Text Available Feature Usage Explorer is a JavaScript library, which automatically detects features in HTML5 based applications and monitors their usage. The collected information can be visualized in a Feature Usage Diagram, which is automatically generated from an input json file. Currently, the users of Feature Usage Explorer have to design their own tool in order to generate the json file from collected usage information. This option remains viable when using the library in order not to constraint the user’s choice of preferred data storage. Feature Usage Explorer can be reused in any HTML5 based applications where an understanding of how users interact with the system is required (i.e. user experience and usability studies, human computer interaction field, or requirement prioritization area.

  7. Designing Multimodal Mobile Interaction for a Text Messaging Application for Visually Impaired Users

    Directory of Open Access Journals (Sweden)

    Carlos Duarte

    2017-12-01

    Full Text Available While mobile devices have experienced important accessibility advances in the past years, people with visual impairments still face important barriers, especially in specific contexts when both their hands are not free to hold the mobile device, like when walking outside. By resorting to a multimodal combination of body based gestures and voice, we aim to achieve full hands and vision free interaction with mobile devices. In this article, we describe this vision and present the design of a prototype, inspired by that vision, of a text messaging application. The article also presents a user study where the suitability of the proposed approach was assessed, and a performance comparison between our prototype and existing SMS applications was conducted. Study participants received positively the prototype, which also supported better performance in tasks that involved text editing.

  8. Flow visualization

    CERN Document Server

    Merzkirch, Wolfgang

    1974-01-01

    Flow Visualization describes the most widely used methods for visualizing flows. Flow visualization evaluates certain properties of a flow field directly accessible to visual perception. Organized into five chapters, this book first presents the methods that create a visible flow pattern that could be investigated by visual inspection, such as simple dye and density-sensitive visualization methods. It then deals with the application of electron beams and streaming birefringence. Optical methods for compressible flows, hydraulic analogy, and high-speed photography are discussed in other cha

  9. Case studies on design, simulation and visualization of control and measurement applications using REX control system

    Energy Technology Data Exchange (ETDEWEB)

    Ozana, Stepan, E-mail: stepan.ozana@vsb.cz; Pies, Martin, E-mail: martin.pies@vsb.cz; Docekal, Tomas, E-mail: docekalt@email.cz [VSB-Technical University of Ostrava, Faculty of Electrical Engineering and Computer Science, Department of Cybernetics and Biomedical Engineering, 17. listopadu 15/2172, Ostrava-Poruba, 700 30 (Czech Republic)

    2016-06-08

    REX Control System is a professional advanced tool for design and implementation of complex control systems that belongs to softPLC category. It covers the entire process starting from simulation of functionality of the application before deployment, through implementation on real-time target, towards analysis, diagnostics and visualization. Basically it consists of two parts: the development tools and the runtime system. It is also compatible with Simulink environment, and the way of implementation of control algorithm is very similar. The control scheme is finally compiled (using RexDraw utility) and uploaded into a chosen real-time target (using RexView utility). There is a wide variety of hardware platforms and real-time operating systems supported by REX Control System such as for example Windows Embedded, Linux, Linux/Xenomai deployed on SBC, IPC, PAC, Raspberry Pi and others with many I/O interfaces. It is modern system designed both for measurement and control applications, offering a lot of additional functions concerning data archiving, visualization based on HTML5, and communication standards. The paper will sum up possibilities of its use in educational process, focused on control of case studies of physical models with classical and advanced control algorithms.

  10. Case studies on design, simulation and visualization of control and measurement applications using REX control system

    International Nuclear Information System (INIS)

    Ozana, Stepan; Pies, Martin; Docekal, Tomas

    2016-01-01

    REX Control System is a professional advanced tool for design and implementation of complex control systems that belongs to softPLC category. It covers the entire process starting from simulation of functionality of the application before deployment, through implementation on real-time target, towards analysis, diagnostics and visualization. Basically it consists of two parts: the development tools and the runtime system. It is also compatible with Simulink environment, and the way of implementation of control algorithm is very similar. The control scheme is finally compiled (using RexDraw utility) and uploaded into a chosen real-time target (using RexView utility). There is a wide variety of hardware platforms and real-time operating systems supported by REX Control System such as for example Windows Embedded, Linux, Linux/Xenomai deployed on SBC, IPC, PAC, Raspberry Pi and others with many I/O interfaces. It is modern system designed both for measurement and control applications, offering a lot of additional functions concerning data archiving, visualization based on HTML5, and communication standards. The paper will sum up possibilities of its use in educational process, focused on control of case studies of physical models with classical and advanced control algorithms.

  11. Case studies on design, simulation and visualization of control and measurement applications using REX control system

    Science.gov (United States)

    Ozana, Stepan; Pies, Martin; Docekal, Tomas

    2016-06-01

    REX Control System is a professional advanced tool for design and implementation of complex control systems that belongs to softPLC category. It covers the entire process starting from simulation of functionality of the application before deployment, through implementation on real-time target, towards analysis, diagnostics and visualization. Basically it consists of two parts: the development tools and the runtime system. It is also compatible with Simulink environment, and the way of implementation of control algorithm is very similar. The control scheme is finally compiled (using RexDraw utility) and uploaded into a chosen real-time target (using RexView utility). There is a wide variety of hardware platforms and real-time operating systems supported by REX Control System such as for example Windows Embedded, Linux, Linux/Xenomai deployed on SBC, IPC, PAC, Raspberry Pi and others with many I/O interfaces. It is modern system designed both for measurement and control applications, offering a lot of additional functions concerning data archiving, visualization based on HTML5, and communication standards. The paper will sum up possibilities of its use in educational process, focused on control of case studies of physical models with classical and advanced control algorithms.

  12. Applicability of visual-analogue scale in patients with orofacial pain

    Directory of Open Access Journals (Sweden)

    Lončar Jovana

    2013-01-01

    Full Text Available Introduction. Orofacial pain occurs in various disorders of the orofacial region. Objective. The aim of this study was to examine applicability of the visual-analogue scale (VAS in patients with orofacial pain (model of acute and chronic pain. Methods. The study involved 60 patients, aged 18-70 years. The first group consisted of patients with dentin hypersensitivity, and the second group of patients with chronic rhinosinusitis. All patients were asked to fill-in a pain questionnaire and to rate pain intensity on the modified visual analogue scale (VAS; 0-10. Air indexing method was performed in the patients with dentin hypersensitivity in order to provoke pain, while the patients with chronic rhinosinusitis underwent CT imaging of paranasal sinuses. Wilcoxon’s test and Pearson’s correlation coefficient were used for statistical analysis. Results. In patients with dentin hypersensitivity provocation increased subjective feeling of pain, but without statistical significance (t=164.5; p>0.05. In patients with chronic rhinosinusitis a significant statistical correlation (r=0.53; p<0.05 was found between subjective pain assessment of VAS and CT findings. Conclusion. Applying VAS in the evaluation of acute and chronic pain can indicate progression or regression of pathological state under clinical conditions. This study showed that VAS, as a method for follow-up of pathological state, is more applicable and efficient when applied in chronic pain evaluation.

  13. Emerging applications of read profiles towards the functional annotation of the genome

    DEFF Research Database (Denmark)

    Pundhir, Sachin; Poirazi, Panayiota; Gorodkin, Jan

    2015-01-01

    is typically a result of the protocol designed to address specific research questions. The sequencing results in reads, which when mapped to a reference genome often leads to the formation of distinct patterns (read profiles). Interpretation of these read profiles is essential for their analysis in relation...... to the research question addressed. Several strategies have been employed at varying levels of abstraction ranging from a somewhat ad hoc to a more systematic analysis of read profiles. These include methods which can compare read profiles, e.g., from direct (non-sequence based) alignments to classification...... of patterns into functional groups. In this review, we highlight the emerging applications of read profiles for the annotation of non-coding RNA and cis-regulatory elements (CREs) such as enhancers and promoters. We also discuss the biological rationale behind their formation....

  14. Combining Induced Pluripotent Stem Cells and Genome Editing Technologies for Clinical Applications.

    Science.gov (United States)

    Chang, Chia-Yu; Ting, Hsiao-Chien; Su, Hong-Lin; Jeng, Jing-Ren

    2018-01-01

    In this review, we introduce current developments in induced pluripotent stem cells (iPSCs), site-specific nuclease (SSN)-mediated genome editing tools, and the combined application of these two novel technologies in biomedical research and therapeutic trials. The sustainable pluripotent property of iPSCs in vitro not only provides unlimited cell sources for basic research but also benefits precision medicines for human diseases. In addition, rapidly evolving SSN tools efficiently tailor genetic manipulations for exploring gene functions and can be utilized to correct genetic defects of congenital diseases in the near future. Combining iPSC and SSN technologies will create new reliable human disease models with isogenic backgrounds in vitro and provide new solutions for cell replacement and precise therapies.

  15. Genomic variant annotation workflow for clinical applications [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Thomas Thurnherr

    2016-10-01

    Full Text Available Annotation and interpretation of DNA aberrations identified through next-generation sequencing is becoming an increasingly important task. Even more so in the context of data analysis pipelines for medical applications, where genomic aberrations are associated with phenotypic and clinical features. Here we describe a workflow to identify potential gene targets in aberrated genes or pathways and their corresponding drugs. To this end, we provide the R/Bioconductor package rDGIdb, an R wrapper to query the drug-gene interaction database (DGIdb. DGIdb accumulates drug-gene interaction data from 15 different resources and allows filtering on different levels. The rDGIdb package makes these resources and tools available to R users. Moreover, rDGIdb queries can be automated through incorporation of the rDGIdb package into NGS sequencing pipelines.

  16. Data Mining Approaches for Genomic Biomarker Development: Applications Using Drug Screening Data from the Cancer Genome Project and the Cancer Cell Line Encyclopedia.

    Directory of Open Access Journals (Sweden)

    David G Covell

    Full Text Available Developing reliable biomarkers of tumor cell drug sensitivity and resistance can guide hypothesis-driven basic science research and influence pre-therapy clinical decisions. A popular strategy for developing biomarkers uses characterizations of human tumor samples against a range of cancer drug responses that correlate with genomic change; developed largely from the efforts of the Cancer Cell Line Encyclopedia (CCLE and Sanger Cancer Genome Project (CGP. The purpose of this study is to provide an independent analysis of this data that aims to vet existing and add novel perspectives to biomarker discoveries and applications. Existing and alternative data mining and statistical methods will be used to a evaluate drug responses of compounds with similar mechanism of action (MOA, b examine measures of gene expression (GE, copy number (CN and mutation status (MUT biomarkers, combined with gene set enrichment analysis (GSEA, for hypothesizing biological processes important for drug response, c conduct global comparisons of GE, CN and MUT as biomarkers across all drugs screened in the CGP dataset, and d assess the positive predictive power of CGP-derived GE biomarkers as predictors of drug response in CCLE tumor cells. The perspectives derived from individual and global examinations of GEs, MUTs and CNs confirm existing and reveal unique and shared roles for these biomarkers in tumor cell drug sensitivity and resistance. Applications of CGP-derived genomic biomarkers to predict the drug response of CCLE tumor cells finds a highly significant ROC, with a positive predictive power of 0.78. The results of this study expand the available data mining and analysis methods for genomic biomarker development and provide additional support for using biomarkers to guide hypothesis-driven basic science research and pre-therapy clinical decisions.

  17. Characterization of the dsDNA prophage sequences in the genome of Neisseria gonorrhoeae and visualization of productive bacteriophage

    Directory of Open Access Journals (Sweden)

    Maugel Timothy K

    2007-07-01

    Full Text Available Abstract Background Bioinformatic analysis of the genome sequence of Neisseria gonorrhoeae revealed the presence of nine probable prophage islands. The distribution, conservation and function of many of these sequences, and their ability to produce bacteriophage particles are unknown. Results Our analysis of the genomic sequence of FA1090 identified five genomic regions (NgoΦ1 – 5 that are related to dsDNA lysogenic phage. The genetic content of the dsDNA prophage sequences were examined in detail and found to contain blocks of genes encoding for proteins homologous to proteins responsible for phage DNA replication, structural proteins and proteins responsible for phage assembly. The DNA sequences from NgoΦ1, NgoΦ2 and NgoΦ3 contain some significant regions of identity. A unique region of NgoΦ2 showed very high similarity with the Pseudomonas aeruginosa generalized transducing phage F116. Comparative analysis at the nucleotide and protein levels suggests that the sequences of NgoΦ1 and NgoΦ2 encode functionally active phages, while NgoΦ3, NgoΦ4 and NgoΦ5 encode incomplete genomes. Expression of the NgoΦ1 and NgoΦ2 repressors in Escherichia coli inhibit the growth of E. coli and the propagation of phage λ. The NgoΦ2 repressor was able to inhibit transcription of N. gonorrhoeae genes and Haemophilus influenzae HP1 phage promoters. The holin gene of NgoΦ1 (identical to that encoded by NgoΦ2, when expressed in E. coli, could serve as substitute for the phage λ s gene. We were able to detect the presence of the DNA derived from NgoΦ1 in the cultures of N. gonorrhoeae. Electron microscopy analysis of culture supernatants revealed the presence of multiple forms of bacteriophage particles. Conclusion These data suggest that the genes similar to dsDNA lysogenic phage present in the gonococcus are generally conserved in this pathogen and that they are able to regulate the expression of other neisserial genes. Since phage particles were

  18. Automated genomic DNA purification options in agricultural applications using MagneSil paramagnetic particles

    Science.gov (United States)

    Bitner, Rex M.; Koller, Susan C.

    2002-06-01

    The automated high throughput purification of genomic DNA form plant materials can be performed using MagneSil paramagnetic particles on the Beckman-Coulter FX, BioMek 2000, and the Tecan Genesis robot. Similar automated methods are available for DNA purifications from animal blood. These methods eliminate organic extractions, lengthy incubations and cumbersome filter plates. The DNA is suitable for applications such as PCR and RAPD analysis. Methods are described for processing traditionally difficult samples such as those containing large amounts of polyphenolics or oils, while still maintaining a high level of DNA purity. The robotic protocols have ben optimized for agricultural applications such as marker assisted breeding, seed-quality testing, and SNP discovery and scoring. In addition to high yield purification of DNA from plant samples or animal blood, the use of Promega's DNA-IQ purification system is also described. This method allows for the purification of a narrow range of DNA regardless of the amount of additional DNA that is present in the initial sample. This simultaneous Isolation and Quantification of DNA allows the DNA to be used directly in applications such as PCR, SNP analysis, and RAPD, without the need for separate quantitation of the DNA.

  19. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

    Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

  20. Engineering and Scientific Applications: Using MatLab(Registered Trademark) for Data Processing and Visualization

    Science.gov (United States)

    Sen, Syamal K.; Shaykhian, Gholam Ali

    2011-01-01

    MatLab(TradeMark)(MATrix LABoratory) is a numerical computation and simulation tool that is used by thousands Scientists and Engineers in many countries. MatLab does purely numerical calculations, which can be used as a glorified calculator or interpreter programming language; its real strength is in matrix manipulations. Computer algebra functionalities are achieved within the MatLab environment using "symbolic" toolbox. This feature is similar to computer algebra programs, provided by Maple or Mathematica to calculate with mathematical equations using symbolic operations. MatLab in its interpreter programming language form (command interface) is similar with well known programming languages such as C/C++, support data structures and cell arrays to define classes in object oriented programming. As such, MatLab is equipped with most of the essential constructs of a higher programming language. MatLab is packaged with an editor and debugging functionality useful to perform analysis of large MatLab programs and find errors. We believe there are many ways to approach real-world problems; prescribed methods to ensure foregoing solutions are incorporated in design and analysis of data processing and visualization can benefit engineers and scientist in gaining wider insight in actual implementation of their perspective experiments. This presentation will focus on data processing and visualizations aspects of engineering and scientific applications. Specifically, it will discuss methods and techniques to perform intermediate-level data processing covering engineering and scientific problems. MatLab programming techniques including reading various data files formats to produce customized publication-quality graphics, importing engineering and/or scientific data, organizing data in tabular format, exporting data to be used by other software programs such as Microsoft Excel, data presentation and visualization will be discussed.

  1. Visual servoing in medical robotics: a survey. Part I: endoscopic and direct vision imaging - techniques and applications.

    Science.gov (United States)

    Azizian, Mahdi; Khoshnam, Mahta; Najmaei, Nima; Patel, Rajni V

    2014-09-01

    Intra-operative imaging is widely used to provide visual feedback to a clinician when he/she performs a procedure. In visual servoing, surgical instruments and parts of tissue/body are tracked by processing the acquired images. This information is then used within a control loop to manoeuvre a robotic manipulator during a procedure. A comprehensive search of electronic databases was completed for the period 2000-2013 to provide a survey of the visual servoing applications in medical robotics. The focus is on medical applications where image-based tracking is used for closed-loop control of a robotic system. Detailed classification and comparative study of various contributions in visual servoing using endoscopic or direct visual images are presented and summarized in tables and diagrams. The main challenges in using visual servoing for medical robotic applications are identified and potential future directions are suggested. 'Supervised automation of medical robotics' is found to be a major trend in this field. Copyright © 2013 John Wiley & Sons, Ltd.

  2. AERYN: A simple standalone application for visualizing and enhancing elemental maps

    International Nuclear Information System (INIS)

    Mouchi, Vincent; Crowley, Quentin G.; Ubide, Teresa

    2016-01-01

    Interpretation of high spatial resolution elemental mineral maps can be hindered by high frequency fluctuations, as well as by strong naturally-occurring or analytically-induced variations. We have developed a new standalone program named AERYN (Aspect Enhancement by Removing Yielded Noise) to produce more reliable element distribution maps from previously reduced geochemical data. The program is Matlab-based, designed with a graphic user interface and is capable of rapidly generating elemental maps from data acquired by a range of analytical techniques. A visual interface aids selection of appropriate outlier rejection and drift-correction parameters, thereby facilitating recognition of subtle elemental fluctuations which may otherwise be obscured. Examples of use are provided for quantitative trace element maps acquired using both laser ablation (LA-) ICP-MS and electron probe microanalysis (EPMA) of the cold-water coral Lophelia pertusa. We demonstrate how AERYN allows recognition of high frequency elemental fluctuations, including those which occur perpendicular to the maximum concentration gradient. Such data treatment compliments commonly used processing methods to provide greater flexibility and control in producing elemental maps from micro-analytical techniques. - Highlights: • Matlab-based application to improve visualization of elemental maps. • Capable of detrending when data set shows drift. • Compatible with processed data text files from LA-ICP-MS, EDS and EPMA. • Option to filter geochemical trends to observe high-frequency fluctuations.

  3. CRISPR/Cas9 Platforms for Genome Editing in Plants: Developments and Applications.

    Science.gov (United States)

    Ma, Xingliang; Zhu, Qinlong; Chen, Yuanling; Liu, Yao-Guang

    2016-07-06

    The clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein9 (Cas9) genome editing system (CRISPR/Cas9) is adapted from the prokaryotic type II adaptive immunity system. The CRISPR/Cas9 tool surpasses other programmable nucleases, such as ZFNs and TALENs, for its simplicity and high efficiency. Various plant-specific CRISPR/Cas9 vector systems have been established for adaption of this technology to many plant species. In this review, we present an overview of current advances on applications of this technology in plants, emphasizing general considerations for establishment of CRISPR/Cas9 vector platforms, strategies for multiplex editing, methods for analyzing the induced mutations, factors affecting editing efficiency and specificity, and features of the induced mutations and applications of the CRISPR/Cas9 system in plants. In addition, we provide a perspective on the challenges of CRISPR/Cas9 technology and its significance for basic plant research and crop genetic improvement. Copyright © 2016 The Author. Published by Elsevier Inc. All rights reserved.

  4. An application of Random Forests to a genome-wide association dataset: Methodological considerations & new findings

    Directory of Open Access Journals (Sweden)

    Hubbard Alan E

    2010-06-01

    Full Text Available Abstract Background As computational power improves, the application of more advanced machine learning techniques to the analysis of large genome-wide association (GWA datasets becomes possible. While most traditional statistical methods can only elucidate main effects of genetic variants on risk for disease, certain machine learning approaches are particularly suited to discover higher order and non-linear effects. One such approach is the Random Forests (RF algorithm. The use of RF for SNP discovery related to human disease has grown in recent years; however, most work has focused on small datasets or simulation studies which are limited. Results Using a multiple sclerosis (MS case-control dataset comprised of 300 K SNP genotypes across the genome, we outline an approach and some considerations for optimally tuning the RF algorithm based on the empirical dataset. Importantly, results show that typical default parameter values are not appropriate for large GWA datasets. Furthermore, gains can be made by sub-sampling the data, pruning based on linkage disequilibrium (LD, and removing strong effects from RF analyses. The new RF results are compared to findings from the original MS GWA study and demonstrate overlap. In addition, four new interesting candidate MS genes are identified, MPHOSPH9, CTNNA3, PHACTR2 and IL7, by RF analysis and warrant further follow-up in independent studies. Conclusions This study presents one of the first illustrations of successfully analyzing GWA data with a machine learning algorithm. It is shown that RF is computationally feasible for GWA data and the results obtained make biologic sense based on previous studies. More importantly, new genes were identified as potentially being associated with MS, suggesting new avenues of investigation for this complex disease.

  5. From motor cortex to visual cortex: the application of noninvasive brain stimulation to amblyopia.

    Science.gov (United States)

    Thompson, Benjamin; Mansouri, Behzad; Koski, Lisa; Hess, Robert F

    2012-04-01

    Noninvasive brain stimulation is a technique for inducing changes in the excitability of discrete neural populations in the human brain. A current model of the underlying pathological processes contributing to the loss of motor function after stroke has motivated a number of research groups to investigate the potential therapeutic application of brain stimulation to stroke rehabilitation. The loss of motor function is modeled as resulting from a combination of reduced excitability in the lesioned motor cortex and an increased inhibitory drive from the nonlesioned hemisphere over the lesioned hemisphere. This combination of impaired neural function and pathological suppression resonates with current views on the cause of the visual impairment in amblyopia. Here, we discuss how the rationale for using noninvasive brain stimulation in stroke rehabilitation can be applied to amblyopia, review a proof-of-principle study demonstrating that brain stimulation can temporarily improve amblyopic eye function, and propose future research avenues. Copyright © 2010 Wiley Periodicals, Inc.

  6. Continuous modelling study of numerical volumes - Applications to the visualization of anatomical structures

    International Nuclear Information System (INIS)

    Goret, C.

    1990-12-01

    Several technics of imaging (IRM, image scanners, tomoscintigraphy, echography) give numerical informations presented by means of a stack of parallel cross-sectional images. Since many years, 3-D mathematical tools have been developed and allow the 3 D images synthesis of surfaces. In first part, we give the technics of numerical volume exploitation and their medical applications to diagnosis and therapy. The second part is about a continuous modelling of the volume with a tensor product of cubic splines. We study the characteristics of this representation and its clinical validation. Finally, we treat of the problem of surface visualization of objects contained in the volume. The results show the interest of this model and allow to propose specifications for 3-D workstation realization [fr

  7. Quality control in diagnostic radiology: software (Visual Basic 6) and database applications

    International Nuclear Information System (INIS)

    Md Saion Salikin; Muhammad Farid Abdul Khalid

    2002-01-01

    Quality Assurance programme in diagnostic Radiology is being implemented by the Ministry of Health (MoH) in Malaysia. Under this program the performance of an x-ray machine used for diagnostic purpose is tested by using the approved procedure which is commonly known as Quality Control in diagnostic radiology. The quality control or performance tests are carried out b a class H licence holder issued the Atomic Energy Licensing Act 1984. There are a few computer applications (software) that are available in the market which can be used for this purpose. A computer application (software) using Visual Basics 6 and Microsoft Access, is being developed to expedite data handling, analysis and storage as well as report writing of the quality control tests. In this paper important features of the software for quality control tests are explained in brief. A simple database is being established for this purpose which is linked to the software. Problems encountered in the preparation of database are discussed in this paper. A few examples of practical usage of the software and database applications are presented in brief. (Author)

  8. Icarus: visualizer for de novo assembly evaluation.

    Science.gov (United States)

    Mikheenko, Alla; Valin, Gleb; Prjibelski, Andrey; Saveliev, Vladislav; Gurevich, Alexey

    2016-11-01

    : Data visualization plays an increasingly important role in NGS data analysis. With advances in both sequencing and computational technologies, it has become a new bottleneck in genomics studies. Indeed, evaluation of de novo genome assemblies is one of the areas that can benefit from the visualization. However, even though multiple quality assessment methods are now available, existing visualization tools are hardly suitable for this purpose. Here, we present Icarus-a novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on the tool QUAST. Icarus can be used in studies where a related reference genome is available, as well as for non-model organisms. The tool is available online and as a standalone application. http://cab.spbu.ru/software/icarus CONTACT: aleksey.gurevich@spbu.ruSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  9. CALCMIN - an EXCEL™ Visual Basic application for calculating mineral structural formulae from electron microprobe analyses

    Science.gov (United States)

    Brandelik, Andreas

    2009-07-01

    CALCMIN, an open source Visual Basic program, was implemented in EXCEL™. The program was primarily developed to support geoscientists in their routine task of calculating structural formulae of minerals on the basis of chemical analysis mainly obtained by electron microprobe (EMP) techniques. Calculation programs for various minerals are already included in the form of sub-routines. These routines are arranged in separate modules containing a minimum of code. The architecture of CALCMIN allows the user to easily develop new calculation routines or modify existing routines with little knowledge of programming techniques. By means of a simple mouse-click, the program automatically generates a rudimentary framework of code using the object model of the Visual Basic Editor (VBE). Within this framework simple commands and functions, which are provided by the program, can be used, for example, to perform various normalization procedures or to output the results of the computations. For the clarity of the code, element symbols are used as variables initialized by the program automatically. CALCMIN does not set any boundaries in complexity of the code used, resulting in a wide range of possible applications. Thus, matrix and optimization methods can be included, for instance, to determine end member contents for subsequent thermodynamic calculations. Diverse input procedures are provided, such as the automated read-in of output files created by the EMP. Furthermore, a subsequent filter routine enables the user to extract specific analyses in order to use them for a corresponding calculation routine. An event-driven, interactive operating mode was selected for easy application of the program. CALCMIN leads the user from the beginning to the end of the calculation process.

  10. PENGEMBANGAN MEDIA PEMBELAJARAN MENGGUNAKAN POWERPOINT DISERTAI VISUAL BASIC FOR APPLICATION MATERI JARAK PADA BANGUN RUANG KELAS X

    Directory of Open Access Journals (Sweden)

    Siti Marfuah

    2016-10-01

    Full Text Available Penelitian ini bertujuan : (1 menghasilkan media pembelajaran menggunakan powerpoint disertai visual basic for application materi jarak pada bangun ruang yang valid dan praktis di kelas X, dan (2 mengetahui efek potensial dari pengembangan media pembelajaran menggunakan powerpoint disertai visual basic for application materi jarak pada bangun ruang di kelas X. Jenis penelitian yang digunakan adalah Design Research tipe Development Study. Subjek penelitian ini adalah siswa kelas X SMA Negeri 4 Palembang tahun ajaran 2014/2015. Teknik pengumpulan data adalah dengan walkthrough,, tes, angket, dan wawancara. Hasil dari penelitian ini adalah: (1 Penelitian ini telah menghasilkan media pembelajaran menggunakan powerpoint disertai visual basic for application materi jarak pada bangun ruang yang valid dan praktis. (2 media pembelajaran  yang dikembangkan memiliki efek potensial terhadap hasil belajar dan sikap positif siswa. Kata Kunci : Pengembangan, Media Pembelajaran, Powerpoint, Jarak pada Bangun Ruang This design research typed Development Study aims to: (1 develop valid and practical learning media using power point and visual basic for application for Distance in three-dimensional objects topic in class X, and (2 to determine the potential effects media developed by using power point and visual basic for application for Distance in three-dimensional objects topic in class X. The subjects were students of class X SMA Negeri 4 Palembang academic year 2014/2015. Data were collected through walkthrough, tests, questionnaires, and interviews. The study results show that (1 This research has produced valid and practical learning media using power point and visual basic for application for Distance in three-dimensional objects topic; (2 the learning media developed has potential effects on students learning outcomes and students positive attitude. Keywords: development, learning media, powerpoint, distance in three-dimensional object

  11. State of the art of parallel scientific visualization applications on PC clusters; Etat de l'art des applications de visualisation scientifique paralleles sur grappes de PC

    Energy Technology Data Exchange (ETDEWEB)

    Juliachs, M

    2004-07-01

    In this state of the art on parallel scientific visualization applications on PC clusters, we deal with both surface and volume rendering approaches. We first analyze available PC cluster configurations and existing parallel rendering software components for parallel graphics rendering. CEA/DIF has been studying cluster visualization since 2001. This report is part of a study to set up a new visualization research platform. This platform consisting of an eight-node PC cluster under Linux and a tiled display was installed in collaboration with Versailles-Saint-Quentin University in August 2003. (author)

  12. State of the art of parallel scientific visualization applications on PC clusters; Etat de l'art des applications de visualisation scientifique paralleles sur grappes de PC

    Energy Technology Data Exchange (ETDEWEB)

    Juliachs, M

    2004-07-01

    In this state of the art on parallel scientific visualization applications on PC clusters, we deal with both surface and volume rendering approaches. We first analyze available PC cluster configurations and existing parallel rendering software components for parallel graphics rendering. CEA/DIF has been studying cluster visualization since 2001. This report is part of a study to set up a new visualization research platform. This platform consisting of an eight-node PC cluster under Linux and a tiled display was installed in collaboration with Versailles-Saint-Quentin University in August 2003. (author)

  13. A visualization environment for supercomputing-based applications in computational mechanics

    Energy Technology Data Exchange (ETDEWEB)

    Pavlakos, C.J.; Schoof, L.A.; Mareda, J.F.

    1993-06-01

    In this paper, we characterize a visualization environment that has been designed and prototyped for a large community of scientists and engineers, with an emphasis in superconducting-based computational mechanics. The proposed environment makes use of a visualization server concept to provide effective, interactive visualization to the user`s desktop. Benefits of using the visualization server approach are discussed. Some thoughts regarding desirable features for visualization server hardware architectures are also addressed. A brief discussion of the software environment is included. The paper concludes by summarizing certain observations which we have made regarding the implementation of such visualization environments.

  14. Application of fast neutron radiography to three-dimensional visualization of steady two-phase flow in a rod bundle

    CERN Document Server

    Takenaka, N; Fujii, T; Mizubata, M; Yoshii, K

    1999-01-01

    Three-dimensional void fraction distribution of air-water two-phase flow in a 4x4 rod-bundle near a spacer was visualized by fast neutron radiography using a CT method. One-dimensional cross sectional averaged void fraction distribution was also calculated. The behaviors of low void fraction (thick water) two-phase flow in the rod bundle around the spacer were clearly visualized. It was shown that the void fraction distributions were visualized with a quality similar to those by thermal neutron radiography for low void fraction two-phase flow which is difficult to visualize by thermal neutron radiography. It is concluded that the fast neutron radiography is efficiently applicable to two-phase flow studies.

  15. GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface.

    Science.gov (United States)

    Lajugie, Julien; Fourel, Nicolas; Bouhassira, Eric E

    2015-01-01

    Parallel visualization of multiple individual human genomes is a complex endeavor that is rapidly gaining importance with the increasing number of personal, phased and cancer genomes that are being generated. It requires the display of variants such as SNPs, indels and structural variants that are unique to specific genomes and the introduction of multiple overlapping gaps in the reference sequence. Here, we describe GenPlay Multi-Genome, an application specifically written to visualize and analyze multiple human genomes in parallel. GenPlay Multi-Genome is ideally suited for the comparison of allele-specific expression and functional genomic data obtained from multiple phased genomes in a graphical interface with access to multiple-track operation. It also allows the analysis of data that have been aligned to custom genomes rather than to a standard reference and can be used as a variant calling format file browser and as a tool to compare different genome assembly, such as hg19 and hg38. GenPlay is available under the GNU public license (GPL-3) from http://genplay.einstein.yu.edu. The source code is available at https://github.com/JulienLajugie/GenPlay. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  16. The effect of mood state on visual search times for detecting a target in noise: An application of smartphone technology.

    Science.gov (United States)

    Maekawa, Toru; Anderson, Stephen J; de Brecht, Matthew; Yamagishi, Noriko

    2018-01-01

    The study of visual perception has largely been completed without regard to the influence that an individual's emotional status may have on their performance in visual tasks. However, there is a growing body of evidence to suggest that mood may affect not only creative abilities and interpersonal skills but also the capacity to perform low-level cognitive tasks. Here, we sought to determine whether rudimentary visual search processes are similarly affected by emotion. Specifically, we examined whether an individual's perceived happiness level affects their ability to detect a target in noise. To do so, we employed pop-out and serial visual search paradigms, implemented using a novel smartphone application that allowed search times and self-rated levels of happiness to be recorded throughout each twenty-four-hour period for two weeks. This experience sampling protocol circumvented the need to alter mood artificially with laboratory-based induction methods. Using our smartphone application, we were able to replicate the classic visual search findings, whereby pop-out search times remained largely unaffected by the number of distractors whereas serial search times increased with increasing number of distractors. While pop-out search times were unaffected by happiness level, serial search times with the maximum numbers of distractors (n = 30) were significantly faster for high happiness levels than low happiness levels (p = 0.02). Our results demonstrate the utility of smartphone applications in assessing ecologically valid measures of human visual performance. We discuss the significance of our findings for the assessment of basic visual functions using search time measures, and for our ability to search effectively for targets in real world settings.

  17. Applications of flow cytometry in plant pathology for genome size determination, detection and physiological status.

    Science.gov (United States)

    D'Hondt, Liesbet; Höfte, Monica; Van Bockstaele, Erik; Leus, Leen

    2011-10-01

    Flow cytometers are probably the most multipurpose laboratory devices available. They can analyse a vast and very diverse range of cell parameters. This technique has left its mark on cancer, human immunodeficiency virus and immunology research, and is indispensable in routine clinical diagnostics. Flow cytometry (FCM) is also a well-known tool for the detection and physiological status assessment of microorganisms in drinking water, marine environments, food and fermentation processes. However, flow cytometers are seldom used in plant pathology, despite FCM's major advantages as both a detection method and a research tool. Potential uses of FCM include the characterization of genome sizes of fungal and oomycete populations, multiplexed pathogen detection and the monitoring of the viability, culturability and gene expression of plant pathogens, and many others. This review provides an overview of the history, advantages and disadvantages of FCM, and focuses on the current applications and future possibilities of FCM in plant pathology. © 2011 THE AUTHORS. MOLECULAR PLANT PATHOLOGY © 2011 BSPP AND BLACKWELL PUBLISHING LTD.

  18. Application of Whole Genome Expression Analysis to Assess Bacterial Responses to Environmental Conditions

    Science.gov (United States)

    Vukanti, R. V.; Mintz, E. M.; Leff, L. G.

    2005-05-01

    Bacterial responses to environmental signals are multifactorial and are coupled to changes in gene expression. An understanding of bacterial responses to environmental conditions is possible using microarray expression analysis. In this study, the utility of microarrays for examining changes in gene expression in Escherichia coli under different environmental conditions was assessed. RNA was isolated, hybridized to Affymetrix E. coli Genome 2.0 chips and analyzed using Affymetrix GCOS and Genespring software. Major limiting factors were obtaining enough quality RNA (107-108 cells to get 10μg RNA)and accounting for differences in growth rates under different conditions. Stabilization of RNA prior to isolation and taking extreme precautions while handling RNA were crucial. In addition, use of this method in ecological studies is limited by availability and cost of commercial arrays; choice of primers for cDNA synthesis, reproducibility, complexity of results generated and need to validate findings. This method may be more widely applicable with the development of better approaches for RNA recovery from environmental samples and increased number of available strain-specific arrays. Diligent experimental design and verification of results with real-time PCR or northern blots is needed. Overall, there is a great potential for use of this technology to discover mechanisms underlying organisms' responses to environmental conditions.

  19. Creating a Prototype Web Application for Spacecraft Real-Time Data Visualization on Mobile Devices

    Science.gov (United States)

    Lang, Jeremy S.; Irving, James R.

    2014-01-01

    Mobile devices (smart phones, tablets) have become commonplace among almost all sectors of the workforce, especially in the technical and scientific communities. These devices provide individuals the ability to be constantly connected to any area of interest they may have, whenever and wherever they are located. The Huntsville Operations Support Center (HOSC) is attempting to take advantage of this constant connectivity to extend the data visualization component of the Payload Operations and Integration Center (POIC) to a person's mobile device. POIC users currently have a rather unique capability to create custom user interfaces in order to view International Space Station (ISS) payload health and status telemetry. These displays are used at various console positions within the POIC. The Software Engineering team has created a Mobile Display capability that will allow authenticated users to view the same displays created for the console positions on the mobile device of their choice. Utilizing modern technologies including ASP.net, JavaScript, and HTML5, we have created a web application that renders the user's displays in any modern desktop or mobile web browser, regardless of the operating system on the device. Additionally, the application is device aware which enables it to render its configuration and selection menus with themes that correspond to the particular device. The Mobile Display application uses a communication mechanism known as signalR to push updates to the web client. This communication mechanism automatically detects the best communication protocol between the client and server and also manages disconnections and reconnections of the client to the server. One benefit of this application is that the user can monitor important telemetry even while away from their console position. If expanded to the scientific community, this application would allow a scientist to view a snapshot of the state of their particular experiment at any time or place

  20. Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC and its application for DNA methylation analysis

    Directory of Open Access Journals (Sweden)

    Ottaviani Diego

    2008-05-01

    Full Text Available Abstract Background The major histocompatibility complex (MHC is essential for human immunity and is highly associated with common diseases, including cancer. While the genetics of the MHC has been studied intensively for many decades, very little is known about the epigenetics of this most polymorphic and disease-associated region of the genome. Methods To facilitate comprehensive epigenetic analyses of this region, we have generated a genomic tiling array of 2 Kb resolution covering the entire 4 Mb MHC region. The array has been designed to be compatible with chromatin immunoprecipitation (ChIP, methylated DNA immunoprecipitation (MeDIP, array comparative genomic hybridization (aCGH and expression profiling, including of non-coding RNAs. The array comprises 7832 features, consisting of two replicates of both forward and reverse strands of MHC amplicons and appropriate controls. Results Using MeDIP, we demonstrate the application of the MHC array for DNA methylation profiling and the identification of tissue-specific differentially methylated regions (tDMRs. Based on the analysis of two tissues and two cell types, we identified 90 tDMRs within the MHC and describe their characterisation. Conclusion A tiling array covering the MHC region was developed and validated. Its successful application for DNA methylation profiling indicates that this array represents a useful tool for molecular analyses of the MHC in the context of medical genomics.

  1. Cloning-free genome engineering in Sinorhizobium meliloti advances applications of Cre/loxP site-specific recombination.

    Science.gov (United States)

    Döhlemann, Johannes; Brennecke, Meike; Becker, Anke

    2016-09-10

    The soil-dwelling α-proteobacterium Sinorhizobium meliloti serves as model for studies of symbiotic nitrogen fixation, a highly important process in sustainable agriculture. Here, we report advancements of the genetic toolbox accelerating genome editing in S. meliloti. The hsdMSR operon encodes a type-I restriction-modification (R-M) system. Transformation of S. meliloti is counteracted by the restriction endonuclease HsdR degrading DNA which lacks the appropriate methylation pattern. We provide a stable S. meliloti hsdR deletion mutant showing enhanced transformation with Escherichia coli-derived plasmid DNA and demonstrate that using an E. coli plasmid donor, expressing S. meliloti methyl transferase genes, is an alternative strategy of increasing the transformation efficiency of S. meliloti. Furthermore, we devise a novel cloning-free genome editing (CFGE) method for S. meliloti, Agrobacterium tumefaciens and Xanthomonas campestris, and demonstrate the applicability of this method for intricate applications of the Cre/lox recombination system in S. meliloti. An enhanced Cre/lox system, allowing for serial deletions of large genomic regions, was established. An assay of lox spacer mutants identified a set of lox sites mediating specific recombination. The availability of several non-promiscuous Cre recognition sites enables simultaneous specific Cre/lox recombination events. CFGE combined with Cre/lox recombination is put forward as powerful approach for targeted genome editing, involving serial steps of manipulation to expedite the genetic accessibility of S. meliloti as chassis. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Molecular studies in olive (Olea europaea L.): overview on DNA markers applications and recent advances in genome analysis.

    Science.gov (United States)

    Bracci, T; Busconi, M; Fogher, C; Sebastiani, L

    2011-04-01

    Olive (Olea europaea L.) is one of the oldest agricultural tree crops worldwide and is an important source of oil with beneficial properties for human health. This emblematic tree crop of the Mediterranean Basin, which has conserved a very wide germplasm estimated in more than 1,200 cultivars, is a diploid species (2n = 2x = 46) that is present in two forms, namely wild (Olea europaea subsp. europaea var. sylvestris) and cultivated (Olea europaea subsp. europaea var. europaea). In spite of its economic and nutritional importance, there are few data about the genetic of olive if compared with other fruit crops. Available molecular data are especially related to the application of molecular markers to the analysis of genetic variability in Olea europaea complex and to develop efficient molecular tools for the olive oil origin traceability. With regard to genomic research, in the last years efforts are made for the identification of expressed sequence tag, with particular interest in those sequences expressed during fruit development and in pollen allergens. Very recently the sequencing of chloroplast genome provided new information on the olive nucleotide sequence, opening the olive genomic era. In this article, we provide an overview of the most relevant results in olive molecular studies. A particular attention was given to DNA markers and their application that constitute the most part of published researches. The first important results in genome analysis were reported.

  3. Polymerase spiral reaction (PSR): a novel, visual isothermal amplification method for detection of canine parvovirus 2 genomic DNA.

    Science.gov (United States)

    Gupta, Vikas; Chakravarti, Soumendu; Chander, Vishal; Majumder, Saurabh; Bhat, Shabir Ahmad; Gupta, Vivek Kumar; Nandi, Sukdeb

    2017-07-01

    Canine parvovirus-2 (CPV-2), which is ubiquitously distributed worldwide, causes severe and often fatal gastroenteritis in dogs. Accurate, differential and rapid diagnosis of canine parvoviral enteritis remains a challenge for clinicians. A recently developed isothermal amplification technique, polymerase spiral reaction (PSR), was optimized for the first time for a viral pathogen with reference recombinant plasmid standards from different CPV-2 antigenic variants (CPV-2, CPV-2a, CPV-2b and CPV-2c) and subsequently validated using clinical samples. Addition of chromogenic substrate SYBR Green I after the completion of the reaction resulted in bright green fluorescence in positive samples, while negative samples and a no-template control remained orange. These results were further substantiated through visualization of a laddering pattern of the PSR-amplified product in an agarose gel in positive cases and the absence of this pattern in no-template control and negative samples. The PSR assay was found to be highly specific, as it did not react with other putative canine pathogens (canine adenovirus 1 and canine distemper virus). The sensitivity of the newly developed PSR technique was compared with that of conventional PCR, real-time PCR and LAMP, using a serial tenfold dilution of canine parvovirus DNA. The detection limit of PSR was found to be at the femtogram level, which is comparable with that of real-time PCR and LAMP, which are ten times more sensitive than conventional PCR. The assay was validated using 90 clinical samples, of which 54 were found positive, while only 45 samples were positive in conventional PCR. This novel assay, which is fully compliant with the 'ASSURED' concept for disease diagnosis, provides a simple, rapid, specific, sensitive and cost-effective method for diagnosis of canine parvoviral enteritis in veterinary clinics.

  4. Selective visual attention to drive cognitive brain machine interfaces: from concepts to neurofeedback and rehabilitation applications

    Directory of Open Access Journals (Sweden)

    Elaine eAstrand

    2014-08-01

    Full Text Available Brain Machine Interfaces (BMI using motor cortical activity to drive an external effector like a screen cursor or a robotic arm have seen enormous success and proven their great rehabilitation potential. An emerging parallel effort is now directed to BMIs controlled by endogenous cognitive activity, also called cognitive BMIs. While more challenging, this approach opens new dimensions to the rehabilitation of cognitive disorders. In the present work, we focus on BMIs driven by visuospatial attention signals and we provide a critical review of these studies in the light of the accumulated knowledge about the psychophysics, anatomy and neurophysiology of visual spatial attention. Importantly, we provide a unique comparative overview of the several studies, ranging from noninvasive to invasive human and non-human primates studies, that decode attention-related information from ongoing neuronal activity. We discuss these studies in the light of the challenges attention-driven cognitive BMIs have to face. In a second part of the review, we discuss past and current attention-based neurofeedback studies, describing both the covert effects of neurofeedback onto neuronal activity and its overt behavioral effects. Importantly, we compare neurofeedback studies based on the amplitude of cortical activity to studies based on the enhancement of cortical information content. Last, we discuss several lines of future research and applications for attention-driven cognitive BCIs, including the rehabilitation of cognitive deficits, restored communication in locked-in patients, and open-field applications for enhanced cognition in normal subjects. The core motivation of this work is the key idea that the improvement of current cognitive BMIs for therapeutic and open field applications needs to be grounded in a proper interdisciplinary understanding of the physiology of the cognitive function of interest, be it spatial attention, working memory or any other

  5. Evaluation of the Effectiveness of a Tablet Computer Application (App) in Helping Students with Visual Impairments Solve Mathematics Problems

    Science.gov (United States)

    Beal, Carole R.; Rosenblum, L. Penny

    2018-01-01

    Introduction: The authors examined a tablet computer application (iPad app) for its effectiveness in helping students studying prealgebra to solve mathematical word problems. Methods: Forty-three visually impaired students (that is, those who are blind or have low vision) completed eight alternating mathematics units presented using their…

  6. Application and API for Real-time Visualization of Ground-motions and Tsunami

    Science.gov (United States)

    Aoi, S.; Kunugi, T.; Suzuki, W.; Kubo, T.; Nakamura, H.; Azuma, H.; Fujiwara, H.

    2015-12-01

    limited and it is not practical to regularly visualize all the data. The application has automatic starting (pop-up) function triggered by EEW. Similar WebAPI and application for tsunami are being prepared using the pressure data recorded by dense offshore observation network (S-net), which is under construction along the Japan Trench.

  7. CRISPR/Cas9 Genome Editing: A Promising Tool for Therapeutic Applications of Induced Pluripotent Stem Cells.

    Science.gov (United States)

    Zhang, Yanli; Sastre, Danuta; Wang, Feng

    2018-01-01

    Induced pluripotent stem cells hold tremendous potential for biological and therapeutic applications. The development of efficient technologies for targeted genome alteration of stem cells in disease models is a prerequisite for utilizing stem cells to their full potential. The revolutionary technology for genome editing known as the clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 9 (Cas9) system is recently recognized as a powerful tool for editing DNA at specific loci. The ease of use of the CRISPR-Cas9 technology will allow us to improve our understanding of genomic variation in disease processes via cellular and animal models. More recently, this system was modified to repress (CRISPR interference, CRISPRi) or activate (CRISPR activation, CRISPRa) gene expression without alterations in the DNA, which amplified the scope of applications of CRISPR systems for stem cell biology. Here, we highlight latest advances of CRISPR-associated applications in human pluripotent stem cells. The challenges and future prospects of CRISPR-based systems for human research are also discussed. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  8. Data-Proximate Analysis and Visualization in the Cloud using Cloudstream, an Open-Source Application Streaming Technology Stack

    Science.gov (United States)

    Fisher, W. I.

    2017-12-01

    The rise in cloud computing, coupled with the growth of "Big Data", has lead to a migration away from local scientific data storage. The increasing size of remote scientific data sets increase, however, makes it difficult for scientists to subject them to large-scale analysis and visualization. These large datasets can take an inordinate amount of time to download; subsetting is a potential solution, but subsetting services are not yet ubiquitous. Data providers may also pay steep prices, as many cloud providers meter data based on how much data leaves their cloud service. The solution to this problem is a deceptively simple one; move data analysis and visualization tools to the cloud, so that scientists may perform data-proximate analysis and visualization. This results in increased transfer speeds, while egress costs are lowered or completely eliminated. Moving standard desktop analysis and visualization tools to the cloud is enabled via a technique called "Application Streaming". This technology allows a program to run entirely on a remote virtual machine while still allowing for interactivity and dynamic visualizations. When coupled with containerization technology such as Docker, we are able to easily deploy legacy analysis and visualization software to the cloud whilst retaining access via a desktop, netbook, a smartphone, or the next generation of hardware, whatever it may be. Unidata has created a Docker-based solution for easily adapting legacy software for Application Streaming. This technology stack, dubbed Cloudstream, allows desktop software to run in the cloud with little-to-no effort. The docker container is configured by editing text files, and the legacy software does not need to be modified in any way. This work will discuss the underlying technologies used by Cloudstream, and outline how to use Cloudstream to run and access an existing desktop application to the cloud.

  9. The Human Genome Project: applications in the diagnosis and treatment of neurologic disease.

    Science.gov (United States)

    Evans, G A

    1998-10-01

    The Human Genome Project (HGP), an international program to decode the entire DNA sequence of the human genome in 15 years, represents the largest biological experiment ever conducted. This set of information will contain the blueprint for the construction and operation of a human being. While the primary driving force behind the genome project is the potential to vastly expand the amount of genetic information available for biomedical research, the ramifications for other fields of study in biological research, the biotechnology and pharmaceutical industry, our understanding of evolution, effects on agriculture, and implications for bioethics are likely to be profound.

  10. Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering.

    Science.gov (United States)

    Wang, Harris H; Church, George M

    2011-01-01

    Engineering at the scale of whole genomes requires fundamentally new molecular biology tools. Recent advances in recombineering using synthetic oligonucleotides enable the rapid generation of mutants at high efficiency and specificity and can be implemented at the genome scale. With these techniques, libraries of mutants can be generated, from which individuals with functionally useful phenotypes can be isolated. Furthermore, populations of cells can be evolved in situ by directed evolution using complex pools of oligonucleotides. Here, we discuss ways to utilize these multiplexed genome engineering methods, with special emphasis on experimental design and implementation. Copyright © 2011 Elsevier Inc. All rights reserved.

  11. Discrete Frenet frame, inflection point solitons, and curve visualization with applications to folded proteins

    Science.gov (United States)

    Hu, Shuangwei; Lundgren, Martin; Niemi, Antti J.

    2011-06-01

    We develop a transfer matrix formalism to visualize the framing of discrete piecewise linear curves in three-dimensional space. Our approach is based on the concept of an intrinsically discrete curve. This enables us to more effectively describe curves that in the limit where the length of line segments vanishes approach fractal structures in lieu of continuous curves. We verify that in the case of differentiable curves the continuum limit of our discrete equation reproduces the generalized Frenet equation. In particular, we draw attention to the conceptual similarity between inflection points where the curvature vanishes and topologically stable solitons. As an application we consider folded proteins, their Hausdorff dimension is known to be fractal. We explain how to employ the orientation of Cβ carbons of amino acids along a protein backbone to introduce a preferred framing along the backbone. By analyzing the experimentally resolved fold geometries in the Protein Data Bank we observe that this Cβ framing relates intimately to the discrete Frenet framing. We also explain how inflection points (a.k.a. soliton centers) can be located in the loops and clarify their distinctive rôle in determining the loop structure of folded proteins.

  12. Physiologically based pharmacokinetic modeling using microsoft excel and visual basic for applications.

    Science.gov (United States)

    Marino, Dale J

    2005-01-01

    Abstract Physiologically based pharmacokinetic (PBPK) models are mathematical descriptions depicting the relationship between external exposure and internal dose. These models have found great utility for interspecies extrapolation. However, specialized computer software packages, which are not widely distributed, have typically been used for model development and utilization. A few physiological models have been reported using more widely available software packages (e.g., Microsoft Excel), but these tend to include less complex processes and dose metrics. To ascertain the capability of Microsoft Excel and Visual Basis for Applications (VBA) for PBPK modeling, models for styrene, vinyl chloride, and methylene chloride were coded in Advanced Continuous Simulation Language (ACSL), Excel, and VBA, and simulation results were compared. For styrene, differences between ACSL and Excel or VBA compartment concentrations and rates of change were less than +/-7.5E-10 using the same numerical integration technique and time step. Differences using VBA fixed step or ACSL Gear's methods were generally Excel and VBA PBPK model dose metrics differed by no more than -0.013% or -0.23%, respectively, from ACSL results. These differences are likely attributable to different step sizes rather than different numerical integration techniques. These results indicate that Microsoft Excel and VBA can be useful tools for utilizing PBPK models, and given the availability of these software programs, it is hoped that this effort will help facilitate the use and investigation of PBPK modeling.

  13. Imaging of postthalamic visual fiber tracts by anisotropic diffusion weighted MRI and diffusion tensor imaging: principles and applications

    International Nuclear Information System (INIS)

    Reinges, Marcus H.T.; Schoth, Felix; Coenen, Volker A.; Krings, Timo

    2004-01-01

    Diffusion weighted MRI offers the possibility to study the course of the cerebral white matter tracts. In the present manuscript, the basics, the technique and the limitations of diffusion tensor imaging and anisotropic diffusion weighted MRI are presented and their applications in various neurological and neurosurgical diseases are discussed with special emphasis on the visual system. A special focus is laid on the combination of fiber tract imaging, anatomical imaging and functional MRI for presurgical planning and intraoperative neuronavigation of lesions near the visual system

  14. Neural correlates of olfactory and visual memory performance in 3D-simulated mazes after intranasal insulin application.

    Science.gov (United States)

    Brünner, Yvonne F; Rodriguez-Raecke, Rea; Mutic, Smiljana; Benedict, Christian; Freiherr, Jessica

    2016-10-01

    This fMRI study intended to establish 3D-simulated mazes with olfactory and visual cues and examine the effect of intranasally applied insulin on memory performance in healthy subjects. The effect of insulin on hippocampus-dependent brain activation was explored using a double-blind and placebo-controlled design. Following intranasal administration of either insulin (40IU) or placebo, 16 male subjects participated in two experimental MRI sessions with olfactory and visual mazes. Each maze included two separate runs. The first was an encoding maze during which subjects learned eight olfactory or eight visual cues at different target locations. The second was a recall maze during which subjects were asked to remember the target cues at spatial locations. For eleven included subjects in the fMRI analysis we were able to validate brain activation for odor perception and visuospatial tasks. However, we did not observe an enhancement of declarative memory performance in our behavioral data or hippocampal activity in response to insulin application in the fMRI analysis. It is therefore possible that intranasal insulin application is sensitive to the methodological variations e.g. timing of task execution and dose of application. Findings from this study suggest that our method of 3D-simulated mazes is feasible for studying neural correlates of olfactory and visual memory performance. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. Orientation-modulated attention effect on visual evoked potential: Application for PIN system using brain-computer interface.

    Science.gov (United States)

    Wilaiprasitporn, Theerawit; Yagi, Tohru

    2015-01-01

    This research demonstrates the orientation-modulated attention effect on visual evoked potential. We combined this finding with our previous findings about the motion-modulated attention effect and used the result to develop novel visual stimuli for a personal identification number (PIN) application based on a brain-computer interface (BCI) framework. An electroencephalography amplifier with a single electrode channel was sufficient for our application. A computationally inexpensive algorithm and small datasets were used in processing. Seven healthy volunteers participated in experiments to measure offline performance. Mean accuracy was 83.3% at 13.9 bits/min. Encouraged by these results, we plan to continue developing the BCI-based personal identification application toward real-time systems.

  16. Updates on genome-wide association findings in eating disorders and future application to precision medicine.

    Science.gov (United States)

    Breithaupt, Lauren; Hubel, Christopher; Bulik, Cynthia M

    2018-02-22

    Heterogeneity, frequent diagnostic fluctuation across presentations, and global concerns with the absence of effective treatments all encourage science that moves the field toward individualized or precision medicine in eating disorders. We review recent advances in psychiatric genetics focusing on genome-wide association studies (GWAS) in eating disorders and enumerate the prospects and challenges of a genomics-driven approach towards personalized intervention. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  17. Isolation and characterization of repeat elements of the oak genome and their application in population analysis

    International Nuclear Information System (INIS)

    Fluch, S.; Burg, K.

    1998-01-01

    Four minisatellite sequence elements have been identified and isolated from the genome of the oak species Quercus petraea and Quercus robur. Minisatellites 1 and 2 are putative members of repeat families, while minisatellites 3 and 4 show repeat length variation among individuals of test populations. A 590 base pair (bp) long element has also been identified which reveals individual-specific autoradiographic patterns when used as probe in Southern hybridisations of genomic oak DNA. (author)

  18. Development of Highly Informative Genome-Wide Single Sequence Repeat Markers for Breeding Applications in Sesame and Construction of a Web Resource: SisatBase

    Directory of Open Access Journals (Sweden)

    Komivi Dossa

    2017-08-01

    Full Text Available The sequencing of the full nuclear genome of sesame (Sesamum indicum L. provides the platform for functional analyses of genome components and their application in breeding programs. Although the importance of microsatellites markers or simple sequence repeats (SSR in crop genotyping, genetics, and breeding applications is well established, only a little information exist concerning SSRs at the whole genome level in sesame. In addition, SSRs represent a suitable marker type for sesame molecular breeding in developing countries where it is mainly grown. In this study, we identified 138,194 genome-wide SSRs of which 76.5% were physically mapped onto the 13 pseudo-chromosomes. Among these SSRs, up to three primers pairs were supplied for 101,930 SSRs and used to in silico amplify the reference genome together with two newly sequenced sesame accessions. A total of 79,957 SSRs (78% were polymorphic between the three genomes thereby suggesting their promising use in different genomics-assisted breeding applications. From these polymorphic SSRs, 23 were selected and validated to have high polymorphic potential in 48 sesame accessions from different growing areas of Africa. Furthermore, we have developed an online user-friendly database, SisatBase (http://www.sesame-bioinfo.org/SisatBase/, which provides free access to SSRs data as well as an integrated platform for functional analyses. Altogether, the reference SSR and SisatBase would serve as useful resources for genetic assessment, genomic studies, and breeding advancement in sesame, especially in developing countries.

  19. epidemix—An interactive multi-model application for teaching and visualizing infectious disease transmission

    Directory of Open Access Journals (Sweden)

    Ulrich Muellner

    2018-06-01

    Full Text Available Mathematical models of disease transmission are used to improve our understanding of patterns of infection and to identify factors influencing them. During recent public and animal health crises, such as pandemic influenza, Ebola, Zika, foot-and-mouth disease, models have made important contributions in addressing policy questions, especially through the assessment of the trajectory and scale of outbreaks, and the evaluation of control interventions. However, their mathematical formulation means that they may appear as a “black box” to those without the appropriate mathematical background. This may lead to a negative perception of their utility for guiding policy, and generate expectations, which are not in line with what these models can deliver. It is therefore important for policymakers, as well as public health and animal health professionals and researchers who collaborate with modelers and use results generated by these models for policy development or research purpose, to understand the key concepts and assumptions underlying these models.The software application epidemix (http://shinyapps.rvc.ac.uk presented here aims to make mathematical models of disease transmission accessible to a wider audience of users. By developing a visual interface for a suite of eight models, users can develop an understanding of the impact of various modelling assumptions – especially mixing patterns – on the trajectory of an epidemic and the impact of control interventions, without having to directly deal with the complexity of mathematical equations and programming languages. Models are compartmental or individual-based, deterministic or stochastic, and assume homogeneous or heterogeneous-mixing patterns (with the probability of transmission depending on the underlying structure of contact networks, or the spatial distribution of hosts. This application is intended to be used by scientists teaching mathematical modelling short courses to non

  20. Application of visual servoing for grasping and placing operation in slaughterhouse

    DEFF Research Database (Denmark)

    Wu, Haiyan; Andersen, Thomas Timm; Andersen, Nils Axel

    2017-01-01

    of the target the color information provided by a visual sensor is utilized. The control command for the robot is generated based on the real time visual feedback. An industrial robot arm UR10 is applied to complete the operation. A lab-scale experimental setup is constructed for system validation...

  1. Based on matlab 3d visualization programming in the application of the uranium exploration

    International Nuclear Information System (INIS)

    Qi Jianquan

    2012-01-01

    Combined geological theory, geophysical curve and Matlab programming three dimensional visualization applied to the production of uranium exploration. With a simple Matlab programming, numerical processing and graphical visualization of convenient features, and effective in identifying ore bodies, recourse to ore, ore body delineation of the scope of analysis has played the role of sedimentary environment. (author)

  2. CompaGB: An open framework for genome browsers comparison

    Directory of Open Access Journals (Sweden)

    Chiapello Hélène

    2011-05-01

    Full Text Available Abstract Background Tools to visualize and explore genomes hold a central place in genomics and the diversity of genome browsers has increased dramatically over the last few years. It often turns out to be a daunting task to compare and choose a well-adapted genome browser, as multidisciplinary knowledge is required to carry out this task and the number of tools, functionalities and features are overwhelming. Findings To assist in this task, we propose a community-based framework based on two cornerstones: (i the implementation of industry promoted software qualification method (QSOS adapted for genome browser evaluations, and (ii a web resource providing numerous facilities either for visualizing comparisons or performing new evaluations. We formulated 60 criteria specifically for genome browsers, and incorporated another 65 directly from QSOS's generic section. Those criteria aim to answer versatile needs, ranging from a biologist whose interest primarily lies into user-friendly and informative functionalities, a bioinformatician who wants to integrate the genome browser into a wider framework, or a computer scientist who might choose a software according to more technical features. We developed a dedicated web application to enrich the existing QSOS functionalities (weighting of criteria, user profile with features of interest to a community-based framework: easy management of evolving data, user comments... Conclusions The framework is available at http://genome.jouy.inra.fr/CompaGB. It is open to anyone who wishes to participate in the evaluations. It helps the scientific community to (1 choose a genome browser that would better fit their particular project, (2 visualize features comparatively with easily accessible formats, such as tables or radar plots and (3 perform their own evaluation against the defined criteria. To illustrate the CompaGB functionalities, we have evaluated seven genome browsers according to the implemented methodology

  3. Implementation of a patient-facing genomic test report in the electronic health record using a web-application interface.

    Science.gov (United States)

    Williams, Marc S; Kern, Melissa S; Lerch, Virginia R; Billet, Jonathan; Williams, Janet L; Moore, Gregory J

    2018-05-30

    Genomic medicine is emerging into clinical care. Communication of genetic laboratory results to patients and providers is hampered by the complex technical nature of the laboratory reports. This can lead to confusion and misinterpretation of the results resulting in inappropriate care. Patients usually do not receive a copy of the report leading to further opportunities for miscommunication. To address these problems, interpretive reports were created using input from the intended end users, patients and providers. This paper describes the technical development and deployment of the first patient-facing genomic test report (PGR) within an electronic health record (EHR) ecosystem using a locally developed standards-based web-application interface. A patient-facing genomic test report with a companion provider report was configured for implementation within the EHR using a locally developed software platform, COMPASS™. COMPASS™ is designed to manage secure data exchange, as well as patient and provider access to patient reported data capture and clinical display tools. COMPASS™ is built using a Software as a Service (SaaS) approach which exposes an API that apps can interact with. An authoring tool was developed that allowed creation of patient-specific PGRs and the accompanying provider reports. These were converted to a format that allowed them to be presented in the patient portal and EHR respectively using the existing COMPASS™ interface thus allowing patients, caregivers and providers access to individual reports designed for the intended end user. The PGR as developed was shown to enhance patient and provider communication around genomic results. It is built on current standards but is designed to support integration with other tools and be compatible with emerging opportunities such as SMART on FHIR. This approach could be used to support genomic return of results as the tool is scalable and generalizable.

  4. Efficient privacy-preserving string search and an application in genomics.

    Science.gov (United States)

    Shimizu, Kana; Nuida, Koji; Rätsch, Gunnar

    2016-06-01

    Personal genomes carry inherent privacy risks and protecting privacy poses major social and technological challenges. We consider the case where a user searches for genetic information (e.g. an allele) on a server that stores a large genomic database and aims to receive allele-associated information. The user would like to keep the query and result private and the server the database. We propose a novel approach that combines efficient string data structures such as the Burrows-Wheeler transform with cryptographic techniques based on additive homomorphic encryption. We assume that the sequence data is searchable in efficient iterative query operations over a large indexed dictionary, for instance, from large genome collections and employing the (positional) Burrows-Wheeler transform. We use a technique called oblivious transfer that is based on additive homomorphic encryption to conceal the sequence query and the genomic region of interest in positional queries. We designed and implemented an efficient algorithm for searching sequences of SNPs in large genome databases. During search, the user can only identify the longest match while the server does not learn which sequence of SNPs the user queried. In an experiment based on 2184 aligned haploid genomes from the 1000 Genomes Project, our algorithm was able to perform typical queries within [Formula: see text] 4.6 s and [Formula: see text] 10.8 s for client and server side, respectively, on laptop computers. The presented algorithm is at least one order of magnitude faster than an exhaustive baseline algorithm. https://github.com/iskana/PBWT-sec and https://github.com/ratschlab/PBWT-sec shimizu-kana@aist.go.jp or Gunnar.Ratsch@ratschlab.org Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  5. SIGMA: A System for Integrative Genomic Microarray Analysis of Cancer Genomes

    Directory of Open Access Journals (Sweden)

    Davies Jonathan J

    2006-12-01

    Full Text Available Abstract Background The prevalence of high resolution profiling of genomes has created a need for the integrative analysis of information generated from multiple methodologies and platforms. Although the majority of data in the public domain are gene expression profiles, and expression analysis software are available, the increase of array CGH studies has enabled integration of high throughput genomic and gene expression datasets. However, tools for direct mining and analysis of array CGH data are limited. Hence, there is a great need for analytical and display software tailored to cross platform integrative analysis of cancer genomes. Results We have created a user-friendly java application to facilitate sophisticated visualization and analysis such as cross-tumor and cross-platform comparisons. To demonstrate the utility of this software, we assembled array CGH data representing Affymetrix SNP chip, Stanford cDNA arrays and whole genome tiling path array platforms for cross comparison. This cancer genome database contains 267 profiles from commonly used cancer cell lines representing 14 different tissue types. Conclusion In this study we have developed an application for the visualization and analysis of data from high resolution array CGH platforms that can be adapted for analysis of multiple types of high throughput genomic datasets. Furthermore, we invite researchers using array CGH technology to deposit both their raw and processed data, as this will be a continually expanding database of cancer genomes. This publicly available resource, the System for Integrative Genomic Microarray Analysis (SIGMA of cancer genomes, can be accessed at http://sigma.bccrc.ca.

  6. Evaluation of different sources of DNA for use in genome wide studies and forensic application.

    Science.gov (United States)

    Al Safar, Habiba S; Abidi, Fatima H; Khazanehdari, Kamal A; Dadour, Ian R; Tay, Guan K

    2011-02-01

    In the field of epidemiology, Genome-Wide Association Studies (GWAS) are commonly used to identify genetic predispositions of many human diseases. Large repositories housing biological specimens for clinical and genetic investigations have been established to store material and data for these studies. The logistics of specimen collection and sample storage can be onerous, and new strategies have to be explored. This study examines three different DNA sources (namely, degraded genomic DNA, amplified degraded genomic DNA and amplified extracted DNA from FTA card) for GWAS using the Illumina platform. No significant difference in call rate was detected between amplified degraded genomic DNA extracted from whole blood and amplified DNA retrieved from FTA™ cards. However, using unamplified-degraded genomic DNA reduced the call rate to a mean of 42.6% compared to amplified DNA extracted from FTA card (mean of 96.6%). This study establishes the utility of FTA™ cards as a viable storage matrix for cells from which DNA can be extracted to perform GWAS analysis.

  7. Three invariant Hi-C interaction patterns: Applications to genome assembly.

    Science.gov (United States)

    Oddes, Sivan; Zelig, Aviv; Kaplan, Noam

    2018-06-01

    Assembly of reference-quality genomes from next-generation sequencing data is a key challenge in genomics. Recently, we and others have shown that Hi-C data can be used to address several outstanding challenges in the field of genome assembly. This principle has since been developed in academia and industry, and has been used in the assembly of several major genomes. In this paper, we explore the central principles underlying Hi-C-based assembly approaches, by quantitatively defining and characterizing three invariant Hi-C interaction patterns on which these approaches can build: Intrachromosomal interaction enrichment, distance-dependent interaction decay and local interaction smoothness. Specifically, we evaluate to what degree each invariant pattern holds on a single locus level in different species, cell types and Hi-C map resolutions. We find that these patterns are generally consistent across species and cell types but are affected by sequencing depth, and that matrix balancing improves consistency of loci with all three invariant patterns. Finally, we overview current Hi-C-based assembly approaches in light of these invariant patterns and demonstrate how local interaction smoothness can be used to easily detect scaffolding errors in extremely sparse Hi-C maps. We suggest that simultaneously considering all three invariant patterns may lead to better Hi-C-based genome assembly methods. Copyright © 2018 Elsevier Inc. All rights reserved.

  8. Development and application of visual support module for remote operator in 3D virtual environment

    International Nuclear Information System (INIS)

    Choi, Kyung Hyun; Cho, Soo Jeong; Yang, Kyung Boo; Bae, Chang Hyun

    2006-02-01

    In this research, the 3D graphic environment was developed for remote operation, and included the visual support module. The real operation environment was built by employing a experiment robot, and also the identical virtual model was developed. The well-designed virtual models can be used to retrieve the necessary conditions for developing the devices and processes. The integration of 3D virtual models, the experimental operation environment, and the visual support module was used for evaluating the operation efficiency and accuracy by applying different methods such as only monitor image and with visual support module

  9. Development and application of visual support module for remote operator in 3D virtual environment

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Kyung Hyun; Cho, Soo Jeong; Yang, Kyung Boo [Cheju Nat. Univ., Jeju (Korea, Republic of); Bae, Chang Hyun [Pusan Nat. Univ., Busan (Korea, Republic of)

    2006-02-15

    In this research, the 3D graphic environment was developed for remote operation, and included the visual support module. The real operation environment was built by employing a experiment robot, and also the identical virtual model was developed. The well-designed virtual models can be used to retrieve the necessary conditions for developing the devices and processes. The integration of 3D virtual models, the experimental operation environment, and the visual support module was used for evaluating the operation efficiency and accuracy by applying different methods such as only monitor image and with visual support module.

  10. A portable Si/CdTe Compton camera and its applications to the visualization of radioactive substances

    Energy Technology Data Exchange (ETDEWEB)

    Takeda, Shin' ichiro, E-mail: takeda@astro.isas.jaxa.jp [Institute of Space and Astronautical Science (ISAS)/JAXA, 3-1-1 Yoshinodai, Chuo-ku, Sagamihara, Kanagawa 252-5210 (Japan); Harayama, Atsushi [Institute of Space and Astronautical Science (ISAS)/JAXA, 3-1-1 Yoshinodai, Chuo-ku, Sagamihara, Kanagawa 252-5210 (Japan); Ichinohe, Yuto [Institute of Space and Astronautical Science (ISAS)/JAXA, 3-1-1 Yoshinodai, Chuo-ku, Sagamihara, Kanagawa 252-5210 (Japan); University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033 (Japan); Odaka, Hirokazu [Institute of Space and Astronautical Science (ISAS)/JAXA, 3-1-1 Yoshinodai, Chuo-ku, Sagamihara, Kanagawa 252-5210 (Japan); Watanabe, Shin; Takahashi, Tadayuki [Institute of Space and Astronautical Science (ISAS)/JAXA, 3-1-1 Yoshinodai, Chuo-ku, Sagamihara, Kanagawa 252-5210 (Japan); University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033 (Japan); Tajima, Hiroyasu [Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601 (Japan); Genba, Kei; Matsuura, Daisuke; Ikebuchi, Hiroshi; Kuroda, Yoshikatsu [Mitsubishi Heavy Industries, 1200 Higashi-Tanaka, Komaki, Aichi 485-8561 (Japan); Tomonaka, Tetsuya [Mitsubishi Heavy Industry, 2-1-1 Shinhama, Arai-cho, Takasago, Hyogo 676-8686 (Japan)

    2015-07-01

    Gamma-ray imagers with the potential for visualizing the distribution of radioactive materials are required in the fields of astrophysics, medicine, nuclear applications, and homeland security. Based on the technology of the Si/CdTe Compton camera, we have manufactured the first commercial Compton camera for practical use. Through field tests in Fukushima, we demonstrated that the camera is capable of hot spot detection and the evaluation of radioactive decontamination.

  11. A portable Si/CdTe Compton camera and its applications to the visualization of radioactive substances

    International Nuclear Information System (INIS)

    Takeda, Shin'ichiro; Harayama, Atsushi; Ichinohe, Yuto; Odaka, Hirokazu; Watanabe, Shin; Takahashi, Tadayuki; Tajima, Hiroyasu; Genba, Kei; Matsuura, Daisuke; Ikebuchi, Hiroshi; Kuroda, Yoshikatsu; Tomonaka, Tetsuya

    2015-01-01

    Gamma-ray imagers with the potential for visualizing the distribution of radioactive materials are required in the fields of astrophysics, medicine, nuclear applications, and homeland security. Based on the technology of the Si/CdTe Compton camera, we have manufactured the first commercial Compton camera for practical use. Through field tests in Fukushima, we demonstrated that the camera is capable of hot spot detection and the evaluation of radioactive decontamination

  12. Modern Geodata Management: Application of Interdisciplinary Interpretation and Visualization in Central America

    Directory of Open Access Journals (Sweden)

    T. Damm

    2009-01-01

    Full Text Available In the last years new methods of data acquisition and processing in geosciences, inspired by growing computer performance, have led to an increased amount of data, and this development will proceed surely. In this paper we present the conception and technical realization of an interdisciplinary research group's geodata management as a combination of a metadata catalog together with web mapping technology. Clearly related with the storage and retrieval of different datasets is the need of visualization. 3D visualization in geoscientific interpretation is a useful tool, if numerous, heterogenic datasets have to be visualized at the same time. Moreover, advanced sensing technology often generates native three-dimensional datasets. Using a case study from the Collaborative Research Centre “SFB 574”, we present the possibilities of our stereoscopic projection system and want to explain the benefit of 3D visualization for research in general and university education in particular, as low-cost systems become available nowadays.

  13. Volume of visual field assessed with kinetic perimetry and its application to static perimetry

    Directory of Open Access Journals (Sweden)

    Christoforidis JB

    2011-04-01

    Full Text Available John B ChristoforidisCollege of Medicine, The Ohio State University, Columbus, OH, USABackground: The purpose of this study was to quantify the volume of the kinetic visual field with a single unit that accounts for visual field area and differential luminance sensitivity.Methods: Kinetic visual field perimetry was performed with a Goldmann perimeter using I4e, I3e, I2e, and I1e targets. The visual fields of 25 normal volunteers (17 women, eight men of mean age 33.9 ± 10.1 (range 17–64 years were obtained and digitized. Isopter areas were measured with a method devised to correct cartographic distortion due to polar projection inherent in perimetry and are expressed in steradians. The third dimension of each isopter represents sensitivity to target luminance and was calculated as log (target luminance-1. If luminance is expressed in cd/m2, the values for the third dimension are 0.5 for I4e, 1.0 for I3e, 1.5 for I2e, and 2.0 for I1e. The resulting unit is a steradian (log 103 (cd/m2-1 which is referred to as a Goldmann. In addition, the visual fields of four patients with representative visual defect patterns were examined and compared with normal subjects.Results: Mean isopter areas for normal subjects were 3.092 ± 0.242 steradians for I4e, 2.349 ± 0.280 steradians for I3e, 1.242 ± 0.263 steradians for I2e, and 0.251 ± 0.114 steradians for the I1e target. Isopter volumes were 1.546 ± 0.121 Goldmanns for the I4e target, 1.174 ± 0.140 Goldmanns for I3e, 0.621 ± 0.131 Goldmanns for I2e, and 0.126 ± 0.057 Goldmanns for I1e. The total mean visual field volume in our study for the I target was 3.467 ± 0.371 Goldmanns.Conclusion: The volume of the island of vision may be used to quantify a visual field with a single value which contains information about both visual field extension and differential luminance sensitivity. This technique may be used to assess the progression or stability of visual field defects over time. A similar method may

  14. BoreholeAR: A mobile tablet application for effective borehole database visualization using an augmented reality technology

    Science.gov (United States)

    Lee, Sangho; Suh, Jangwon; Park, Hyeong-Dong

    2015-03-01

    Boring logs are widely used in geological field studies since the data describes various attributes of underground and surface environments. However, it is difficult to manage multiple boring logs in the field as the conventional management and visualization methods are not suitable for integrating and combining large data sets. We developed an iPad application to enable its user to search the boring log rapidly and visualize them using the augmented reality (AR) technique. For the development of the application, a standard borehole database appropriate for a mobile-based borehole database management system was designed. The application consists of three modules: an AR module, a map module, and a database module. The AR module superimposes borehole data on camera imagery as viewed by the user and provides intuitive visualization of borehole locations. The map module shows the locations of corresponding borehole data on a 2D map with additional map layers. The database module provides data management functions for large borehole databases for other modules. Field survey was also carried out using more than 100,000 borehole data.

  15. A medical application integrating remote 3D visualization tools to access picture archiving and communication system on mobile devices.

    Science.gov (United States)

    He, Longjun; Ming, Xing; Liu, Qian

    2014-04-01

    With computing capability and display size growing, the mobile device has been used as a tool to help clinicians view patient information and medical images anywhere and anytime. However, for direct interactive 3D visualization, which plays an important role in radiological diagnosis, the mobile device cannot provide a satisfactory quality of experience for radiologists. This paper developed a medical system that can get medical images from the picture archiving and communication system on the mobile device over the wireless network. In the proposed application, the mobile device got patient information and medical images through a proxy server connecting to the PACS server. Meanwhile, the proxy server integrated a range of 3D visualization techniques, including maximum intensity projection, multi-planar reconstruction and direct volume rendering, to providing shape, brightness, depth and location information generated from the original sectional images for radiologists. Furthermore, an algorithm that changes remote render parameters automatically to adapt to the network status was employed to improve the quality of experience. Finally, performance issues regarding the remote 3D visualization of the medical images over the wireless network of the proposed application were also discussed. The results demonstrated that this proposed medical application could provide a smooth interactive experience in the WLAN and 3G networks.

  16. Design of Application Software : Visualization of Electronic Encyclopedia with Multimedia Basis

    International Nuclear Information System (INIS)

    Laggoune, Hayet; Madenda, Sarifuddin; Gunawan, Teddy

    2001-01-01

    This paper discusses a multimedia program which visualizes an electronic dictionary / encyclopedia. This program uses different types of files such as text, sound, graphic and video. These files are related to each corresponding word as defined in the dictionary. This software is easy to use and allow searching, adding, editing or deleting data from the dictionary. It can also visualizes the word contain as text, graphic, sound or video

  17. Clinical application of multifocal visual evoked potentials in children with epilepsy caused by intracranial disease

    International Nuclear Information System (INIS)

    Yukawa, Eiichi; Kim, Yeong-Jin; Kawasaki, Kensuke; Yoshii, Toshiaki; Hara, Yoshiaki

    2006-01-01

    We investigated whether visual field defects could be objectively evaluated using multifocal visual evoked potential (m-VEP) in two children with epilepsy caused by intracranial disease in whom it was difficult to measure the visual field. To determine normal waves in m-VEP, recording was performed using a visual evoked response imaging system (VERIS) Junior Science program (Mayo, Aichi, Japan) in 20 healthy children (20 eyes) peak latency and amplitude were used for assessment. In the two children with epilepsy, m-VEPs were recorded, and compared with the results of static perimetry or the lesions observed by Magnetic Resonance Imaging (MRI). In the 20 healthy children, there was no significant difference in the peak latency or amplitude among 4 quadrants by one-way analysis of variance. m-VEP in the children with epilepsy showed abnormal waves, corresponding to the visual field defects in the static perimetry or the lesions observed by MRI. Objective evaluation of visual field defects using m-VEP may be useful in children with epilepsy caused by intracranial disease in whom kinetic/static perimetry as a subjective examination is difficult. (author)

  18. Performance of an iPad Application to Detect Moderate and Advanced Visual Field Loss in Nepal.

    Science.gov (United States)

    Johnson, Chris A; Thapa, Suman; George Kong, Yu Xiang; Robin, Alan L

    2017-10-01

    To evaluate the accuracy and efficiency of Visual Fields Easy (VFE), a free iPad app, for performing suprathreshold perimetric screening. Prospective, cross-sectional validation study. We performed screening visual fields using a calibrated iPad 2 with the VFE application on 206 subjects (411 eyes): 210 normal (NL), 183 glaucoma (GL), and 18 diabetic retinopathy (DR) at Tilganga Institute of Ophthalmology, Kathmandu, Nepal. We correlated the results with a Humphrey Field Analyzer using 24-2 SITA Standard tests on 373 of these eyes (198 NL, 160 GL, 15 DR). The number of missed locations on the VFE correlated with mean deviation (MD, r = 0.79), pattern standard deviation (PSD, r = 0.60), and number of locations that were worse than the 95% confidence limits for total deviation (r = 0.51) and pattern deviation (r = 0.68) using SITA Standard. iPad suprathreshold perimetry was able to detect most visual field deficits with moderate (MD of -6 to -12 dB) and advanced (MD worse than -12 dB) loss, but had greater difficulty in detecting early (MD better than -6 dB) loss, primarily owing to an elevated false-positive response rate. The average time to perform the Visual Fields Easy test was 3 minutes, 18 seconds (standard deviation = 16.88 seconds). The Visual Fields Easy test procedure is a portable, fast, effective procedure for detecting moderate and advanced visual field loss. Improvements are currently underway to monitor eye and head tracking during testing, reduce testing time, improve performance, and eliminate the need to touch the video screen surface. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Draft genome sequence of Pseudomonas corrugata, a phytopathogenic bacterium with potential industrial applications.

    Science.gov (United States)

    Licciardello, G; Jackson, R W; Bella, P; Strano, C P; Catara, A F; Arnold, D L; Venturi, V; Silby, M W; Catara, V

    2014-04-10

    Pseudomonas corrugata was first described as the causal agent of a tomato disease called 'pith necrosis' yet it is considered as a biological resource in various fields such as biocontrol of plant diseases and production of industrially promising microbial biopolymers (mcl-PHA). Here we report the first draft genome sequence of this species. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Application of CRISPR/Cas9 Genome Editing to Improve Recombinant Protein Production in CHO Cells

    DEFF Research Database (Denmark)

    Grav, Lise Marie; Julie la Cour Karottki, Karen; Lee, Jae Seong

    2017-01-01

    and yields. In this chapter, we present our protocol on how to use the genome editing tool Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) to knockout engineering target genes in CHO cells. As an example, we refer to the glutamine synthetase (GS...

  1. Direct extraction of genomic DNA from maize with aqueous ionic liquid buffer systems for applications in genetically modified organisms analysis.

    Science.gov (United States)

    Gonzalez García, Eric; Ressmann, Anna K; Gaertner, Peter; Zirbs, Ronald; Mach, Robert L; Krska, Rudolf; Bica, Katharina; Brunner, Kurt

    2014-12-01

    To date, the extraction of genomic DNA is considered a bottleneck in the process of genetically modified organisms (GMOs) detection. Conventional DNA isolation methods are associated with long extraction times and multiple pipetting and centrifugation steps, which makes the entire procedure not only tedious and complicated but also prone to sample cross-contamination. In recent times, ionic liquids have emerged as innovative solvents for biomass processing, due to their outstanding properties for dissolution of biomass and biopolymers. In this study, a novel, easily applicable, and time-efficient method for the direct extraction of genomic DNA from biomass based on aqueous-ionic liquid solutions was developed. The straightforward protocol relies on extraction of maize in a 10 % solution of ionic liquids in aqueous phosphate buffer for 5 min at room temperature, followed by a denaturation step at 95 °C for 10 min and a simple filtration to remove residual biopolymers. A set of 22 ionic liquids was tested in a buffer system and 1-ethyl-3-methylimidazolium dimethylphosphate, as well as the environmentally benign choline formate, were identified as ideal candidates. With this strategy, the quality of the genomic DNA extracted was significantly improved and the extraction protocol was notably simplified compared with a well-established method.

  2. CRISPR/Cas9 for Human Genome Engineering and Disease Research.

    Science.gov (United States)

    Xiong, Xin; Chen, Meng; Lim, Wendell A; Zhao, Dehua; Qi, Lei S

    2016-08-31

    The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system, a versatile RNA-guided DNA targeting platform, has been revolutionizing our ability to modify, manipulate, and visualize the human genome, which greatly advances both biological research and therapeutics development. Here, we review the current development of CRISPR/Cas9 technologies for gene editing, transcription regulation, genome imaging, and epigenetic modification. We discuss the broad application of this system to the study of functional genomics, especially genome-wide genetic screening, and to therapeutics development, including establishing disease models, correcting defective genetic mutations, and treating diseases.

  3. Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping

    Directory of Open Access Journals (Sweden)

    Harvey Steven P

    2007-03-01

    Full Text Available Abstract Background The facultative, intracellular bacterium Burkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease of humans and animals. We identified and categorized tandem repeat arrays and their distribution throughout the genome of B. pseudomallei strain K96243 in order to develop a genetic typing method for B. pseudomallei. We then screened 104 of the potentially polymorphic loci across a diverse panel of 31 isolates including B. pseudomallei, B. mallei and B. thailandensis in order to identify loci with varying degrees of polymorphism. A subset of these tandem repeat arrays were subsequently developed into a multiple-locus VNTR analysis to examine 66 B. pseudomallei and 21 B. mallei isolates from around the world, as well as 95 lineages from a serial transfer experiment encompassing ~18,000 generations. Results B. pseudomallei contains a preponderance of tandem repeat loci throughout its genome, many of which are duplicated elsewhere in the genome. The majority of these loci are composed of repeat motif lengths of 6 to 9 bp with 4 to 10 repeat units and are predominately located in intergenic regions of the genome. Across geographically diverse B. pseudomallei and B.mallei isolates, the 32 VNTR loci displayed between 7 and 28 alleles, with Nei's diversity values ranging from 0.47 and 0.94. Mutation rates for these loci are comparable (>10-5 per locus per generation to that of the most diverse tandemly repeated regions found in other less diverse bacteria. Conclusion The frequency, location and duplicate nature of tandemly repeated regions within the B. pseudomallei genome indicate that these tandem repeat regions may play a role in generating and maintaining adaptive genomic variation. Multiple-locus VNTR analysis revealed extensive diversity within the global isolate set containing B. pseudomallei and B. mallei, and it detected genotypic differences within clonal lineages of both species that were

  4. Application of High-performance Visual Analysis Methods to Laser Wakefield Particle Acceleration Data

    International Nuclear Information System (INIS)

    Rubel, Oliver; Prabhat, Mr.; Wu, Kesheng; Childs, Hank; Meredith, Jeremy; Geddes, Cameron G.R.; Cormier-Michel, Estelle; Ahern, Sean; Weber, Gunther H.; Messmer, Peter; Hagen, Hans; Hamann, Bernd; Bethel, E. Wes

    2008-01-01

    Our work combines and extends techniques from high-performance scientific data management and visualization to enable scientific researchers to gain insight from extremely large, complex, time-varying laser wakefield particle accelerator simulation data. We extend histogram-based parallel coordinates for use in visual information display as well as an interface for guiding and performing data mining operations, which are based upon multi-dimensional and temporal thresholding and data subsetting operations. To achieve very high performance on parallel computing platforms, we leverage FastBit, a state-of-the-art index/query technology, to accelerate data mining and multi-dimensional histogram computation. We show how these techniques are used in practice by scientific researchers to identify, visualize and analyze a particle beam in a large, time-varying dataset

  5. Visual Hallucinations Due to Rivastigmine Transdermal Patch Application in Alzheimer's Disease; The First Case Report

    Directory of Open Access Journals (Sweden)

    Yıldız Değirmenci

    2016-12-01

    Full Text Available Rivastigmine is a well-known dual acting acetylcholinesterase and butyrylcholinesterase inhibitor, which is effective on behavioral and psychiatric symptoms including hallucinations, as well as cognitive symptoms of dementia. The most common adverse effects of rivastigmine related to cholinergic stimulation in brain and peripheral tissues are gastrointestinal, cardiorespiratory, extrapyramidal, genitourinary, musculoskeletal symptoms, sleep disturbances, and skin irritations with the transdermal patch form in particular. Despite to the previous reports revealing the improving effects of the drug on hallucinations, we presented a-80 year old women with Alzheimer's disease suffering from visual hallucinations whose complaints began with rivastigmine treatment. Since the patient had recent memory disturbance without any behavioral and/or psychiatric symptoms before rivastigmine administration, and visual hallucinations disappeared with the discontinuation of the drug, visual hallucinations were attributed to rivastigmine.

  6. Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles.

    Science.gov (United States)

    Mustafin, Zakhar Sergeevich; Lashin, Sergey Alexandrovich; Matushkin, Yury Georgievich; Gunbin, Konstantin Vladimirovich; Afonnikov, Dmitry Arkadievich

    2017-01-27

    There are many available software tools for visualization and analysis of biological networks. Among them, Cytoscape ( http://cytoscape.org/ ) is one of the most comprehensive packages, with many plugins and applications which extends its functionality by providing analysis of protein-protein interaction, gene regulatory and gene co-expression networks, metabolic, signaling, neural as well as ecological-type networks including food webs, communities networks etc. Nevertheless, only three plugins tagged 'network evolution' found in Cytoscape official app store and in literature. We have developed a new Cytoscape 3.0 application Orthoscape aimed to facilitate evolutionary analysis of gene networks and visualize the results. Orthoscape aids in analysis of evolutionary information available for gene sets and networks by highlighting: (1) the orthology relationships between genes; (2) the evolutionary origin of gene network components; (3) the evolutionary pressure mode (diversifying or stabilizing, negative or positive selection) of orthologous groups in general and/or branch-oriented mode. The distinctive feature of Orthoscape is the ability to control all data analysis steps via user-friendly interface. Orthoscape allows its users to analyze gene networks or separated gene sets in the context of evolution. At each step of data analysis, Orthoscape also provides for convenient visualization and data manipulation.

  7. Utility estimation of the application of auditory-visual-tactile sense feedback in respiratory gated radiation therapy

    Energy Technology Data Exchange (ETDEWEB)

    Jo, Jung Hun; KIm, Byeong Jin; Roh, Shi Won; Lee, Hyeon Chan; Jang, Hyeong Jun; Kim, Hoi Nam [Dept. of Radiation Oncology, Biomedical Engineering, Seoul St. Mary' s Hospital, Seoul (Korea, Republic of); Song, Jae Hoon [Dept. of Biomedical Engineering, Seoul St. Mary' s Hospital, Seoul (Korea, Republic of); Kim, Young Jae [Dept. of Radiological Technology, Gwang Yang Health Collage, Gwangyang (Korea, Republic of)

    2013-03-15

    The purpose of this study was to evaluate the possibility to optimize the gated treatment delivery time and maintenance of stable respiratory by the introduction of breath with the assistance of auditory-visual-tactile sense. The experimenter's respiration were measured by ANZAI 4D system. We obtained natural breathing signal, monitor-induced breathing signal, monitor and ventilator-induced breathing signal, and breath-hold signal using real time monitor during 10 minutes beam-on-time. In order to check the stability of respiratory signals distributed in each group were compared with means, standard deviation, variation value, beam{sub t}ime of the respiratory signal. The stability of each respiratory was measured in consideration of deviation change studied in each respiratory time lapse. As a result of an analysis of respiratory signal, all experimenters has showed that breathing signal used both Real time monitor and Ventilator was the most stable and shortest time. In this study, it was evaluated that respiratory gated radiation therapy with auditory-visual-tactual sense and without auditory-visual-tactual sense feedback. The study showed that respiratory gated radiation therapy delivery time could significantly be improved by the application of video feedback when this is combined with audio-tactual sense assistance. This delivery technique did prove its feasibility to limit the tumor motion during treatment delivery for all patients to a defined value while maintaining the accuracy and proved the applicability of the technique in a conventional clinical schedule.

  8. Utility estimation of the application of auditory-visual-tactile sense feedback in respiratory gated radiation therapy

    International Nuclear Information System (INIS)

    Jo, Jung Hun; KIm, Byeong Jin; Roh, Shi Won; Lee, Hyeon Chan; Jang, Hyeong Jun; Kim, Hoi Nam; Song, Jae Hoon; Kim, Young Jae

    2013-01-01

    The purpose of this study was to evaluate the possibility to optimize the gated treatment delivery time and maintenance of stable respiratory by the introduction of breath with the assistance of auditory-visual-tactile sense. The experimenter's respiration were measured by ANZAI 4D system. We obtained natural breathing signal, monitor-induced breathing signal, monitor and ventilator-induced breathing signal, and breath-hold signal using real time monitor during 10 minutes beam-on-time. In order to check the stability of respiratory signals distributed in each group were compared with means, standard deviation, variation value, beam t ime of the respiratory signal. The stability of each respiratory was measured in consideration of deviation change studied in each respiratory time lapse. As a result of an analysis of respiratory signal, all experimenters has showed that breathing signal used both Real time monitor and Ventilator was the most stable and shortest time. In this study, it was evaluated that respiratory gated radiation therapy with auditory-visual-tactual sense and without auditory-visual-tactual sense feedback. The study showed that respiratory gated radiation therapy delivery time could significantly be improved by the application of video feedback when this is combined with audio-tactual sense assistance. This delivery technique did prove its feasibility to limit the tumor motion during treatment delivery for all patients to a defined value while maintaining the accuracy and proved the applicability of the technique in a conventional clinical schedule

  9. Arctic Research Mapping Application (ARMAP): visualize project-level information for U.S. funded research in the Arctic

    Science.gov (United States)

    Kassin, A.; Cody, R. P.; Barba, M.; Escarzaga, S. M.; Score, R.; Dover, M.; Gaylord, A. G.; Manley, W. F.; Habermann, T.; Tweedie, C. E.

    2015-12-01

    The Arctic Research Mapping Application (ARMAP; http://armap.org/) is a suite of online applications and data services that support Arctic science by providing project tracking information (who's doing what, when and where in the region) for United States Government funded projects. In collaboration with 17 research agencies, project locations are displayed in a visually enhanced web mapping application. Key information about each project is presented along with links to web pages that provide additional information. The mapping application includes new reference data layers and an updated ship tracks layer. Visual enhancements are achieved by redeveloping the front-end from FLEX to HTML5 and JavaScript, which now provide access to mobile users utilizing tablets and cell phone devices. New tools have been added that allow users to navigate, select, draw, measure, print, use a time slider, and more. Other module additions include a back-end Apache SOLR search platform that provides users with the capability to perform advance searches throughout the ARMAP database. Furthermore, a new query builder interface has been developed in order to provide more intuitive controls to generate complex queries. These improvements have been made to increase awareness of projects funded by numerous entities in the Arctic, enhance coordination for logistics support, help identify geographic gaps in research efforts and potentially foster more collaboration amongst researchers working in the region. Additionally, ARMAP can be used to demonstrate past, present, and future research efforts supported by the U.S. Government.

  10. Designing human centered GeoVisualization application--the SanaViz--for telehealth users: a case study.

    Science.gov (United States)

    Joshi, Ashish; de Araujo Novaes, Magdala; Machiavelli, Josiane; Iyengar, Sriram; Vogler, Robert; Johnson, Craig; Zhang, Jiajie; Hsu, Chiehwen E

    2012-01-01

    Public health data is typically organized by geospatial unit. GeoVisualization (GeoVis) allows users to see information visually on a map. Examine telehealth users' perceptions towards existing public health GeoVis applications and obtains users' feedback about features important for the design and development of Human Centered GeoVis application "the SanaViz". We employed a cross sectional study design using mixed methods approach for this pilot study. Twenty users involved with the NUTES telehealth center at Federal University of Pernambuco (UFPE), Recife, Brazil were enrolled. Open and closed ended questionnaires were used to gather data. We performed audio recording for the interviews. Information gathered included socio-demographics, prior spatial skills and perception towards use of GeoVis to evaluate telehealth services. Card sorting and sketching methods were employed. Univariate analysis was performed for the continuous and categorical variables. Qualitative analysis was performed for open ended questions. Existing Public Health GeoVis applications were difficult to use. Results found interaction features zooming, linking and brushing and representation features Google maps, tables and bar chart as most preferred GeoVis features. Early involvement of users is essential to identify features necessary to be part of the human centered GeoVis application "the SanaViz".

  11. Sequence based polymorphic (SBP marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome

    Directory of Open Access Journals (Sweden)

    Sahu Binod B

    2012-01-01

    Full Text Available Abstract Background Molecular markers facilitate both genotype identification, essential for modern animal and plant breeding, and the isolation of genes based on their map positions. Advancements in sequencing technology have made possible the identification of single nucleotide polymorphisms (SNPs for any genomic regions. Here a sequence based polymorphic (SBP marker technology for generating molecular markers for targeted genomic regions in Arabidopsis is described. Results A ~3X genome coverage sequence of the Arabidopsis thaliana ecotype, Niederzenz (Nd-0 was obtained by applying Illumina's sequencing by synthesis (Solexa technology. Comparison of the Nd-0 genome sequence with the assembled Columbia-0 (Col-0 genome sequence identified putative single nucleotide polymorphisms (SNPs throughout the entire genome. Multiple 75 base pair Nd-0 sequence reads containing SNPs and originating from individual genomic DNA molecules were the basis for developing co-dominant SBP markers. SNPs containing Col-0 sequences, supported by transcript sequences or sequences from multiple BAC clones, were compared to the respective Nd-0 sequences to identify possible restriction endonuclease enzyme site variations. Small amplicons, PCR amplified from both ecotypes, were digested with suitable restriction enzymes and resolved on a gel to reveal the sequence based polymorphisms. By applying this technology, 21 SBP markers for the marker poor regions of the Arabidopsis map representing polymorphisms between Col-0 and Nd-0 ecotypes were generated. Conclusions The SBP marker technology described here allowed the development of molecular markers for targeted genomic regions of Arabidopsis. It should facilitate isolation of co-dominant molecular markers for targeted genomic regions of any animal or plant species, whose genomic sequences have been assembled. This technology will particularly facilitate the development of high density molecular marker maps, essential for

  12. In silico analysis of human metabolism: Reconstruction, contextualization and application of genome-scale models

    DEFF Research Database (Denmark)

    Geng, Jun; Nielsen, Jens

    2017-01-01

    The arising prevalence of metabolic diseases calls for a holistic approach for analysis of the underlying nature of abnormalities in cellular functions. Through mathematic representation and topological analysis of cellular metabolism, GEnome scale metabolic Models (GEMs) provide a promising fram...... that correctly describe interactions between cells or tissues, and we therefore discuss how GEMs can be integrated with blood circulation models. Finally, we end the review with proposing some possible future research directions....

  13. Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

    DEFF Research Database (Denmark)

    Khurana, Ekta; Fu, Yao; Colonna, Vincenza

    2013-01-01

    Identifying Important Identifiers Each of us has millions of sequence variations in our genomes. Signatures of purifying or negative selection should help identify which of those variations is functionally important. Khurana et al. (1235587) used sequence polymorphisms from 1092 humans across 14...... sites tended to occur in network hub promoters. Many recurrent somatic cancer variants occurred in noncoding regulatory regions and thus might indicate mutations that drive cancer....

  14. Adapting an existing visualization application for browser-based deployment: A case study from the Tropical Rainfall Measuring Mission

    Science.gov (United States)

    Kelley, Owen A.

    2013-02-01

    THOR, the Tool for High-resolution Observation Review, is a data viewer for the Tropical Rainfall Measuring Mission (TRMM) and the upcoming Global Precipitation Measurement (GPM) mission. THOR began as a desktop application, but now it can be accessed with a web browser, making THOR one of the first online tools for visualizing TRMM satellite data (http://pps.gsfc.nasa.gov/thor). In this effort, the reuse of the existing visualization code was maximized and the complexity of new code was minimized by avoiding unnecessary functionality, frameworks, or libraries. The simplicity of this approach makes it potentially attractive to researchers wishing to adapt their visualization applications for online deployment. To enable THOR to run within a web browser, three new pieces of code are written. First, the graphical user interface (GUI) of the desktop application is translated into HTML, JavaScript, and CSS. Second, a simple communication mechanism is developed over HTTP. Third, a virtual GUI is created on the server that interfaces with the image-generating routines of the existing desktop application so that these routines do not need to be modified for online use. While the basic functionality of THOR is now available online, prototyping is ongoing for enhanced 3D imaging and other aspects of both THOR Desktop and THOR Online. Because TRMM data products are complex and periodically reprocessed with improved algorithms, having a tool such as THOR is important to analysts at the Precipitation Processing System where the algorithms are tested and the products generated, stored, and distributed. Researchers also have found THOR useful for taking a first look at individual files before writing their own software to perform specialized calculations and analyses.

  15. Application of representational difference analysis to identify genomic differences between Bradyrhizobium elkanii and B. Japonicum species.

    Science.gov (United States)

    Soares, René Arderius; Passaglia, Luciane Maria Pereira

    2010-10-01

    Bradyrhizobium elkanii is successfully used in the formulation of commercial inoculants and, together with B. japonicum, it fully supplies the plant nitrogen demands. Despite the similarity between B. japonicum and B. elkanii species, several works demonstrated genetic and physiological differences between them. In this work Representational Difference Analysis (RDA) was used for genomic comparison between B. elkanii SEMIA 587, a crop inoculant strain, and B. japonicum USDA 110, a reference strain. Two hundred sequences were obtained. From these, 46 sequences belonged exclusively to the genome of B. elkanii strain, and 154 showed similarity to sequences from B. japonicum genome. From the 46 sequences with no similarity to sequences from B. japonicum, 39 showed no similarity to sequences in public databases and seven showed similarity to sequences of genes coding for known proteins. These seven sequences were divided in three groups: similar to sequences from other Bradyrhizobium strains, similar to sequences from other nitrogen-fixing bacteria, and similar to sequences from non nitrogen-fixing bacteria. These new sequences could be used as DNA markers in order to investigate the rates of genetic material gain and loss in natural Bradyrhizobium strains.

  16. Versatile Gene-Specific Sequence Tags for Arabidopsis Functional Genomics: Transcript Profiling and Reverse Genetics Applications

    Science.gov (United States)

    Hilson, Pierre; Allemeersch, Joke; Altmann, Thomas; Aubourg, Sébastien; Avon, Alexandra; Beynon, Jim; Bhalerao, Rishikesh P.; Bitton, Frédérique; Caboche, Michel; Cannoot, Bernard; Chardakov, Vasil; Cognet-Holliger, Cécile; Colot, Vincent; Crowe, Mark; Darimont, Caroline; Durinck, Steffen; Eickhoff, Holger; de Longevialle, Andéol Falcon; Farmer, Edward E.; Grant, Murray; Kuiper, Martin T.R.; Lehrach, Hans; Léon, Céline; Leyva, Antonio; Lundeberg, Joakim; Lurin, Claire; Moreau, Yves; Nietfeld, Wilfried; Paz-Ares, Javier; Reymond, Philippe; Rouzé, Pierre; Sandberg, Goran; Segura, Maria Dolores; Serizet, Carine; Tabrett, Alexandra; Taconnat, Ludivine; Thareau, Vincent; Van Hummelen, Paul; Vercruysse, Steven; Vuylsteke, Marnik; Weingartner, Magdalena; Weisbeek, Peter J.; Wirta, Valtteri; Wittink, Floyd R.A.; Zabeau, Marc; Small, Ian

    2004-01-01

    Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes and which are compatible with both approaches. The GSTs were carefully selected to ensure that each of them shared no significant similarity with any other region in the Arabidopsis genome. They were synthesized by PCR amplification from genomic DNA. Spotted microarrays fabricated from the GSTs show good dynamic range, specificity, and sensitivity in transcript profiling experiments. The GSTs have also been transferred to bacterial plasmid vectors via recombinational cloning protocols. These cloned GSTs constitute the ideal starting point for a variety of functional approaches, including reverse genetics. We have subcloned GSTs on a large scale into vectors designed for gene silencing in plant cells. We show that in planta expression of GST hairpin RNA results in the expected phenotypes in silenced Arabidopsis lines. These versatile GST resources provide novel and powerful tools for functional genomics. PMID:15489341

  17. Comparison of L-system applications towards plant modelling, music rendering and score generation using visual language programming

    Science.gov (United States)

    Lim, Chen Kim; Tan, Kian Lam; Yusran, Hazwanni; Suppramaniam, Vicknesh

    2017-10-01

    Visual language or visual representation has been used in the past few years in order to express the knowledge in graphic. One of the important graphical elements is fractal and L-Systems is a mathematic-based grammatical model for modelling cell development and plant topology. From the plant model, L-Systems can be interpreted as music sound and score. In this paper, LSound which is a Visual Language Programming (VLP) framework has been developed to model plant to music sound and generate music score and vice versa. The objectives of this research has three folds: (i) To expand the grammar dictionary of L-Systems music based on visual programming, (ii) To design and produce a user-friendly and icon based visual language framework typically for L-Systems musical score generation which helps the basic learners in musical field and (iii) To generate music score from plant models and vice versa using L-Systems method. This research undergoes a four phases methodology where the plant is first modelled, then the music is interpreted, followed by the output of music sound through MIDI and finally score is generated. LSound is technically compared to other existing applications in the aspects of the capability of modelling the plant, rendering the music and generating the sound. It has been found that LSound is a flexible framework in which the plant can be easily altered through arrow-based programming and the music score can be altered through the music symbols and notes. This work encourages non-experts to understand L-Systems and music hand-in-hand.

  18. Application of a visual soil examination and evaluation technique at site and farm level

    NARCIS (Netherlands)

    Sonneveld, M.P.W.; Heuvelink, G.B.M.; Moolenaar, S.W.

    2014-01-01

    Visual soil examination and evaluation (VSEE) techniques are semi-quantitative methods that provide rapid and cost-effective information on soil quality. These are mostly applied at site or field level, but there is an increased need for soil quality indicators at farm level to allow integration

  19. Audio visual interaction in the context of multi-media applications

    NARCIS (Netherlands)

    Kohlrausch, A.G.; Par, van de S.L.J.D.E.; Blauert, J.

    2005-01-01

    In our natural environment, we simultaneously receive information through various sensory modalities. The properties of these stimuli are coupled by physical laws, so that, e. g., auditory and visual stimuli caused by the same event have a specific temporal, spatial and contextual relation when

  20. APPLICATION OF COMPUTER-AIDED TOMOGRAPHY TO VISUALIZE AND QUANTIFY BIOGENIC STRUCTURES IN MARINE SEDIMENTS

    Science.gov (United States)

    We used computer-aided tomography (CT) for 3D visualization and 2D analysis ofmarine sediment cores from 3 stations (at 10, 75 and 118 m depths) with different environmentalimpact. Biogenic structures such as tubes and burrows were quantified and compared among st...

  1. Real-time tracking of visually attended objects in virtual environments and its application to LOD.

    Science.gov (United States)

    Lee, Sungkil; Kim, Gerard Jounghyun; Choi, Seungmoon

    2009-01-01

    This paper presents a real-time framework for computationally tracking objects visually attended by the user while navigating in interactive virtual environments. In addition to the conventional bottom-up (stimulus-driven) saliency map, the proposed framework uses top-down (goal-directed) contexts inferred from the user's spatial and temporal behaviors, and identifies the most plausibly attended objects among candidates in the object saliency map. The computational framework was implemented using GPU, exhibiting high computational performance adequate for interactive virtual environments. A user experiment was also conducted to evaluate the prediction accuracy of the tracking framework by comparing objects regarded as visually attended by the framework to actual human gaze collected with an eye tracker. The results indicated that the accuracy was in the level well supported by the theory of human cognition for visually identifying single and multiple attentive targets, especially owing to the addition of top-down contextual information. Finally, we demonstrate how the visual attention tracking framework can be applied to managing the level of details in virtual environments, without any hardware for head or eye tracking.

  2. An Assessment of the Tinder Mobile Dating Application for Individuals Who Are Visually Impaired

    Science.gov (United States)

    Kapperman, Gaylen; Kelly, Stacy M.; Kilmer, Kylie; Smith, Thomas J.

    2017-01-01

    People with visual impairments (that is, those who are blind or have low vision) have a disadvantage in the process of being selected as a romantic partner. It is further underscored that these difficulties with dating and fitting in among sighted individuals extend beyond formative years into adulthood (Sacks & Wolffe, 2006). Thus, the…

  3. FluoRender: An application of 2D image space methods for 3D and 4D confocal microscopy data visualization in neurobiology research

    KAUST Repository

    Wan, Yong; Otsuna, Hideo; Chien, Chi-Bin; Hansen, Charles

    2012-01-01

    2D image space methods are processing methods applied after the volumetric data are projected and rendered into the 2D image space, such as 2D filtering, tone mapping and compositing. In the application domain of volume visualization, most 2D image space methods can be carried out more efficiently than their 3D counterparts. Most importantly, 2D image space methods can be used to enhance volume visualization quality when applied together with volume rendering methods. In this paper, we present and discuss the applications of a series of 2D image space methods as enhancements to confocal microscopy visualizations, including 2D tone mapping, 2D compositing, and 2D color mapping. These methods are easily integrated with our existing confocal visualization tool, FluoRender, and the outcome is a full-featured visualization system that meets neurobiologists' demands for qualitative analysis of confocal microscopy data. © 2012 IEEE.

  4. FluoRender: An application of 2D image space methods for 3D and 4D confocal microscopy data visualization in neurobiology research

    KAUST Repository

    Wan, Yong

    2012-02-01

    2D image space methods are processing methods applied after the volumetric data are projected and rendered into the 2D image space, such as 2D filtering, tone mapping and compositing. In the application domain of volume visualization, most 2D image space methods can be carried out more efficiently than their 3D counterparts. Most importantly, 2D image space methods can be used to enhance volume visualization quality when applied together with volume rendering methods. In this paper, we present and discuss the applications of a series of 2D image space methods as enhancements to confocal microscopy visualizations, including 2D tone mapping, 2D compositing, and 2D color mapping. These methods are easily integrated with our existing confocal visualization tool, FluoRender, and the outcome is a full-featured visualization system that meets neurobiologists\\' demands for qualitative analysis of confocal microscopy data. © 2012 IEEE.

  5. Applications of synchrotron microradiography in materials science-in situ visualization of the growth of metallic alloy crystals

    International Nuclear Information System (INIS)

    Wang Tongmin; Zhu Jing; Cao Fei; Wang Kun; Bao Yongming; Xie Honglan; Huang Wanxia

    2012-01-01

    Metals and their alloys are an important type of structural and functional material and have been widely used in the aerospace, automobile, shipbuilding and other industries. The macro-properties of metallic alloys actually depend on their microstructures. The evolution of their microstructures generally involves a dynamic process of crystal growth on the scale of micrometers. The crystal growth of these alloys is still a puzzle to us due to their opacity. Conventional metallography techniques are limited by the high temperature of the phase changes so it is not possible to perform in situ observation of the evolving crystal morphology. The in situ visualization of the crystal growth has now become possible with the application of synchrotron radiation imaging techniques, which are just the right key to unravel the mystery mentioned above. In this paper, the development and current state-of-the-art of in situ crystal growth visualization are reviewed. Some typical application examples are presented, and promising applications in materials science are further expected. (authors)

  6. Animal models in genomic research: Techniques, applications, and roles for nurses.

    Science.gov (United States)

    Osier, Nicole D; Pham, Lan; Savarese, Amanda; Sayles, Kendra; Alexander, Sheila A

    2016-11-01

    Animal research has been conducted by scientists for over two millennia resulting in a better understanding of human anatomy, physiology, and pathology, as well as testing of novel therapies. In the molecular genomic era, pre-clinical models represent a key tool for understanding the genomic underpinnings of health and disease and are relevant to precision medicine initiatives. Nurses contribute to improved health by collecting and translating evidence from clinically relevant pre-clinical models. Using animal models, nurses can ask questions that would not be feasible or ethical to address in humans, and establish the safety and efficacy of interventions before translating them to clinical trials. Two advantages of using pre-clinical models are reduced variability between test subjects and the opportunity for precisely controlled experimental exposures. Standardized care controls the effects of diet and environment, while the availability of inbred strains significantly reduces the confounding effects of genetic differences. Outside the laboratory, nurses can contribute to the approval and oversight of animal studies, as well as translation to clinical trials and, ultimately, patient care. This review is intended as a primer on the use of animal models to advance nursing science; specifically, the paper discusses the utility of preclinical models for studying the pathophysiologic and genomic contributors to health and disease, testing interventions, and evaluating effects of environmental exposures. Considerations specifically geared to nurse researchers are also introduced, including discussion of how to choose an appropriate model and controls, potential confounders, as well as legal and ethical concerns. Finally, roles for nurse clinicians in pre-clinical research are also highlighted. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.

    Science.gov (United States)

    Fungtammasan, Arkarachai; Ananda, Guruprasad; Hile, Suzanne E; Su, Marcia Shu-Wei; Sun, Chen; Harris, Robert; Medvedev, Paul; Eckert, Kristin; Makova, Kateryna D

    2015-05-01

    Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCR-free protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution. © 2015 Fungtammasan et al.; Published by Cold Spring Harbor Laboratory Press.

  8. An Interactive Mobile Application for the Visually Impaired to Have Access to Listening Audio Books with Handy Books Portal

    Directory of Open Access Journals (Sweden)

    Avanthika Meenakshi

    2015-01-01

    Full Text Available Mobile phones are used in almost all aspects of life by people. But in the case of visually impaired, they are still a step behind in using smart phones for various purposes. Having interactive android OS, navigation and travel aiding apps using sensors and voice user interfaces (VUI or the voice response systems, we are still a step lagging in giving them an application for educational purposes. This paper proposes a complete new idea of having a portal where they can store audio books aided with interactive system so that they can use them whenever needed.

  9. Novel probabilistic models of spatial genetic ancestry with applications to stratification correction in genome-wide association studies.

    Science.gov (United States)

    Bhaskar, Anand; Javanmard, Adel; Courtade, Thomas A; Tse, David

    2017-03-15

    Genetic variation in human populations is influenced by geographic ancestry due to spatial locality in historical mating and migration patterns. Spatial population structure in genetic datasets has been traditionally analyzed using either model-free algorithms, such as principal components analysis (PCA) and multidimensional scaling, or using explicit spatial probabilistic models of allele frequency evolution. We develop a general probabilistic model and an associated inference algorithm that unify the model-based and data-driven approaches to visualizing and inferring population structure. Our spatial inference algorithm can also be effectively applied to the problem of population stratification in genome-wide association studies (GWAS), where hidden population structure can create fictitious associations when population ancestry is correlated with both the genotype and the trait. Our algorithm Geographic Ancestry Positioning (GAP) relates local genetic distances between samples to their spatial distances, and can be used for visually discerning population structure as well as accurately inferring the spatial origin of individuals on a two-dimensional continuum. On both simulated and several real datasets from diverse human populations, GAP exhibits substantially lower error in reconstructing spatial ancestry coordinates compared to PCA. We also develop an association test that uses the ancestry coordinates inferred by GAP to accurately account for ancestry-induced correlations in GWAS. Based on simulations and analysis of a dataset of 10 metabolic traits measured in a Northern Finland cohort, which is known to exhibit significant population structure, we find that our method has superior power to current approaches. Our software is available at https://github.com/anand-bhaskar/gap . abhaskar@stanford.edu or ajavanma@usc.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved

  10. Dye visualization near a three-dimensional stagnation point: application to the vortex breakdown bubble

    DEFF Research Database (Denmark)

    Brøns, Morten; Thompson, M. C.; Hourigan, K.

    2009-01-01

    flows are typically visualized. Predictions based on the model are made for the steady vortex breakdown bubble in a torsionally driven cylinder and compared with computational fluid dynamics predictions and experimental observations. Previous experimental observations using tracer visualization...... techniques have suggested that even for low-Reynolds-number flows, the steady vortex breakdown bubble in a torsionally driven cylinder is not axisymmetric and has an inflow/outflow asymmetry at its tail. Recent numerical and theoretical studies show that the asymmetry of the vortex breakdown bubble......, and consequently its open nature, can be explained by the very small imperfections that are present in any experimental rig. Distinct from this, here it is shown that even for a perfectly axisymmetric flow and breakdown bubble, the combined effect of dye diffusion and the inevitable small errors in the dye...

  11. ANLIZE: a molecular mechanics force field visualization tool and its application to 18-crown-6.

    Science.gov (United States)

    Stolworthy, L D; Shirts, R B

    1997-03-01

    We describe a software tool that allows one to visualize and analyze the importance of each individual steric interaction in a molecular mechanics force field. ANLIZE is presently implemented for the Dreiding force field for use with the Cerius2 software package, but could be implemented in any molecular mechanics package with a graphical user interface. ANLIZE calculates individual interactions in the force field, sorts them by size, and displays them in several ways from a menu of choices. This allows the user to scan through selected interactions to visualize which interactions are the primary determinants of preferred conformations. The features of ANLIZE are illustrated using 18-crown-6 as an example, and the factors governing conformational preference in 18-crown-6 are demonstrated. Users of molecular mechanics packages are encouraged to demand this functionality from commercial software producers.

  12. Application of neutron radiography to visualize the distribution of lithium in lithium batteries

    International Nuclear Information System (INIS)

    Kamata, Masahiro; Esaka, Takao; Fujine, Sigenori; Yoneda, Kenji; Kanda, Keiji.

    1995-01-01

    The authors have tried to visualize the motion of lithium ions in lithium ion conductors such as Li 1.33 Ti 1.67 O 4 at high temperatures using neutron radiography (NR) technique and confirmed that NR is very effective to the 6 Li containing systems. This means NR may be used as a non-destructive investigating method to study the electrode reactions and the mass transfer in lithium batteries. Here in this work, it was tried to visualize the distribution of lithium in commercial lithium batteries before and after discharge using NR technique. Obtained NR images will be presented with brief explanation on NR method. Further explanations on the principle of NR and on the NR facilities were presented elsewhere. (J.P.N.)

  13. Use of artificial intelligence techniques for visual inspection systems prototyping. Application to magnetoscopy

    International Nuclear Information System (INIS)

    Pallas, Christophe

    1987-01-01

    The automation of visual inspection is a complex task that requires collaboration between experts, for example inspection specialist, vision specialist. on-line operators. Solving such problems through prototyping promotes this collaboration: the use of a non specific programming environment allows rapid, concrete checking of method validity, thus leading incrementally to the final system. In this context, artificial intelligence techniques permit easy, extensible, and modular design of the prototype, together with heuristic solution building. We define and achieve the SPOR prototyping environment, based on object-oriented programming and rules-basis managing. The feasibility and the validity of an heuristic method for automated visual inspection in fluoroscopy have been proved through prototyping in SPOR. (author) [fr

  14. Gauging the impact of gender grammaticization in different languages : application of a linguistic-visual paradigm

    OpenAIRE

    Sato, Sayaka; Gygax, Pascal M.; Gabriel, Ute

    2016-01-01

    Employing a linguistic-visual paradigm, we investigated whether the grammaticization of gender information impacts readers’ gender representations. French and German were taken as comparative languages, taking into account the male gender bias associated to both languages, as well as the comparative gender biases associated to their plural determiners (French: les [generic] vs. German: die [morphologically feminine]). Bilingual speakers of French and German had to judge whether a pair of faci...

  15. A Visual Programming Methodology for Tactical Aircrew Scheduling and Other Applications

    Science.gov (United States)

    1991-12-01

    34Program Visualization: Graphical Support for Software Development," Computer, August 1985, pp. 27-35. 7 Bruno, Giorgio, Antonio Elia, and Pietro ...fl wFORMULAi24O.rgirl .1. ELECrcnvaldt .14 uSELECT(- di ~l) -1- -I&Q.BOLS3:1 S 128 _L .dbox2f) -LL -IFNOT(G541,RETURNO) .12 .ATA.FINDO AL -SELECT

  16. MSTools-Web based application for visualization and presentation of HXMS data

    Czech Academy of Sciences Publication Activity Database

    Kavan, Daniel; Man, Petr

    2011-01-01

    Roč. 302, 1-3 (2011), s. 53-58 ISSN 1387-3806 R&D Projects: GA ČR(CZ) GAP207/10/1040; GA AV ČR KJB500200612; GA MŠk LC545; GA MŠk LC07017 Institutional research plan: CEZ:AV0Z50200510 Keywords : Hydrogen/deuterium exchange * Data visualization * Software Subject RIV: EE - Microbiology, Virology Impact factor: 2.549, year: 2011

  17. Establishment and Application of a Visual DNA Microarray for the Detection of Food-borne Pathogens.

    Science.gov (United States)

    Li, Yongjin

    2016-01-01

    The accurate detection and identification of food-borne pathogenic microorganisms is critical for food safety nowadays. In the present work, a visual DNA microarray was established and applied to detect pathogens commonly found in food, including Salmonella enterica, Shigella flexneri, E. coli O157:H7 and Listeria monocytogenes in food samples. Multiplex PCR (mPCR) was employed to simultaneously amplify specific gene fragments, fimY for Salmonella, ipaH for Shigella, iap for L. monocytogenes and ECs2841 for E. coli O157:H7, respectively. Biotinylated PCR amplicons annealed to the microarray probes were then reacted with a streptavidin-alkaline phosphatase conjugate and nitro blue tetrazolium/5-bromo-4-chloro-3'-indolylphosphate, p-toluidine salt (NBT/BCIP); the positive results were easily visualized as blue dots formatted on the microarray surface. The performance of a DNA microarray was tested against 14 representative collection strains and mock-contamination food samples. The combination of mPCR and a visual micro-plate chip specifically and sensitively detected Salmonella enterica, Shigella flexneri, E. coli O157:H7 and Listeria monocytogenes in standard strains and food matrices with a sensitivity of ∼10(2) CFU/mL of bacterial culture. Thus, the developed method is advantageous because of its high throughput, cost-effectiveness and ease of use.

  18. A Hyperbolic Ontology Visualization Tool for Model Application Programming Interface Documentation

    Science.gov (United States)

    Hyman, Cody

    2011-01-01

    Spacecraft modeling, a critically important portion in validating planned spacecraft activities, is currently carried out using a time consuming method of mission to mission model implementations and integration. A current project in early development, Integrated Spacecraft Analysis (ISCA), aims to remedy this hindrance by providing reusable architectures and reducing time spent integrating models with planning and sequencing tools. The principle objective of this internship was to develop a user interface for an experimental ontology-based structure visualization of navigation and attitude control system modeling software. To satisfy this, a number of tree and graph visualization tools were researched and a Java based hyperbolic graph viewer was selected for experimental adaptation. Early results show promise in the ability to organize and display large amounts of spacecraft model documentation efficiently and effectively through a web browser. This viewer serves as a conceptual implementation for future development but trials with both ISCA developers and end users should be performed to truly evaluate the effectiveness of continued development of such visualizations.

  19. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems.

    Directory of Open Access Journals (Sweden)

    Sophie S Abby

    Full Text Available Biologists often wish to use their knowledge on a few experimental models of a given molecular system to identify homologs in genomic data. We developed a generic tool for this purpose.Macromolecular System Finder (MacSyFinder provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include functional analogs, and the multiple uses of a same component by different systems. Models are used to search for molecular systems in complete genomes or in unstructured data like metagenomes. The components of the systems are searched by sequence similarity using Hidden Markov model (HMM protein profiles. The assignment of hits to a given system is decided based on compliance with the content and organization of the system model. A graphical interface, MacSyView, facilitates the analysis of the results by showing overviews of component content and genomic context. To exemplify the use of MacSyFinder we built models to detect and class CRISPR-Cas systems following a previously established classification. We show that MacSyFinder allows to easily define an accurate "Cas-finder" using publicly available protein profiles.MacSyFinder is a standalone application implemented in Python. It requires Python 2.7, Hmmer and makeblastdb (version 2.2.28 or higher. It is freely available with its source code under a GPLv3 license at https://github.com/gem-pasteur/macsyfinder. It is compatible with all platforms supporting Python and Hmmer/makeblastdb. The "Cas-finder" (models and HMM profiles is distributed as a compressed tarball archive as Supporting Information.

  20. Application of genomics-assisted breeding for generation of climate resilient crops: Progress and prospects

    Directory of Open Access Journals (Sweden)

    Chittaranjan eKole

    2015-08-01

    Full Text Available Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to surge further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood and submergence, and pests along with increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives towards identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have been proven helpful in enhancing the stress adaptation of crop plants, and recent advancement in next-generation sequencing along with high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB. In view of this, the present review elaborates the progress and prospects of GAB in improving climate change resilience in crop plants towards circumventing global food insecurity.

  1. Application for TJ-II Signals Visualization: User's Guide; Aplicacion para la Visualizacion de Senales de TJ-II: Guia del Usuario

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez, E.; Portas, A. B.; Vega, J. [Ciemat, Madrid (Spain)

    2000-07-01

    In this documents are described the functionalities of the application developed by the Data Acquisition Group for TJ-II signal visualization. There are two versions of the application, the On-line version, used for signal visualization during TJ-II operation, and the Off-line version, used for signal visualization without TJ-II operation. Both versions of the application consist in a graphical user interface developed for X/Motif, in which most of the actions can be done using the mouse buttons. The functionalities of both versions of the application are described in this user's guide, beginning at the application start-up and explaining in detail all the options that it provides and the actions that can be done with each graphic control. (Author) 8 refs.

  2. Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence-Function Space and Genome Context to Discover Novel Functions.

    Science.gov (United States)

    Gerlt, John A

    2017-08-22

    The exponentially increasing number of protein and nucleic acid sequences provides opportunities to discover novel enzymes, metabolic pathways, and metabolites/natural products, thereby adding to our knowledge of biochemistry and biology. The challenge has evolved from generating sequence information to mining the databases to integrating and leveraging the available information, i.e., the availability of "genomic enzymology" web tools. Web tools that allow identification of biosynthetic gene clusters are widely used by the natural products/synthetic biology community, thereby facilitating the discovery of novel natural products and the enzymes responsible for their biosynthesis. However, many novel enzymes with interesting mechanisms participate in uncharacterized small-molecule metabolic pathways; their discovery and functional characterization also can be accomplished by leveraging information in protein and nucleic acid databases. This Perspective focuses on two genomic enzymology web tools that assist the discovery novel metabolic pathways: (1) Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST) for generating sequence similarity networks to visualize and analyze sequence-function space in protein families and (2) Enzyme Function Initiative-Genome Neighborhood Tool (EFI-GNT) for generating genome neighborhood networks to visualize and analyze the genome context in microbial and fungal genomes. Both tools have been adapted to other applications to facilitate target selection for enzyme discovery and functional characterization. As the natural products community has demonstrated, the enzymology community needs to embrace the essential role of web tools that allow the protein and genome sequence databases to be leveraged for novel insights into enzymological problems.

  3. A new method for detecting signal regions in ordered sequences of real numbers, and application to viral genomic data.

    Science.gov (United States)

    Gog, Julia R; Lever, Andrew M L; Skittrall, Jordan P

    2018-01-01

    We present a fast, robust and parsimonious approach to detecting signals in an ordered sequence of numbers. Our motivation is in seeking a suitable method to take a sequence of scores corresponding to properties of positions in virus genomes, and find outlying regions of low scores. Suitable statistical methods without using complex models or making many assumptions are surprisingly lacking. We resolve this by developing a method that detects regions of low score within sequences of real numbers. The method makes no assumptions a priori about the length of such a region; it gives the explicit location of the region and scores it statistically. It does not use detailed mechanistic models so the method is fast and will be useful in a wide range of applications. We present our approach in detail, and test it on simulated sequences. We show that it is robust to a wide range of signal morphologies, and that it is able to capture multiple signals in the same sequence. Finally we apply it to viral genomic data to identify regions of evolutionary conservation within influenza and rotavirus.

  4. Safety analysis of a Russian phage cocktail: From MetaGenomic analysis to oral application in healthy human subjects

    Energy Technology Data Exchange (ETDEWEB)

    McCallin, Shawna, E-mail: semccallin@yahoo.com [Nestlé Research Centre, Nestec Ltd, Vers-chez-les-Blanc, CH-1000 Lausanne 26 (Switzerland); Alam Sarker, Shafiqul, E-mail: sasarker@icddrb.org [International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sharani, Mohakhali, Dhaka 1212 (Bangladesh); Barretto, Caroline, E-mail: Caroline.Barretto@rdls.nestle.com [Nestlé Research Centre, Nestec Ltd, Vers-chez-les-Blanc, CH-1000 Lausanne 26 (Switzerland); Sultana, Shamima, E-mail: shamima@icddrb.org [International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sharani, Mohakhali, Dhaka 1212 (Bangladesh); Berger, Bernard, E-mail: bernard.berger@rdls.nestle.com [Nestlé Research Centre, Nestec Ltd, Vers-chez-les-Blanc, CH-1000 Lausanne 26 (Switzerland); Huq, Sayeda, E-mail: sayeeda@mail.icddrb.org [International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sharani, Mohakhali, Dhaka 1212 (Bangladesh); Krause, Lutz, E-mail: ltz.krause@gmail.com [Nestlé Research Centre, Nestec Ltd, Vers-chez-les-Blanc, CH-1000 Lausanne 26 (Switzerland); Bibiloni, Rodrigo, E-mail: Rodrigo.Bibiloni@agresearch.co.nz [Nestlé Research Centre, Nestec Ltd, Vers-chez-les-Blanc, CH-1000 Lausanne 26 (Switzerland); Schmitt, Bertrand, E-mail: bertrand.schmitt@rdls.nestle.com [Nestlé Research Centre, Nestec Ltd, Vers-chez-les-Blanc, CH-1000 Lausanne 26 (Switzerland); Reuteler, Gloria, E-mail: gloria.reuteler@rdls.nestle.com [Nestlé Research Centre, Nestec Ltd, Vers-chez-les-Blanc, CH-1000 Lausanne 26 (Switzerland); Brüssow, Harald, E-mail: harald.bruessow@rdls.nestle.com [Nestlé Research Centre, Nestec Ltd, Vers-chez-les-Blanc, CH-1000 Lausanne 26 (Switzerland)

    2013-09-01

    Phage therapy has a long tradition in Eastern Europe, where preparations are comprised of complex phage cocktails whose compositions have not been described. We investigated the composition of a phage cocktail from the Russian pharmaceutical company Microgen targeting Escherichia coli/Proteus infections. Electron microscopy identified six phage types, with numerically T7-like phages dominating over T4-like phages. A metagenomic approach using taxonomical classification, reference mapping and de novo assembly identified 18 distinct phage types, including 7 genera of Podoviridae, 2 established and 2 proposed genera of Myoviridae, and 2 genera of Siphoviridae. De novo assembly yielded 7 contigs greater than 30 kb, including a 147-kb Myovirus genome and a 42-kb genome of a potentially new phage. Bioinformatic analysis did not reveal undesired genes and a small human volunteer trial did not associate adverse effects with oral phage exposure. - Highlights: • We analyzed the composition of a commercial Russian phage cocktail. • The cocktail consists of at least 10 different phage genera. • No undesired genes were detected. • No adverse effects were seen upon oral application in a small human clinical trial.

  5. Genome-wide analysis of SSR and ILP markers in trees: diversity profiling, alternate distribution, and applications in duplication.

    Science.gov (United States)

    Xia, Xinyao; Luan, Lin Lin; Qin, Guanghua; Yu, Li Fang; Wang, Zhi Wei; Dong, Wan Chen; Song, Yumin; Qiao, Yuling; Zhang, Xian Sheng; Sang, Ya Lin; Yang, Long

    2017-12-20

    Molecular markers are efficient tools for breeding and genetic studies. However, despite their ecological and economic importance, their development and application have long been hampered. In this study, we identified 524,170 simple sequence repeat (SSR), 267,636 intron length polymorphism (ILP), and 11,872 potential intron polymorphism (PIP) markers from 16 tree species based on recently available genome sequences. Larger motifs, including hexamers and heptamers, accounted for most of the seven different types of SSR loci. Within these loci, A/T bases comprised a significantly larger proportion of sequence than G/C. SSR and ILP markers exhibited an alternative distribution pattern. Most SSRs were monomorphic markers, and the proportions of polymorphic markers were positively correlated with genome size. By verifying with all 16 tree species, 54 SSR, 418 ILP, and four PIP universal markers were obtained, and their efficiency was examined by PCR. A combination of five SSR and six ILP markers were used for the phylogenetic analysis of 30 willow samples, revealing a positive correlation between genetic diversity and geographic distance. We also found that SSRs can be used as tools for duplication analysis. Our findings provide important foundations for the development of breeding and genetic studies in tree species.

  6. Safety analysis of a Russian phage cocktail: From MetaGenomic analysis to oral application in healthy human subjects

    International Nuclear Information System (INIS)

    McCallin, Shawna; Alam Sarker, Shafiqul; Barretto, Caroline; Sultana, Shamima; Berger, Bernard; Huq, Sayeda; Krause, Lutz; Bibiloni, Rodrigo; Schmitt, Bertrand; Reuteler, Gloria; Brüssow, Harald

    2013-01-01

    Phage therapy has a long tradition in Eastern Europe, where preparations are comprised of complex phage cocktails whose compositions have not been described. We investigated the composition of a phage cocktail from the Russian pharmaceutical company Microgen targeting Escherichia coli/Proteus infections. Electron microscopy identified six phage types, with numerically T7-like phages dominating over T4-like phages. A metagenomic approach using taxonomical classification, reference mapping and de novo assembly identified 18 distinct phage types, including 7 genera of Podoviridae, 2 established and 2 proposed genera of Myoviridae, and 2 genera of Siphoviridae. De novo assembly yielded 7 contigs greater than 30 kb, including a 147-kb Myovirus genome and a 42-kb genome of a potentially new phage. Bioinformatic analysis did not reveal undesired genes and a small human volunteer trial did not associate adverse effects with oral phage exposure. - Highlights: • We analyzed the composition of a commercial Russian phage cocktail. • The cocktail consists of at least 10 different phage genera. • No undesired genes were detected. • No adverse effects were seen upon oral application in a small human clinical trial

  7. Genetical Genomics for Evolutionary Studies

    NARCIS (Netherlands)

    Prins, J.C.P.; Smant, G.; Jansen, R.C.

    2012-01-01

    Genetical genomics combines acquired high-throughput genomic data with genetic analysis. In this chapter, we discuss the application of genetical genomics for evolutionary studies, where new high-throughput molecular technologies are combined with mapping quantitative trait loci (QTL) on the genome

  8. Radiation hybrid maps of the D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes.

    Science.gov (United States)

    Kumar, Ajay; Seetan, Raed; Mergoum, Mohamed; Tiwari, Vijay K; Iqbal, Muhammad J; Wang, Yi; Al-Azzam, Omar; Šimková, Hana; Luo, Ming-Cheng; Dvorak, Jan; Gu, Yong Q; Denton, Anne; Kilian, Andrzej; Lazo, Gerard R; Kianian, Shahryar F

    2015-10-16

    The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high resolution genome maps with saturated marker scaffolds to anchor and orient BAC contigs/ sequence scaffolds for whole genome assembly. Radiation hybrid (RH) mapping has proven to be an excellent tool for the development of such maps for it offers much higher and more uniform marker resolution across the length of the chromosome compared to genetic mapping and does not require marker polymorphism per se, as it is based on presence (retention) vs. absence (deletion) marker assay. In this study, a 178 line RH panel was genotyped with SSRs and DArT markers to develop the first high resolution RH maps of the entire D-genome of Ae. tauschii accession AL8/78. To confirm map order accuracy, the AL8/78-RH maps were compared with:1) a DArT consensus genetic map constructed using more than 100 bi-parental populations, 2) a RH map of the D-genome of reference hexaploid wheat 'Chinese Spring', and 3) two SNP-based genetic maps, one with anchored D-genome BAC contigs and another with anchored D-genome sequence scaffolds. Using marker sequences, the RH maps were also anchored with a BAC contig based physical map and draft sequence of the D-genome of Ae. tauschii. A total of 609 markers were mapped to 503 unique positions on the seven D-genome chromosomes, with a total map length of 14,706.7 cR. The average distance between any two marker loci was 29.2 cR which corresponds to 2.1 cM or 9.8 Mb. The average mapping resolution across the D-genome was estimated to be 0.34 Mb (Mb/cR) or 0.07 cM (cM/cR). The RH maps showed almost perfect agreement with several published maps with regard to chromosome assignments of markers. The mean rank correlations between the position of markers on AL8/78 maps and the four published maps, ranged from 0.75 to 0.92, suggesting a good agreement in marker order. With 609 mapped markers, a total of 2481 deletions for the whole D-genome were detected with an average

  9. Integrated and visual performance evaluation model for thermal systems and its application to an HTGR cogeneration system

    International Nuclear Information System (INIS)

    Qi, Zhang; Yoshikawa, Hidekazu; Ishii, Hirotake; Shimoda, Hiroshi

    2010-01-01

    An integrated and visual model EXCEM-MFM (EXergy, Cost, Energy and Mass - Multilevel Flow Model) has been proposed in this study to comprehensively analyze and evaluate the performances of thermal systems by coupling two models: EXCEM model and MFM. In the EXCEM-MFM model, MFM is used to provide analysis frameworks for exergy, cost, energy and mass four parameters, and EXCEM is used to calculate the flow values of these four parameters for MFM based on the provided framework. In this study, we used the tools and technologies of computer science and software engineering to materialize the model. Moreover, the feasibility and application potential of this proposed EXCEM-MFM model has been demonstrated by the example application of a comprehensive performance study of a typical High Temperature Gas Reactor (HTGR) cogeneration system by taking into account the thermodynamic and economic perspectives. (author)

  10. Modern tools for development of interactive web map applications for visualization spatial data on the internet

    Directory of Open Access Journals (Sweden)

    Horáková Bronislava

    2009-11-01

    Full Text Available In the last few years has begun the development of dynamic web applications, often called Web2.0. From this development wascreated a technology called Mashups. Mashups may easily combine huge amounts of data sources and functionalities of existing as wellas future web applications and services. Therefore they are used to develop a new device, which offers new possibilities of informationusage. This technology provides possibilities of developing basic as well as robust web applications not only for IT or GIS specialists,but also for common users. Software companies have developed web projects for building mashup application also called mashupeditors.

  11. Data Visualization with Flash Builder Designing RIA and AIR Applications with Remote Data Sources

    CERN Document Server

    Rocchi, Cesare

    2011-01-01

    Design and create functional applications that interact with remote data sources. You get a thorough introduction to the latest Flash Builder tools learning how you can use the built-in wizards, MXML or pure ActionScript 3 to build information-rich applications for the browser or AIR applications. Hand's on tutorials guide you through each iteration including building user interaction, charting, incorporating audio and video, customizing the UI; and a code repository provides re-usable code that you can modify and deploy in your own applications. *Hand's o

  12. Visualization rhetoric: framing effects in narrative visualization.

    Science.gov (United States)

    Hullman, Jessica; Diakopoulos, Nicholas

    2011-12-01

    Narrative visualizations combine conventions of communicative and exploratory information visualization to convey an intended story. We demonstrate visualization rhetoric as an analytical framework for understanding how design techniques that prioritize particular interpretations in visualizations that "tell a story" can significantly affect end-user interpretation. We draw a parallel between narrative visualization interpretation and evidence from framing studies in political messaging, decision-making, and literary studies. Devices for understanding the rhetorical nature of narrative information visualizations are presented, informed by the rigorous application of concepts from critical theory, semiotics, journalism, and political theory. We draw attention to how design tactics represent additions or omissions of information at various levels-the data, visual representation, textual annotations, and interactivity-and how visualizations denote and connote phenomena with reference to unstated viewing conventions and codes. Classes of rhetorical techniques identified via a systematic analysis of recent narrative visualizations are presented, and characterized according to their rhetorical contribution to the visualization. We describe how designers and researchers can benefit from the potentially positive aspects of visualization rhetoric in designing engaging, layered narrative visualizations and how our framework can shed light on how a visualization design prioritizes specific interpretations. We identify areas where future inquiry into visualization rhetoric can improve understanding of visualization interpretation. © 2011 IEEE

  13. Constructing an AIRS Climatology for Data Visualization and Analysis to Serve the Climate Science and Application Communities

    Science.gov (United States)

    Ding, Feng; Keim, Elaine; Hearty, Thomas J.; Wei, Jennifer; Savtchenko, Andrey; Theobald, Michael; Vollmer, Bruce

    2016-01-01

    The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) is the home of processing, archiving, and distribution services for NASA sounders: the present Aqua AIRS mission and the succeeding SNPP CrIS mission. The AIRS mission is entering its 15th year of global observations of the atmospheric state, including temperature and humidity profiles, outgoing longwave radiation, cloud properties, and trace gases. The GES DISC, in collaboration with the AIRS Project, released product from the version 6 algorithm in early 2013. Giovanni, a Web-based application developed by the GES DISC, provides a simple and intuitive way to visualize, analyze, and access vast amounts of Earth science remote sensing data without having to download the data. Most important variables from version 6 AIRS product are available in Giovanni. We are developing a climatology product using 14-year AIRS retrievals. The study can be a good start for the long term climatology from NASA sounders: the AIRS and the succeeding CrIS. This presentation will show the impacts to the climatology product from different aggregation methods. The climatology can serve climate science and application communities in data visualization and analysis, which will be demonstrated using a variety of functions in version 4 Giovanni. The highlights of these functions include user-defined monthly and seasonal climatology, inter annual seasonal time series, anomaly analysis.

  14. HERA: A dynamic web application for visualizing community exposure to flood hazards based on storm and sea level rise scenarios

    Science.gov (United States)

    Jones, Jeanne M.; Henry, Kevin; Wood, Nathan; Ng, Peter; Jamieson, Matthew

    2017-12-01

    The Hazard Exposure Reporting and Analytics (HERA) dynamic web application was created to provide a platform that makes research on community exposure to coastal-flooding hazards influenced by sea level rise accessible to planners, decision makers, and the public in a manner that is both easy to use and easily accessible. HERA allows users to (a) choose flood-hazard scenarios based on sea level rise and storm assumptions, (b) appreciate the modeling uncertainty behind a chosen hazard zone, (c) select one or several communities to examine exposure, (d) select the category of population or societal asset, and (e) choose how to look at results. The application is designed to highlight comparisons between (a) varying levels of sea level rise and coastal storms, (b) communities, (c) societal asset categories, and (d) spatial scales. Through a combination of spatial and graphical visualizations, HERA aims to help individuals and organizations to craft more informed mitigation and adaptation strategies for climate-driven coastal hazards. This paper summarizes the technologies used to maximize the user experience, in terms of interface design, visualization approaches, and data processing.

  15. HERA: A dynamic web application for visualizing community exposure to flood hazards based on storm and sea level rise scenarios

    Science.gov (United States)

    Jones, Jeanne M.; Henry, Kevin; Wood, Nathan J.; Ng, Peter; Jamieson, Matthew

    2017-01-01

    The Hazard Exposure Reporting and Analytics (HERA) dynamic web application was created to provide a platform that makes research on community exposure to coastal-flooding hazards influenced by sea level rise accessible to planners, decision makers, and the public in a manner that is both easy to use and easily accessible. HERA allows users to (a) choose flood-hazard scenarios based on sea level rise and storm assumptions, (b) appreciate the modeling uncertainty behind a chosen hazard zone, (c) select one or several communities to examine exposure, (d) select the category of population or societal asset, and (e) choose how to look at results. The application is designed to highlight comparisons between (a) varying levels of sea level rise and coastal storms, (b) communities, (c) societal asset categories, and (d) spatial scales. Through a combination of spatial and graphical visualizations, HERA aims to help individuals and organizations to craft more informed mitigation and adaptation strategies for climate-driven coastal hazards. This paper summarizes the technologies used to maximize the user experience, in terms of interface design, visualization approaches, and data processing.

  16. Computational Modeling of Cephalad Fluid Shift for Application to Microgravity-Induced Visual Impairment

    Science.gov (United States)

    Nelson, Emily S.; Best, Lauren M.; Myers, Jerry G.; Mulugeta, Lealem

    2013-01-01

    An improved understanding of spaceflight-induced ocular pathology, including the loss of visual acuity, globe flattening, optic disk edema and distension of the optic nerve and optic nerve sheath, is of keen interest to space medicine. Cephalad fluid shift causes a profoundly altered distribution of fluid within the compartments of the head and body, and may indirectly generate phenomena that are biomechanically relevant to visual function, such as choroidal engorgement, compromised drainage of blood and cerebrospinal fluid (CSF), and altered translaminar pressure gradient posterior to the eye. The experimental body of evidence with respect to the consequences of fluid shift has not yet been able to provide a definitive picture of the sequence of events. On earth, elevated intracranial pressure (ICP) is associated with idiopathic intracranial hypertension (IIH), which can produce ocular pathologies that look similar to those seen in some astronauts returning from long-duration flight. However, the clinically observable features of the Visual Impairment and Intracranial Pressure (VIIP) syndrome in space and IIH on earth are not entirely consistent. Moreover, there are at present no experimental measurements of ICP in microgravity. By its very nature, physiological measurements in spaceflight are sparse, and the space environment does not lend itself to well-controlled experiments. In the absence of such data, numerical modeling can play a role in the investigation of biomechanical causal pathways that are suspected of involvement in VIIP. In this work, we describe the conceptual framework for modeling the altered compartmental fluid distribution that represents an equilibrium fluid distribution resulting from the loss of hydrostatic pressure gradient.

  17. Application of single-image camera calibration for ultrasound augmented laparoscopic visualization.

    Science.gov (United States)

    Liu, Xinyang; Su, He; Kang, Sukryool; Kane, Timothy D; Shekhar, Raj

    2015-03-01

    Accurate calibration of laparoscopic cameras is essential for enabling many surgical visualization and navigation technologies such as the ultrasound-augmented visualization system that we have developed for laparoscopic surgery. In addition to accuracy and robustness, there is a practical need for a fast and easy camera calibration method that can be performed on demand in the operating room (OR). Conventional camera calibration methods are not suitable for the OR use because they are lengthy and tedious. They require acquisition of multiple images of a target pattern in its entirety to produce satisfactory result. In this work, we evaluated the performance of a single-image camera calibration tool ( rdCalib ; Percieve3D, Coimbra, Portugal) featuring automatic detection of corner points in the image, whether partial or complete, of a custom target pattern. Intrinsic camera parameters of a 5-mm and a 10-mm standard Stryker ® laparoscopes obtained using rdCalib and the well-accepted OpenCV camera calibration method were compared. Target registration error (TRE) as a measure of camera calibration accuracy for our optical tracking-based AR system was also compared between the two calibration methods. Based on our experiments, the single-image camera calibration yields consistent and accurate results (mean TRE = 1.18 ± 0.35 mm for the 5-mm scope and mean TRE = 1.13 ± 0.32 mm for the 10-mm scope), which are comparable to the results obtained using the OpenCV method with 30 images. The new single-image camera calibration method is promising to be applied to our augmented reality visualization system for laparoscopic surgery.

  18. Application of single-image camera calibration for ultrasound augmented laparoscopic visualization

    Science.gov (United States)

    Liu, Xinyang; Su, He; Kang, Sukryool; Kane, Timothy D.; Shekhar, Raj

    2015-03-01

    Accurate calibration of laparoscopic cameras is essential for enabling many surgical visualization and navigation technologies such as the ultrasound-augmented visualization system that we have developed for laparoscopic surgery. In addition to accuracy and robustness, there is a practical need for a fast and easy camera calibration method that can be performed on demand in the operating room (OR). Conventional camera calibration methods are not suitable for the OR use because they are lengthy and tedious. They require acquisition of multiple images of a target pattern in its entirety to produce satisfactory result. In this work, we evaluated the performance of a single-image camera calibration tool (rdCalib; Percieve3D, Coimbra, Portugal) featuring automatic detection of corner points in the image, whether partial or complete, of a custom target pattern. Intrinsic camera parameters of a 5-mm and a 10-mm standard Stryker® laparoscopes obtained using rdCalib and the well-accepted OpenCV camera calibration method were compared. Target registration error (TRE) as a measure of camera calibration accuracy for our optical tracking-based AR system was also compared between the two calibration methods. Based on our experiments, the single-image camera calibration yields consistent and accurate results (mean TRE = 1.18 ± 0.35 mm for the 5-mm scope and mean TRE = 1.13 ± 0.32 mm for the 10-mm scope), which are comparable to the results obtained using the OpenCV method with 30 images. The new single-image camera calibration method is promising to be applied to our augmented reality visualization system for laparoscopic surgery.

  19. Applications of uncertainty analysis to visual evaluation of density in radiographs

    International Nuclear Information System (INIS)

    Uchida, Suguru; Ohtsuka, Akiyoshi; Fujita, Hiroshi.

    1981-01-01

    Uncertainty analysis, developed as a method of absolute judgment in psychology, is applied to a method of radiographic image evaluation with perceptual fluctuations and to an examination of visual evaluation of density in radiographs. Subjects are composed of three groups of four neurosurgeons, four radiologic technologists and four nonprofessionals. By using a five-category rating scale, each observer is directed to classify 255 radiographs randomly presented without feedback. Characteristics of each observer and each group can be shown quantitatively by calculated information values. It is also described that bivariate uncertainty analysis or entropy method can be used to calculate the degree of agreement of evaluation. (author)

  20. Applications of uncertainty analysis to visual evaluation of density in radiographs

    Energy Technology Data Exchange (ETDEWEB)

    Uchida, S [Gifu Univ. (Japan); Ohtsuka, A; Fujita, H

    1981-03-01

    Uncertainty analysis, developed as a method of absolute judgment in psychology, is applied to a method of radiographic image evaluation with perceptual fluctuations and to an examination of visual evaluation of density in radiographs. Subjects are composed of three groups of four neurosurgeons, four radiologic technologists and four nonprofessionals. By using a five-category rating scale, each observer is directed to classify 255 radiographs randomly presented without feedback. Characteristics of each observer and each group can be shown quantitatively by calculated information values. It is also described that bivariate uncertainty analysis or entropy method can be used to calculate the degree of agreement of evaluation.

  1. Application of TensorFlow to recognition of visualized results of fragment molecular orbital (FMO) calculations

    OpenAIRE

    Saitou, Sona; Iijima, Jun; Fujimoto, Mayu; Mochizuki, Yuji; Okuwaki, Koji; Doi, Hideo; Komeiji, Yuto

    2018-01-01

    We have applied Google's TensorFlow deep learning toolkit to recognize the visualized results of the fragment molecular orbital (FMO) calculations. Typical protein structures of alpha-helix and beta-sheet provide some characteristic patterns in the two-dimensional map of inter-fragment interaction energy termed as IFIE-map (Kurisaki et al., Biophys. Chem. 130 (2007) 1). A thousand of IFIE-map images with labels depending on the existences of alpha-helix and beta-sheet were prepared by employi...

  2. Virtual reality aided visualization of fluid flow simulations with application in medical education and diagnostics.

    Science.gov (United States)

    Djukic, Tijana; Mandic, Vesna; Filipovic, Nenad

    2013-12-01

    Medical education, training and preoperative diagnostics can be drastically improved with advanced technologies, such as virtual reality. The method proposed in this paper enables medical doctors and students to visualize and manipulate three-dimensional models created from CT or MRI scans, and also to analyze the results of fluid flow simulations. Simulation of fluid flow using the finite element method is performed, in order to compute the shear stress on the artery walls. The simulation of motion through the artery is also enabled. The virtual reality system proposed here could shorten the length of training programs and make the education process more effective. © 2013 Published by Elsevier Ltd.

  3. Real time application of whole genome sequencing for outbreak investigation - What is an achievable turnaround time?

    Science.gov (United States)

    McGann, Patrick; Bunin, Jessica L; Snesrud, Erik; Singh, Seema; Maybank, Rosslyn; Ong, Ana C; Kwak, Yoon I; Seronello, Scott; Clifford, Robert J; Hinkle, Mary; Yamada, Stephen; Barnhill, Jason; Lesho, Emil

    2016-07-01

    Whole genome sequencing (WGS) is increasingly employed in clinical settings, though few assessments of turnaround times (TAT) have been performed in real-time. In this study, WGS was used to investigate an unfolding outbreak of vancomycin resistant Enterococcus faecium (VRE) among 3 patients in the ICU of a tertiary care hospital. Including overnight culturing, a TAT of just 48.5 h for a comprehensive report was achievable using an Illumina Miseq benchtop sequencer. WGS revealed that isolates from patient 2 and 3 differed from that of patient 1 by a single nucleotide polymorphism (SNP), indicating nosocomial transmission. However, the unparalleled resolution provided by WGS suggested that nosocomial transmission involved two separate events from patient 1 to patient 2 and 3, and not a linear transmission suspected by the time line. Rapid TAT's are achievable using WGS in the clinical setting and can provide an unprecedented level of resolution for outbreak investigations. Published by Elsevier Inc.

  4. The Estimation of Human Genome Radiosensitivity-Applicability in Radiation Protection

    International Nuclear Information System (INIS)

    Joksic, G.; Nikolic, M.; Vuckovic, M.

    1997-01-01

    The individual variability in response to radiation was examined in a group of 77 healthy individuals, 35-45 years aged, employing Cytochalasin-blocking micronucleus test. Blood samples were irradiated by the most explored therapeutical gamma dose of 2 Gy ( 60 Co) in vitro. The results of our examination demonstrated statistically significant difference in the yield of spontaneously occurring micronuclei between genders of the same age group, while in the yields of induced micronuclei no statistical significance was observed. Out of 77 persons, 4% showed extreme radiosensitivity, while 2% showed extreme radioresistance. Since both extremes are genetically controlled, such genomes could easily be recognized employing CB micronuclei test. It would be useful to perform this type of analysis instead of 'null control' chromosomal aberration analysis for all professionals working in ionizing radiation zone. Persons with such genetic predisposition should be advised to work out of ionizing radiation zone. (author)

  5. Sparse multivariate factor analysis regression models and its applications to integrative genomics analysis.

    Science.gov (United States)

    Zhou, Yan; Wang, Pei; Wang, Xianlong; Zhu, Ji; Song, Peter X-K

    2017-01-01

    The multivariate regression model is a useful tool to explore complex associations between two kinds of molecular markers, which enables the understanding of the biological pathways underlying disease etiology. For a set of correlated response variables, accounting for such dependency can increase statistical power. Motivated by integrative genomic data analyses, we propose a new methodology-sparse multivariate factor analysis regression model (smFARM), in which correlations of response variables are assumed to follow a factor analysis model with latent factors. This proposed method not only allows us to address the challenge that the number of association parameters is larger than the sample size, but also to adjust for unobserved genetic and/or nongenetic factors that potentially conceal the underlying response-predictor associations. The proposed smFARM is implemented by the EM algorithm and the blockwise coordinate descent algorithm. The proposed methodology is evaluated and compared to the existing methods through extensive simulation studies. Our results show that accounting for latent factors through the proposed smFARM can improve sensitivity of signal detection and accuracy of sparse association map estimation. We illustrate smFARM by two integrative genomics analysis examples, a breast cancer dataset, and an ovarian cancer dataset, to assess the relationship between DNA copy numbers and gene expression arrays to understand genetic regulatory patterns relevant to the disease. We identify two trans-hub regions: one in cytoband 17q12 whose amplification influences the RNA expression levels of important breast cancer genes, and the other in cytoband 9q21.32-33, which is associated with chemoresistance in ovarian cancer. © 2016 WILEY PERIODICALS, INC.

  6. PCR-SSCP analysis and its application to human genome study

    International Nuclear Information System (INIS)

    Hayashi, Kenshi

    1994-01-01

    A large amount of DNA sequence data are now available owing to the development of the human genome project. These data are deposited in public databases, e.g. DDBJ, GebBank and EMBL, and freely accessible to scientific community. One of the major advantages of having these databases is that we can now detect sequence differences between individuals in a large scale. Using the sequence informations, we can design primer sequences, amplify various target regions of the sample DNA's by PCR and detect abnormal sequence changes from reference, or normal sequences. Detecting sequence changes, or mutations, are essential part of searching genes responsible for hereditary diseases and also DNA diagnosis of hereditary diseases or cancer. We can also measure mutation frequency of the human genome by knowing its variability. Our group has developed and been improving a method, PCR-SSCP analysis, as an extremely rapid and easy technique for detection of sequence differences between sample DNA's. Knowing the sensitivity (percentage detection of mutations) of this technique is important in evaluating usefulness of it for the purposes stated above. Considerable number of experiences on PCR-SSCP analysis of fragments shorter than 300 b.p. are accumulating. We summarize here the sensitivity of PCR-SSCP analysis for various sequence context of this size range examined in various electrophoretic conditions conducted in many laboratories. Data on mutation detection by this technique for longer fragments are limited. We also present oue effort for defining electrophoretic conditions of PCR-SSCP analysis when examining longer (350 to 600 b.p.) fragments. (author)

  7. The Application of Restriction Landmark Genome Scanning Method for Surveillance of Non-Mendelian Inheritance in F1 Hybrids

    Directory of Open Access Journals (Sweden)

    Tomoko Takamiya

    2009-01-01

    Full Text Available We analyzed inheritance of DNA methylation in reciprocal F1 hybrids (subsp. japonica cv. Nipponbare × subsp. indica cv. Kasalath of rice (Oryza sativa L. using restriction landmark genome scanning (RLGS, and detected differing RLGS spots between the parents and reciprocal F1 hybrids. MspI/HpaII restriction sites in the DNA from these different spots were suspected to be heterozygously methylated in the Nipponbare parent. These spots segregated in F1 plants, but did not segregate in selfed progeny of Nipponbare, showing non-Mendelian inheritance of the methylation status. As a result of RT-PCR and sequencing, a specific allele of the gene nearest to the methylated sites was expressed in reciprocal F1 plants, showing evidence of biased allelic expression. These results show the applicability of RLGS for scanning of non-Mendelian inheritance of DNA methylation and biased allelic expression.

  8. Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products.

    Science.gov (United States)

    Holst-Jensen, Arne; Spilsberg, Bjørn; Arulandhu, Alfred J; Kok, Esther; Shi, Jianxin; Zel, Jana

    2016-07-01

    The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however, inevitably introduce a bias and are prone to miss unknown targets. Here we review the application of high-throughput sequencing technologies and the preparation of fit-for-purpose whole genome shotgun sequencing libraries for the detection and characterization of genetically modified and derived products. The potential impact of these new sequencing technologies for the characterization, breeding selection, risk assessment, and traceability of genetically modified organisms and genetically modified products is yet to be fully acknowledged. The published literature is reviewed, and the prospects for future developments and use of the new sequencing technologies for these purposes are discussed.

  9. Guest editors' introduction : Highlights from IEEE Pacific Visualization

    NARCIS (Netherlands)

    Wijk, van J.J.; North, S.; Shen, H.-W.

    2010-01-01

    This article looks briefly at four articles based on papers from the 2010 IEEE Pacific Visualization Symposium. These articles, which strongly focus on visual design and applications, cover a range of applications in scientific visualization, information visualization, and graph visualization,

  10. Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface

    Directory of Open Access Journals (Sweden)

    Bushell Michael E

    2011-05-01

    Full Text Available Abstract Background Constraint-based approaches facilitate the prediction of cellular metabolic capabilities, based, in turn on predictions of the repertoire of enzymes encoded in the genome. Recently, genome annotations have been used to reconstruct genome scale metabolic reaction networks for numerous species, including Homo sapiens, which allow simulations that provide valuable insights into topics, including predictions of gene essentiality of pathogens, interpretation of genetic polymorphism in metabolic disease syndromes and suggestions for novel approaches to microbial metabolic engineering. These constraint-based simulations are being integrated with the functional genomics portals, an activity that requires efficient implementation of the constraint-based simulations in the web-based environment. Results Here, we present Acorn, an open source (GNU GPL grid computing system for constraint-based simulations of genome scale metabolic reaction networks within an interactive web environment. The grid-based architecture allows efficient execution of computationally intensive, iterative protocols such as Flux Variability Analysis, which can be readily scaled up as the numbers of models (and users increase. The web interface uses AJAX, which facilitates efficient model browsing and other search functions, and intuitive implementation of appropriate simulation conditions. Research groups can install Acorn locally and create user accounts. Users can also import models in the familiar SBML format and link reaction formulas to major functional genomics portals of choice. Selected models and simulation results can be shared between different users and made publically available. Users can construct pathway map layouts and import them into the server using a desktop editor integrated within the system. Pathway maps are then used to visualise numerical results within the web environment. To illustrate these features we have deployed Acorn and created a

  11. Application Of Empirical Phase Diagrams For Multidimensional Data Visualization Of High Throughput Microbatch Crystallization Experiments.

    Science.gov (United States)

    Klijn, Marieke E; Hubbuch, Jürgen

    2018-04-27

    Protein phase diagrams are a tool to investigate cause and consequence of solution conditions on protein phase behavior. The effects are scored according to aggregation morphologies such as crystals or amorphous precipitates. Solution conditions affect morphological features, such as crystal size, as well as kinetic features, such as crystal growth time. Common used data visualization techniques include individual line graphs or symbols-based phase diagrams. These techniques have limitations in terms of handling large datasets, comprehensiveness or completeness. To eliminate these limitations, morphological and kinetic features obtained from crystallization images generated with high throughput microbatch experiments have been visualized with radar charts in combination with the empirical phase diagram (EPD) method. Morphological features (crystal size, shape, and number, as well as precipitate size) and kinetic features (crystal and precipitate onset and growth time) are extracted for 768 solutions with varying chicken egg white lysozyme concentration, salt type, ionic strength and pH. Image-based aggregation morphology and kinetic features were compiled into a single and easily interpretable figure, thereby showing that the EPD method can support high throughput crystallization experiments in its data amount as well as its data complexity. Copyright © 2018. Published by Elsevier Inc.

  12. Gauging the impact of gender grammaticization in different languages: Application of a linguistic-visual paradigm

    Directory of Open Access Journals (Sweden)

    Sayaka eSato

    2016-02-01

    Full Text Available Employing a linguistic-visual paradigm, we investigated whether the grammaticization of gender information impacts readers’ gender representations. French and German were taken as comparative languages, taking into account the male gender bias associated to both languages, as well as the comparative gender biases associated to their plural determiners (French: les [generic] vs. German: die [morphologically feminine]. Bilingual speakers of French and German had to judge whether a pair of facial images representing two men or a man and a woman could represent a gender stereotypical role noun prime (e.g., nurses. The prime was presented in the masculine plural form with or without a plural determiner. Results indicated that the overt grammaticization of the male gender in the masculine form dominated the representation of the role nouns (though interpretable as generic. However, the effect of the determiner was not found, indicating that only gender information associated to a human reference role noun had impacted readers’ representations. The results, discussed in the framework of the thinking-for-speaking hypothesis, demonstrated that linguistic-visual paradigms are well-suited to gauge the impact of both stereotype information and grammaticization when processing role nouns.Keywords: gender representation, gender stereotypes, grammatical gender, generic masculine, thinking-for-speaking hypothesis, bilingualism

  13. Application of Automatic Zooming and Autofocusing in Microassembly using Visual Servoing

    International Nuclear Information System (INIS)

    Jang, Kyung-Nam; Kim, Jong-Seog

    2006-01-01

    In recent years, many industrial products and their components are evolving toward miniaturization. To have more functionalities within less dimensional volume, they are usually made of various materials with different characteristics, and they are manufactured using incompatible manufacturing processes with complex geometrical shapes. For these reasons, the assembly technique for mating micro-parts so called microassembly has become important for advanced manufacturing and drawn extensive research interest. Currently, due to various difficulties arising from handling of extremely small size parts, manual assembly method has been widely used. Since this manual method is somehow timeconsuming and not productive enough, automation of micro-assembly has become an essential part for micro parts manufacturing. As an alternative, the vision sensor is widely used in microassembly. The vision sensor has a wide field of view, and it can obtain the wide range data with high speed without contact. In the previous research works, the orientation of the mating parts has not been considered for corrective motion, and, furthermore, the developed vision systems are not adaptive to accommodate various sizes of the mated parts to avoid such criticism, we propose a visual feedback system that accommodates micro parts of various sizes and parts arbitrarily oriented. In this paper, the system that employs adaptive zooming and auto focusing techniques during visual servoing is described

  14. Semi-Supervised Tensor-Based Graph Embedding Learning and Its Application to Visual Discriminant Tracking.

    Science.gov (United States)

    Hu, Weiming; Gao, Jin; Xing, Junliang; Zhang, Chao; Maybank, Stephen

    2017-01-01

    An appearance model adaptable to changes in object appearance is critical in visual object tracking. In this paper, we treat an image patch as a two-order tensor which preserves the original image structure. We design two graphs for characterizing the intrinsic local geometrical structure of the tensor samples of the object and the background. Graph embedding is used to reduce the dimensions of the tensors while preserving the structure of the graphs. Then, a discriminant embedding space is constructed. We prove two propositions for finding the transformation matrices which are used to map the original tensor samples to the tensor-based graph embedding space. In order to encode more discriminant information in the embedding space, we propose a transfer-learning- based semi-supervised strategy to iteratively adjust the embedding space into which discriminative information obtained from earlier times is transferred. We apply the proposed semi-supervised tensor-based graph embedding learning algorithm to visual tracking. The new tracking algorithm captures an object's appearance characteristics during tracking and uses a particle filter to estimate the optimal object state. Experimental results on the CVPR 2013 benchmark dataset demonstrate the effectiveness of the proposed tracking algorithm.

  15. Gauging the Impact of Gender Grammaticization in Different Languages: Application of a Linguistic-Visual Paradigm

    Science.gov (United States)

    Sato, Sayaka; Gygax, Pascal M.; Gabriel, Ute

    2016-01-01

    Employing a linguistic-visual paradigm, we investigated whether the grammaticization of gender information impacts readers’ gender representations. French and German were taken as comparative languages, taking into account the male gender bias associated to both languages, as well as the comparative gender biases associated to their plural determiners (French: les [generic] vs. German: die [morphologically feminine]). Bilingual speakers of French and German had to judge whether a pair of facial images representing two men or a man and a woman could represent a gender stereotypical role noun prime (e.g., nurses). The prime was presented in the masculine plural form with or without a plural determiner. Results indicated that the overt grammaticization of the male gender in the masculine form dominated the representation of the role nouns (though interpretable as generic). However, the effect of the determiner was not found, indicating that only gender information associated to a human reference role noun had impacted readers’ representations. The results, discussed in the framework of the thinking-for-speaking hypothesis, demonstrated that linguistic-visual paradigms are well-suited to gauge the impact of both stereotype information and grammaticization when processing role nouns. PMID:26941663

  16. Application of electroencephalographic techniques to the study of visual impact of renewable energies.

    Science.gov (United States)

    Grima Murcia, M D; Sánchez Ferrer, Francisco; Sorinas, Jennifer; Ferrandez, J M; Fernandez, Eduardo

    2017-09-15

    Much is currently being studied on the negative visual impact associated to the installation of large wind turbines or photovoltaic farms. However, methodologies for quantitatively assessing landscape impact are scarce. In this work we used electroencephalographic (EEG) recordings to investigate the brain activity of 14 human volunteers when looking at the same landscapes with and without wind turbines, solar panels and nuclear power plants. Our results showed no significant differences for landscapes with solar power systems or without them, and the same happened for wind turbines, what was in agreement with their subjective scores. However, there were clear and significant differences when looking at landscapes with and without nuclear power plants. These differences were more pronounced around a time window of 376-407 msec and showed a clear right lateralization for the pictures containing nuclear power plants. Although more studies are still needed, these results suggest that EEG recordings can be a useful procedure for measuring visual impact. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

    Directory of Open Access Journals (Sweden)

    de Vlieg Jacob

    2008-10-01

    Full Text Available Abstract Background In many genomics projects, numerous lists containing biological identifiers are produced. Often it is useful to see the overlap between different lists, enabling researchers to quickly observe similarities and differences between the data sets they are analyzing. One of the most popular methods to visualize the overlap and differences between data sets is the Venn diagram: a diagram consisting of two or more circles in which each circle corresponds to a data set, and the overlap between the circles corresponds to the overlap between the data sets. Venn diagrams are especially useful when they are 'area-proportional' i.e. the sizes of the circles and the overlaps correspond to the sizes of the data sets. Currently there are no programs available that can create area-proportional Venn diagrams connected to a wide range of biological databases. Results We designed a web application named BioVenn to summarize the overlap between two or three lists of identifiers, using area-proportional Venn diagrams. The user only needs to input these lists of identifiers in the textboxes and push the submit button. Parameters like colors and text size can be adjusted easily through the web interface. The position of the text can be adjusted by 'drag-and-drop' principle. The output Venn diagram can be shown as an SVG or PNG image embedded in the web application, or as a standalone SVG or PNG image. The latter option is useful for batch queries. Besides the Venn diagram, BioVenn outputs lists of identifiers for each of the resulting subsets. If an identifier is recognized as belonging to one of the supported biological databases, the output is linked to that database. Finally, BioVenn can map Affymetrix and EntrezGene identifiers to Ensembl genes. Conclusion BioVenn is an easy-to-use web application to generate area-proportional Venn diagrams from lists of biological identifiers. It supports a wide range of identifiers from the most used

  18. The analysis of visual variables for use in the cartographic design of point symbols for mobile Augmented Reality applications

    Science.gov (United States)

    Halik, Łukasz

    2012-11-01

    The objective of the present deliberations was to systematise our knowledge of static visual variables used to create cartographic symbols, and also to analyse the possibility of their utilisation in the Augmented Reality (AR) applications on smartphone-type mobile devices. This was accomplished by combining the visual variables listed over the years by different researchers. Research approach was to determine the level of usefulness of particular characteristics of visual variables such as selective, associative, quantitative and order. An attempt was made to provide an overview of static visual variables and to describe the AR system which is a new paradigm of the user interface. Changing the approach to the presentation of point objects is caused by applying different perspective in the observation of objects (egocentric view) than it is done on traditional analogue maps (geocentric view). Presented topics will refer to the fast-developing field of cartography, namely mobile cartography. Particular emphasis will be put on smartphone-type mobile devices and their applicability in the process of designing cartographic symbols. Celem artykułu było usystematyzowanie wiedzy na temat statycznych zmiennych wizualnych, które sa kluczowymi składnikami budujacymi sygnatury kartograficzne. Podjeto próbe zestawienia zmiennych wizualnych wyodrebnionych przez kartografów na przestrzeni ostatnich piecdziesieciu lat, zaczynajac od klasyfikacji przedstawionej przez J. Bertin’a. Dokonano analizy stopnia uzytecznosci poszczególnych zmiennych graficznych w aspekcie ich wykorzystania w projektowaniu znaków punktowych dla mobilnych aplikacji tworzonych w technologii Rzeczywistosci Rozszerzonej (Augmented Reality). Zmienne poddano analizie pod wzgledem czterech charakterystyk: selektywnosci, skojarzeniowosci, odzwierciedlenia ilosci oraz porzadku. W artykule zwrócono uwage na odmienne zastosowanie perspektywy pomiedzy tradycyjnymi analogowymi mapami (geocentrycznosc) a

  19. GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks

    Directory of Open Access Journals (Sweden)

    Kam D. Dahlquist

    2016-09-01

    Full Text Available GRNsight is a web application and service for visualizing models of gene regulatory networks (GRNs. A gene regulatory network (GRN consists of genes, transcription factors, and the regulatory connections between them which govern the level of expression of mRNA and protein from genes. The original motivation came from our efforts to perform parameter estimation and forward simulation of the dynamics of a differential equations model of a small GRN with 21 nodes and 31 edges. We wanted a quick and easy way to visualize the weight parameters from the model which represent the direction and magnitude of the influence of a transcription factor on its target gene, so we created GRNsight. GRNsight automatically lays out either an unweighted or weighted network graph based on an Excel spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows, a Simple Interaction Format (SIF text file, or a GraphML XML file. When a user uploads an input file specifying an unweighted network, GRNsight automatically lays out the graph using black lines and pointed arrowheads. For a weighted network, GRNsight uses pointed and blunt arrowheads, and colors the edges and adjusts their thicknesses based on the sign (positive for activation or negative for repression and magnitude of the weight parameter. GRNsight is written in JavaScript, with diagrams facilitated by D3.js, a data visualization library. Node.js and the Express framework handle server-side functions. GRNsight’s diagrams are based on D3.js’s force graph layout algorithm, which was then extensively customized to support the specific needs of GRNs. Nodes are rectangular and support gene labels of up to 12 characters. The edges are arcs, which become straight lines when the nodes are close together. Self-regulatory edges are indicated by a loop. When a user mouses over an edge, the numerical value of the weight parameter is displayed. Visualizations can

  20. On the analysis of genome-wide association studies in family-based designs: a universal, robust analysis approach and an application to four genome-wide association studies.

    Directory of Open Access Journals (Sweden)

    Sungho Won

    2009-11-01

    Full Text Available For genome-wide association studies in family-based designs, we propose a new, universally applicable approach. The new test statistic exploits all available information about the association, while, by virtue of its design, it maintains the same robustness against population admixture as traditional family-based approaches that are based exclusively on the within-family information. The approach is suitable for the analysis of almost any trait type, e.g. binary, continuous, time-to-onset, multivariate, etc., and combinations of those. We use simulation studies to verify all theoretically derived properties of the approach, estimate its power, and compare it with other standard approaches. We illustrate the practical implications of the new analysis method by an application to a lung-function phenotype, forced expiratory volume in one second (FEV1 in 4 genome-wide association studies.

  1. A geometrical description of visual sensation II:A complemented model for visual sensation explicitly taking into account the law of Fechner, and its application to Plateau's irradiation

    OpenAIRE

    Ons, Bart; Verstraelen, Pol

    2010-01-01

    Plateau’s irradiation phenomenon in particular describes what one sees when observing a brighter object on a darker background and a physically congruent darker object on a brighter background: the brighter object is seen as being larger. This phenomenon occurs in many optical visual illusions and it involves some fundamental aspects of human vision. We present a general geometrical model of human visual sensation and perception, hereby taking into account the law of Fechner in addition to th...

  2. Annotation and Visualization in Android: An Application for Education and Real Time Information

    Directory of Open Access Journals (Sweden)

    Renato Barahona Neri

    2013-06-01

    Full Text Available By using Augmented Reality applications, users can get more information while interacting with real objects. The popularity of the Smartphones and the ubiquity of an Internet connection within modern devices, offer the best combination for these kind of applications, which can pull content from heterogeneous sources. The goal with this work is to show the architecture and a basic implementation of a prototype for an AR application that displays information (opinions about physical places as comments overlaid to the place left there by other users, but that also encourage in-situ content creation for collaboration. These applications can also be used in order to improve the interaction between students and physical places, getting facts, or associating quizzes to a specific location; tourism guides, promotions of products, just to mention a few.

  3. An Ontology-Based GIS for Genomic Data Management of Rumen Microbes.

    Science.gov (United States)

    Jelokhani-Niaraki, Saber; Tahmoorespur, Mojtaba; Minuchehr, Zarrin; Nassiri, Mohammad Reza

    2015-03-01

    During recent years, there has been exponential growth in biological information. With the emergence of large datasets in biology, life scientists are encountering bottlenecks in handling the biological data. This study presents an integrated geographic information system (GIS)-ontology application for handling microbial genome data. The application uses a linear referencing technique as one of the GIS functionalities to represent genes as linear events on the genome layer, where users can define/change the attributes of genes in an event table and interactively see the gene events on a genome layer. Our application adopted ontology to portray and store genomic data in a semantic framework, which facilitates data-sharing among biology domains, applications, and experts. The application was developed in two steps. In the first step, the genome annotated data were prepared and stored in a MySQL database. The second step involved the connection of the database to both ArcGIS and Protégé as the GIS engine and ontology platform, respectively. We have designed this application specifically to manage the genome-annotated data of rumen microbial populations. Such a GIS-ontology application offers powerful capabilities for visualizing, managing, reusing, sharing, and querying genome-related data.

  4. An Ontology-Based GIS for Genomic Data Management of Rumen Microbes

    Directory of Open Access Journals (Sweden)

    Saber Jelokhani-Niaraki

    2015-03-01

    Full Text Available During recent years, there has been exponential growth in biological information. With the emergence of large datasets in biology, life scientists are encountering bottlenecks in handling the biological data. This study presents an integrated geographic information system (GIS-ontology application for handling microbial genome data. The application uses a linear referencing technique as one of the GIS functionalities to represent genes as linear events on the genome layer, where users can define/change the attributes of genes in an event table and interactively see the gene events on a genome layer. Our application adopted ontology to portray and store genomic data in a semantic framework, which facilitates data-sharing among biology domains, applications, and experts. The application was developed in two steps. In the first step, the genome annotated data were prepared and stored in a MySQL database. The second step involved the connection of the database to both ArcGIS and Protégé as the GIS engine and ontology platform, respectively. We have designed this application specifically to manage the genome-annotated data of rumen microbial populations. Such a GIS-ontology application offers powerful capabilities for visualizing, managing, reusing, sharing, and querying genome-related data.

  5. An Ontology-Based GIS for Genomic Data Management of Rumen Microbes

    Science.gov (United States)

    Jelokhani-Niaraki, Saber; Minuchehr, Zarrin; Nassiri, Mohammad Reza

    2015-01-01

    During recent years, there has been exponential growth in biological information. With the emergence of large datasets in biology, life scientists are encountering bottlenecks in handling the biological data. This study presents an integrated geographic information system (GIS)-ontology application for handling microbial genome data. The application uses a linear referencing technique as one of the GIS functionalities to represent genes as linear events on the genome layer, where users can define/change the attributes of genes in an event table and interactively see the gene events on a genome layer. Our application adopted ontology to portray and store genomic data in a semantic framework, which facilitates data-sharing among biology domains, applications, and experts. The application was developed in two steps. In the first step, the genome annotated data were prepared and stored in a MySQL database. The second step involved the connection of the database to both ArcGIS and Protégé as the GIS engine and ontology platform, respectively. We have designed this application specifically to manage the genome-annotated data of rumen microbial populations. Such a GIS-ontology application offers powerful capabilities for visualizing, managing, reusing, sharing, and querying genome-related data. PMID:25873847

  6. Synthetic schlieren—application to the visualization and characterization of air convection

    Science.gov (United States)

    Taberlet, Nicolas; Plihon, Nicolas; Auzémery, Lucile; Sautel, Jérémy; Panel, Grégoire; Gibaud, Thomas

    2018-05-01

    Synthetic schlieren is a digital image processing optical method relying on the variation of optical index to visualize the flow of a transparent fluid. In this article, we present a step-by-step, easy-to-implement and affordable experimental realization of this technique. The method is applied to air convection caused by a warm surface. We show that the velocity of rising convection plumes can be linked to the temperature of the warm surface and propose a simple physical argument to explain this dependence. Moreover, using this method, one can reveal the tenuous convection plumes rising from one’s hand, a phenomenon invisible to the naked eye. This spectacular result may help students to realize the power of careful data acquisition combined with astute image processing techniques. This spectacular result may help students to realize the power of careful data acquisition combined with astute image processing techniques (refer to the video abstract).

  7. Application of CRISPR/Cas9 Genome Editing Technology for the Improvement of Crops Cultivated in Tropical Climates: Recent Progress, Prospects, and Challenges

    Directory of Open Access Journals (Sweden)

    Effi Haque

    2018-05-01

    Full Text Available The world population is expected to increase from 7.3 to 9.7 billion by 2050. Pest outbreak and increased abiotic stresses due to climate change pose a high risk to tropical crop production. Although conventional breeding techniques have significantly increased crop production and yield, new approaches are required to further improve crop production in order to meet the global growing demand for food. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9 (CRISPR-associated protein9 genome editing technology has shown great promise for quickly addressing emerging challenges in agriculture. It can be used to precisely modify genome sequence of any organism including plants to achieve the desired trait. Compared to other genome editing tools such as zinc finger nucleases (ZFNs and transcriptional activator-like effector nucleases (TALENs, CRISPR/Cas9 is faster, cheaper, precise and highly efficient in editing genomes even at the multiplex level. Application of CRISPR/Cas9 technology in editing the plant genome is emerging rapidly. The CRISPR/Cas9 is becoming a user-friendly tool for development of non-transgenic genome edited crop plants to counteract harmful effects from climate change and ensure future food security of increasing population in tropical countries. This review updates current knowledge and potentials of CRISPR/Cas9 for improvement of crops cultivated in tropical climates to gain resiliency against emerging pests and abiotic stresses.

  8. Application of CRISPR/Cas9 Genome Editing Technology for the Improvement of Crops Cultivated in Tropical Climates: Recent Progress, Prospects, and Challenges.

    Science.gov (United States)

    Haque, Effi; Taniguchi, Hiroaki; Hassan, Md Mahmudul; Bhowmik, Pankaj; Karim, M Rezaul; Śmiech, Magdalena; Zhao, Kaijun; Rahman, Mahfuzur; Islam, Tofazzal

    2018-01-01

    The world population is expected to increase from 7.3 to 9.7 billion by 2050. Pest outbreak and increased abiotic stresses due to climate change pose a high risk to tropical crop production. Although conventional breeding techniques have significantly increased crop production and yield, new approaches are required to further improve crop production in order to meet the global growing demand for food. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 (CRISPR-associated protein9) genome editing technology has shown great promise for quickly addressing emerging challenges in agriculture. It can be used to precisely modify genome sequence of any organism including plants to achieve the desired trait. Compared to other genome editing tools such as zinc finger nucleases (ZFNs) and transcriptional activator-like effector nucleases (TALENs), CRISPR/Cas9 is faster, cheaper, precise and highly efficient in editing genomes even at the multiplex level. Application of CRISPR/Cas9 technology in editing the plant genome is emerging rapidly. The CRISPR/Cas9 is becoming a user-friendly tool for development of non-transgenic genome edited crop plants to counteract harmful effects from climate change and ensure future food security of increasing population in tropical countries. This review updates current knowledge and potentials of CRISPR/Cas9 for improvement of crops cultivated in tropical climates to gain resiliency against emerging pests and abiotic stresses.

  9. The role of prevention-oriented attitudes towards nature in people's judgment of new applications of genomics techniques in soil ecology

    NARCIS (Netherlands)

    de Boer, J.

    2010-01-01

    New applications of genomics techniques in soil ecology may provide people with fresh insights into the richness of microbial life forms and natural methods to build on the "self-cleaning capacity" of soils. Because genetic modification might also be involved, this paper examines people's judgments

  10. Survey of Network Visualization Tools

    Science.gov (United States)

    2007-12-01

    programming language such as Java, C #, Delphi and Visual basic. AlgoCOMs Network also supports Visual Basic for Applications ( VBA ). Hardware: Users...AlgoCOMs Network also supports Visual Basic for Applications ( VBA ). Hardware: Users: Availability: • Commercially Available Cost $101...Application Monitoring - Constantly watch the health of your mission-critical applications: MS SQL , MS Exchange, MS IIS, Active Directory. Event

  11. Bovine viral diarrhea virus: molecular cloning of genomic RNA and its diagnostic application

    International Nuclear Information System (INIS)

    Brock, K.V.

    1987-01-01

    Molecular cloning of a field isolate of bovine viral diarrhea virus (BVDV) strain 72 RNA was done in this study. The sensitivity and specificity of cloned cDNA sequences in hybridization assays with various BVDV strains were determined. cDNA was synthesized from polyadenylated BVDV RNA templates with oligo-dT primers, reverse transcriptase, and DNA polymerase I. The newly synthesized double-stranded BVDV cDNA was C-tailed with terminal deoxytransferase and annealed into G-tailed, Pst-1-cut pUC9 plasmid. Escherichia coli was transformed with the recombinant plasmids and a library of approximately 200 BVDV specific cDNA clones varying in length from 0.5 to 2.6 kilobases were isolated. The sensitivity and specificity of hybridization between the labelled cDNA and BVDV target sequences were determined. Cloned BVDV sequences were isolated from pUC9 plasmid DNA and labelled with 32 P by nick translation. The detection limit by dot blot hybridization assay was 20 pg of purified genomic BVDV RNA. cDNA hybridization probes were specific for all strains of BVDV tested, regardless of whether they were noncytopathic and cytopathic, but did not hybridize with heterologous bovine viruses tested. Probes did not hybridize with uninfected cell culture or cellular RNA. Hybridization probes were at least as sensitive as infectivity assays in detecting homologous virus

  12. Best practice guidelines for the use of next-generation sequencing applications in genome diagnostics: a national collaborative study of dutch genome diagnostic laboratories

    NARCIS (Netherlands)

    Weiss, Marjan M.; van der Zwaag, Bert; Jongbloed, Jan D. H.; Vogel, Maartje J.; Brüggenwirth, Hennie T.; Lekanne Deprez, Ronald H.; Mook, Olaf; Ruivenkamp, Claudia A. L.; van Slegtenhorst, Marjon A.; van den Wijngaard, Arthur; Waisfisz, Quinten; Nelen, Marcel R.; van der Stoep, Nienke

    2013-01-01

    Next-generation sequencing (NGS) methods are being adopted by genome diagnostics laboratories worldwide. However, implementing NGS-based tests according to diagnostic standards is a challenge for individual laboratories. To facilitate the implementation of NGS in Dutch laboratories, the Dutch

  13. The first draft genome of the aquatic model plant Lemna minor opens the route for future stress physiology research and biotechnological applications

    OpenAIRE

    Van Hoeck, Arne; Horemans, Nele; Monsieurs, Pieter; Cao, Hieu Xuan; Vandenhove, Hildegarde; Blust, Ronny

    2015-01-01

    Background: Freshwater duckweed, comprising the smallest, fastest growing and simplest macrophytes has various applications in agriculture, phytoremediation and energy production. Lemna minor, the so-called common duckweed, is a model system of these aquatic plants for ecotoxicological bioassays, genetic transformation tools and industrial applications. Given the ecotoxic relevance and high potential for biomass production, whole-genome information of this cosmopolitan duckweed is needed. Res...

  14. Recent updates and developments to plant genome size databases

    Science.gov (United States)

    Garcia, Sònia; Leitch, Ilia J.; Anadon-Rosell, Alba; Canela, Miguel Á.; Gálvez, Francisco; Garnatje, Teresa; Gras, Airy; Hidalgo, Oriane; Johnston, Emmeline; Mas de Xaxars, Gemma; Pellicer, Jaume; Siljak-Yakovlev, Sonja; Vallès, Joan; Vitales, Daniel; Bennett, Michael D.

    2014-01-01

    Two plant genome size databases have been recently updated and/or extended: the Plant DNA C-values database (http://data.kew.org/cvalues), and GSAD, the Genome Size in Asteraceae database (http://www.asteraceaegenomesize.com). While the first provides information on nuclear DNA contents across land plants and some algal groups, the second is focused on one of the largest and most economically important angiosperm families, Asteraceae. Genome size data have numerous applications: they can be used in comparative studies on genome evolution, or as a tool to appraise the cost of whole-genome sequencing programs. The growing interest in genome size and increasing rate of data accumulation has necessitated the continued update of these databases. Currently, the Plant DNA C-values database (Release 6.0, Dec. 2012) contains data for 8510 species, while GSAD has 1219 species (Release 2.0, June 2013), representing increases of 17 and 51%, respectively, in the number of species with genome size data, compared with previous releases. Here we provide overviews of the most recent releases of each database, and outline new features of GSAD. The latter include (i) a tool to visually compare genome size data between species, (ii) the option to export data and (iii) a webpage containing information about flow cytometry protocols. PMID:24288377

  15. Novel data visualizations of X-ray data for aviation security applications using the Open Threat Assessment Platform (OTAP)

    Science.gov (United States)

    Gittinger, Jaxon M.; Jimenez, Edward S.; Holswade, Erica A.; Nunna, Rahul S.

    2017-02-01

    This work will demonstrate the implementation of a traditional and non-traditional visualization of x-ray images for aviation security applications that will be feasible with open system architecture initiatives such as the Open Threat Assessment Platform (OTAP). Anomalies of interest to aviation security are fluid, where characteristic signals of anomalies of interest can evolve rapidly. OTAP is a limited scope open architecture baggage screening prototype that intends to allow 3rd-party vendors to develop and easily implement, integrate, and deploy detection algorithms and specialized hardware on a field deployable screening technology [13]. In this study, stereoscopic images were created using an unmodified, field-deployed system and rendered on the Oculus Rift, a commercial virtual reality video gaming headset. The example described in this work is not dependent on the Oculus Rift, and is possible using any comparable hardware configuration capable of rendering stereoscopic images. The depth information provided from viewing the images will aid in the detection of characteristic signals from anomalies of interest. If successful, OTAP has the potential to allow for aviation security to become more fluid in its adaptation to the evolution of anomalies of interest. This work demonstrates one example that is easily implemented using the OTAP platform, that could lead to the future generation of ATR algorithms and data visualization approaches.

  16. Harnessing modern web application technology to create intuitive and efficient data visualization and sharing tools

    Directory of Open Access Journals (Sweden)

    Dylan eWood

    2014-08-01

    Full Text Available Neuroscientists increasingly need to work with big data in order to derive meaningful results in their field. Collecting, organizing and analyzing this data can be a major hurdle on the road to scientific discovery. This hurdle can be lowered using the same technologies that are currently revolutionizing the way that cultural and social media sites represent and share information with their users. Web application technologies and standards such as RESTful webservices, HTML5 and high-performance in-browser JavaScript engines are being utilized to vastly improve the way that the world accesses and shares information. The neuroscience community can also benefit tremendously from these technologies. We present here a web application that allows users to explore and request the complex datasets that need to be shared among the neuroimaging community. The COINS (Collaborative Informatics and Neuroimaging Suite Data Exchange uses web application technologies to facilitate data sharing in three phases: Exploration, Request/Communication, and Download. This paper will focus on the first phase, and how intuitive exploration of large and complex datasets is achieved using a framework that centers around asynchronous client-server communication (AJAX and also exposes a powerful API that can be utilized by other applications to explore available data. First opened to the neuroscience community in August 2012, the Data Exchange has already provided researchers with over 2500 GB of data.

  17. Harnessing modern web application technology to create intuitive and efficient data visualization and sharing tools.

    Science.gov (United States)

    Wood, Dylan; King, Margaret; Landis, Drew; Courtney, William; Wang, Runtang; Kelly, Ross; Turner, Jessica A; Calhoun, Vince D

    2014-01-01

    Neuroscientists increasingly need to work with big data in order to derive meaningful results in their field. Collecting, organizing and analyzing this data can be a major hurdle on the road to scientific discovery. This hurdle can be lowered using the same technologies that are currently revolutionizing the way that cultural and social media sites represent and share information with their users. Web application technologies and standards such as RESTful webservices, HTML5 and high-performance in-browser JavaScript engines are being utilized to vastly improve the way that the world accesses and shares information. The neuroscience community can also benefit tremendously from these technologies. We present here a web application that allows users to explore and request the complex datasets that need to be shared among the neuroimaging community. The COINS (Collaborative Informatics and Neuroimaging Suite) Data Exchange uses web application technologies to facilitate data sharing in three phases: Exploration, Request/Communication, and Download. This paper will focus on the first phase, and how intuitive exploration of large and complex datasets is achieved using a framework that centers around asynchronous client-server communication (AJAX) and also exposes a powerful API that can be utilized by other applications to explore available data. First opened to the neuroscience community in August 2012, the Data Exchange has already provided researchers with over 2500 GB of data.

  18. Immunohistochemical visualization of neurons and specific glial cells for stereological application in the porcine neocortex

    DEFF Research Database (Denmark)

    Lyck, Lise; Jelsing, Jacob; Jensen, Pia Søndergaard

    2006-01-01

    The pig is becoming an increasingly used non-primate model in basic experimental studies of human neurological diseases. In spite of the widespread use of immunohistochemistry and cell type specific markers, the application of immunohistochemistry in the pig brain has not been systematically desc...

  19. Multi-objective evolutionary optimization for constructing neural networks for virtual reality visual data mining: application to geophysical prospecting.

    Science.gov (United States)

    Valdés, Julio J; Barton, Alan J

    2007-05-01

    A method for the construction of virtual reality spaces for visual data mining using multi-objective optimization with genetic algorithms on nonlinear discriminant (NDA) neural networks is presented. Two neural network layers (the output and the last hidden) are used for the construction of simultaneous solutions for: (i) a supervised classification of data patterns and (ii) an unsupervised similarity structure preservation between the original data matrix and its image in the new space. A set of spaces are constructed from selected solutions along the Pareto front. This strategy represents a conceptual improvement over spaces computed by single-objective optimization. In addition, genetic programming (in particular gene expression programming) is used for finding analytic representations of the complex mappings generating the spaces (a composition of NDA and orthogonal principal components). The presented approach is domain independent and is illustrated via application to the geophysical prospecting of caves.

  20. DEEP-SEE: Joint Object Detection, Tracking and Recognition with Application to Visually Impaired Navigational Assistance

    Directory of Open Access Journals (Sweden)

    Ruxandra Tapu

    2017-10-01

    Full Text Available In this paper, we introduce the so-called DEEP-SEE framework that jointly exploits computer vision algorithms and deep convolutional neural networks (CNNs to detect, track and recognize in real time objects encountered during navigation in the outdoor environment. A first feature concerns an object detection technique designed to localize both static and dynamic objects without any a priori knowledge about their position, type or shape. The methodological core of the proposed approach relies on a novel object tracking method based on two convolutional neural networks trained offline. The key principle consists of alternating between tracking using motion information and predicting the object location in time based on visual similarity. The validation of the tracking technique is performed on standard benchmark VOT datasets, and shows that the proposed approach returns state-of-the-art results while minimizing the computational complexity. Then, the DEEP-SEE framework is integrated into a novel assistive device, designed to improve cognition of VI people and to increase their safety when navigating in crowded urban scenes. The validation of our assistive device is performed on a video dataset with 30 elements acquired with the help of VI users. The proposed system shows high accuracy (>90% and robustness (>90% scores regardless on the scene dynamics.

  1. Application of slip-band visualization technique to tensile analysis of laser-welded aluminum alloy

    Science.gov (United States)

    Muchiar, -; Yoshida, Sanichiro J.; Widiastuti, Rini; Kusnowo, A.; Takahashi, Kunimitsu; Sato, Shunichi

    1997-03-01

    Recently we have developed a new optical interferometric technique capable of visualizing slip band occurring in a deforming solid-state object. In this work we applied this technique to a tensile analysis of laser-welded aluminum plate samples, and successfully revealed stress concentration that shows strong relationships with the tensile strength and the fracture mechanism. We believe that this method is a new, convenient way to analyze the deformation characteristics of welded objects and evaluate the quality of welding. The analysis has been made for several types of aluminum alloys under various welding conditions, and has shown the following general results. When the penetration is deep, a slip band starts appearing at the fusion zone in an early stage of the elastic region of the strain-stress curve and stays there till the sample fractures at that point. When the penetration is shallow, a slip band appears only after the yield point and moves vigorously over the whole surface of the sample till a late stage of plastic deformation when the slip band stays at the fusion zone where the sample eventually fractures. When the penetration depth is medium, some intermediate situation of the above two extreme cases is observed.

  2. Application of 4-Face Fuel Visual Inspection System during Outage in Nuclear Power Plant

    International Nuclear Information System (INIS)

    Shin, J. C.; Kim, J. I.; Choi, C. B.; Kim, Y. C.; Kang, C. B.

    2008-01-01

    Recently, as a measure to reduce an outage duration in nuclear power plants (NPPs), a four-face fuel visual inspection system (4-FFVIS) built in 4 cameras was introduced by Ahlberg Electronics, Sweden. The 4- FFVIS is used to inspect the external appearance of irradiated fuel assemblies in order to confirm their integrity against mechanical defects and foreign materials. Until now, however, a typical one-face fuel inspection system(1-FFVIS) has been world-widely utilized in NPPs. The 1-FFVIS requires four turns with 90 degree to inspect every face of the fuel assembly, causing a relatively long inspecting time. But the 4- FFVIS allow us to inspect every face of the fuel assembly at the same time. The inspection time with the 4-FFVIS may be less than two minutes per fuel assembly, whereas that with the 1-FFVIS is about six minutes per fuel assembly. In viewpoint of this merit, the 4-FFVIS is expected to be world-widely used in the near future. In this paper, the technical requirements necessary to develop the 4-FFVIS as well as some improvements to complement the current 4-FFVIS are described

  3. Visualization of polarization state and its application in optics classroom teaching

    Science.gov (United States)

    Lei, Bing; Liu, Wei; Shi, Jianhua; Wang, Wei; Yao, Tianfu; Liu, Shugang

    2017-08-01

    Polarization of light and the related knowledge are key and difficult points in optical teaching, and they are difficult to be understood since they are very abstract concepts. To help students understand the polarization properties of light, some classroom demonstration experiments have been constructed by employing the optical source, polarizers, wave plates optical cage system and polarization axis finder (PAF). The PAF is a polarization indicating device with many linear polarizing components concentric circles, which can visualize the polarization axis's direction of linearly polarized light intuitively. With the help of these demonstration experiment systems, the conversion and difference between the linear polarized light and circularly polarized light have been observed directly by inserting or removing a quarter-wave plate. The rotation phenomenon of linearly polarized light's polarization axis when it propagates through an optical active medium has been observed and studied in experiment, and the strain distribution of some mounted and unmounted lenses have also been demonstrated and observed in experiment conveniently. Furthermore, some typical polarization targets, such as liquid crystal display (LCD), polarized dark glass and skylight, have been observed based on PAF, which is quite suitable to help students understand these targets' polarization properties and the related physical laws. Finally, these demonstration experimental systems have been employed in classroom teaching of our university in physical optics, optoelectronics and photoelectric detection courses, and they are very popular with teachers and students.

  4. Web-based Data Exploration, Exploitation and Visualization Tools for Satellite Sensor VIS/IR Calibration Applications

    Science.gov (United States)

    Gopalan, A.; Doelling, D. R.; Scarino, B. R.; Chee, T.; Haney, C.; Bhatt, R.

    2016-12-01

    The CERES calibration group at NASA/LaRC has developed and deployed a suite of online data exploration and visualization tools targeted towards a range of spaceborne VIS/IR imager calibration applications for the Earth Science community. These web-based tools are driven by the open-source R (Language for Statistical Computing and Visualization) with a web interface for the user to customize the results according to their application. The tool contains a library of geostationary and sun-synchronous imager spectral response functions (SRF), incoming solar spectra, SCIAMACHY and Hyperion Earth reflected visible hyper-spectral data, and IASI IR hyper-spectral data. The suite of six specific web-based tools was designed to provide critical information necessary for sensor cross-calibration. One of the challenges of sensor cross-calibration is accounting for spectral band differences and may introduce biases if not handled properly. The spectral band adjustment factors (SBAF) are a function of the earth target, atmospheric and cloud conditions or scene type and angular conditions, when obtaining sensor radiance pairs. The SBAF will need to be customized for each inter-calibration target and sensor pair. The advantages of having a community open source tool are: 1) only one archive of SCIAMACHY, Hyperion, and IASI datasets needs to be maintained, which is on the order of 50TB. 2) the framework will allow easy incorporation of new satellite SRFs and hyper-spectral datasets and associated coincident atmospheric and cloud properties, such as PW. 3) web tool or SBAF algorithm improvements or suggestions when incorporated can benefit the community at large. 4) The customization effort is on the user rather than on the host. In this paper we discuss each of these tools in detail and explore the variety of advanced options that can be used to constrain the results along with specific use cases to highlight the value-added by these datasets.

  5. The first draft genome of the aquatic model plant Lemna minor opens the route for future stress physiology research and biotechnological applications.

    Science.gov (United States)

    Van Hoeck, Arne; Horemans, Nele; Monsieurs, Pieter; Cao, Hieu Xuan; Vandenhove, Hildegarde; Blust, Ronny

    2015-01-01

    Freshwater duckweed, comprising the smallest, fastest growing and simplest macrophytes has various applications in agriculture, phytoremediation and energy production. Lemna minor, the so-called common duckweed, is a model system of these aquatic plants for ecotoxicological bioassays, genetic transformation tools and industrial applications. Given the ecotoxic relevance and high potential for biomass production, whole-genome information of this cosmopolitan duckweed is needed. The 472 Mbp assembly of the L. minor genome (2n = 40; estimated 481 Mbp; 98.1 %) contains 22,382 protein-coding genes and 61.5 % repetitive sequences. The repeat content explains 94.5 % of the genome size difference in comparison with the greater duckweed, Spirodela polyrhiza (2n = 40; 158 Mbp; 19,623 protein-coding genes; and 15.79 % repetitive sequences). Comparison of proteins from other monocot plants, protein ortholog identification, OrthoMCL, suggests 1356 duckweed-specific groups (3367 proteins, 15.0 % total L. minor proteins) and 795 Lemna-specific groups (2897 proteins, 12.9 % total L. minor proteins). Interestingly, proteins involved in biosynthetic processes in response to various stimuli and hydrolase activities are enriched in the Lemna proteome in comparison with the Spirodela proteome. The genome sequence and annotation of L. minor protein-coding genes provide new insights in biological understanding and biomass production applications of Lemna species.

  6. A boosting framework for visuality-preserving distance metric learning and its application to medical image retrieval.

    Science.gov (United States)

    Yang, Liu; Jin, Rong; Mummert, Lily; Sukthankar, Rahul; Goode, Adam; Zheng, Bin; Hoi, Steven C H; Satyanarayanan, Mahadev

    2010-01-01

    Similarity measurement is a critical component in content-based image retrieval systems, and learning a good distance metric can significantly improve retrieval performance. However, despite extensive study, there are several major shortcomings with the existing approaches for distance metric learning that can significantly affect their application to medical image retrieval. In particular, "similarity" can mean very different things in image retrieval: resemblance in visual appearance (e.g., two images that look like one another) or similarity in semantic annotation (e.g., two images of tumors that look quite different yet are both malignant). Current approaches for distance metric learning typically address only one goal without consideration of the other. This is problematic for medical image retrieval where the goal is to assist doctors in decision making. In these applications, given a query image, the goal is to retrieve similar images from a reference library whose semantic annotations could provide the medical professional with greater insight into the possible interpretations of the query image. If the system were to retrieve images that did not look like the query, then users would be less likely to trust the system; on the other hand, retrieving images that appear superficially similar to the query but are semantically unrelated is undesirable because that could lead users toward an incorrect diagnosis. Hence, learning a distance metric that preserves both visual resemblance and semantic similarity is important. We emphasize that, although our study is focused on medical image retrieval, the problem addressed in this work is critical to many image retrieval systems. We present a boosting framework for distance metric learning that aims to preserve both visual and semantic similarities. The boosting framework first learns a binary representation using side information, in the form of labeled pairs, and then computes the distance as a weighted Hamming

  7. Harvesting Statistical Metadata from an Online Repository for Data Analysis and Visualization : Concept Application on Theseus

    OpenAIRE

    Gebresilassie, Sem

    2014-01-01

    Theses and publications from Finnish universities of applied sciences are accessible from an open online repository called Theseus. This repository has an application programming interface (API) that provides tools for harvesting its contents. By properly utilizing this API, it is possible to gather and reuse metadata of thesis documents for any other objective. This thesis mainly intends to explain how to gather the author name, title, submission year, keywords, subjects, department, u...

  8. Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases

    Directory of Open Access Journals (Sweden)

    J. Alberto Romero Navarro

    2017-11-01

    Full Text Available Chocolate is a highly valued and palatable confectionery product. Chocolate is primarily made from the processed seeds of the tree species Theobroma cacao. Cacao cultivation is highly relevant for small-holder farmers throughout the tropics, yet its productivity remains limited by low yields and widespread pathogens. A panel of 148 improved cacao clones was assembled based on productivity and disease resistance, and phenotypic single-tree replicated clonal evaluation was performed for 8 years. Using high-density markers, the diversity of clones was expressed relative to 10 known ancestral cacao populations, and significant effects of ancestry were observed in productivity and disease resistance. Genome-wide association (GWA was performed, and six markers were significantly associated with frosty pod disease resistance. In addition, genomic selection was performed, and consistent with the observed extensive linkage disequilibrium, high predictive ability was observed at low marker densities for all traits. Finally, quantitative trait locus mapping and differential expression analysis of two cultivars with contrasting disease phenotypes were performed to identify genes underlying frosty pod disease resistance, identifying a significant quantitative trait locus and 35 differentially expressed genes using two independent differential expression analyses. These results indicate that in breeding populations of heterozygous and recently admixed individuals, mapping approaches can be used for low complexity traits like pod color cacao, or in other species single gene disease resistance, however genomic selection for quantitative traits remains highly effective relative to mapping. Our results can help guide the breeding process for sustainable improved cacao productivity.

  9. Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes

    Directory of Open Access Journals (Sweden)

    Francis Andrew R

    2008-11-01

    Full Text Available Abstract Background Molecular typing methods are commonly used to study genetic relationships among bacterial isolates. Many of these methods have become standardized and produce portable data. A popular approach for analyzing such data is to construct graphs, including phylogenies. Inferences from graph representations of data assist in understanding the patterns of transmission of bacterial pathogens, and basing these graph constructs on biological models of evolution of the molecular marker helps make these inferences. Spoligotyping is a widely used method for genotyping isolates of Mycobacterium tuberculosis that exploits polymorphism in the direct repeat region. Our goal was to examine a range of models describing the evolution of spoligotypes in order to develop a visualization method to represent likely relationships among M. tuberculosis isolates. Results We found that inferred mutations of spoligotypes frequently involve the loss of a single or very few adjacent spacers. Using a second-order variant of Akaike's Information Criterion, we selected the Zipf model as the basis for resolving ambiguities in the ancestry of spoligotypes. We developed a method to construct graphs of spoligotypes (which we call spoligoforests. To demonstrate this method, we applied it to a tuberculosis data set from Cuba and compared the method to some existing methods. Conclusion We propose a new approach in analyzing relationships of M. tuberculosis isolates using spoligotypes. The spoligoforest recovers a plausible history of transmission and mutation events based on the selected deletion model. The method may be suitable to study markers based on loci of similar structure from other bacteria. The groupings and relationships in the spoligoforest can be analyzed along with the clinical features of strains to provide an understanding of the evolution of spoligotypes.

  10. Genome-wide survey and analysis of microsatellites in giant panda (Ailuropoda melanoleuca), with a focus on the applications of a novel microsatellite marker system.

    Science.gov (United States)

    Huang, Jie; Li, Yu-Zhi; Du, Lian-Ming; Yang, Bo; Shen, Fu-Jun; Zhang, He-Min; Zhang, Zhi-He; Zhang, Xiu-Yue; Yue, Bi-Song

    2015-02-07

    The giant panda (Ailuropoda melanoleuca) is a critically endangered species endemic to China. Microsatellites have been preferred as the most popular molecular markers and proven effective in estimating population size, paternity test, genetic diversity for the critically endangered species. The availability of the giant panda complete genome sequences provided the opportunity to carry out genome-wide scans for all types of microsatellites markers, which now opens the way for the analysis and development of microsatellites in giant panda. By screening the whole genome sequence of giant panda in silico mining, we identified microsatellites in the genome of giant panda and analyzed their frequency and distribution in different genomic regions. Based on our search criteria, a repertoire of 855,058 SSRs was detected, with mono-nucleotides being the most abundant. SSRs were found in all genomic regions and were more abundant in non-coding regions than coding regions. A total of 160 primer pairs were designed to screen for polymorphic microsatellites using the selected tetranucleotide microsatellite sequences. The 51 novel polymorphic tetranucleotide microsatellite loci were discovered based on genotyping blood DNA from 22 captive giant pandas in this study. Finally, a total of 15 markers, which showed good polymorphism, stability, and repetition in faecal samples, were used to establish the novel microsatellite marker system for giant panda. Meanwhile, a genotyping database for Chengdu captive giant pandas (n = 57) were set up using this standardized system. What's more, a universal individual identification method was established and the genetic diversity were analysed in this study as the applications of this marker system. The microsatellite abundance and diversity were characterized in giant panda genomes. A total of 154,677 tetranucleotide microsatellites were identified and 15 of them were discovered as the polymorphic and stable loci. The individual

  11. Health Food Program Applications with Microsoft Visual Basic 6.0 From PT. Kompak Indopola

    OpenAIRE

    Satrio Dwi Seto; Drs. Sunarto Usna, MMSi

    2003-01-01

    Humans are familiar with as a health food supplement to meet the deficiencies in thedaily food and almost all health food ingredients consisting of vitamins and minerals.Health food is not a material change to the daily feed source.Its use is itself balanced by the functions and expenditures. If only someone had asource of food substances that are sufficient, there is no need to consume excesshealth food.Application program created to provide information on health foods PT CompactIndopola. Th...

  12. Stereoscopic Three-Dimensional Visualization Applied to Multimodal Brain Images: Clinical Applications and a Functional Connectivity Atlas.

    Directory of Open Access Journals (Sweden)

    Gonzalo M Rojas

    2014-11-01

    Full Text Available Effective visualization is central to the exploration and comprehension of brain imaging data. While MRI data are acquired in three-dimensional space, the methods for visualizing such data have rarely taken advantage of three-dimensional stereoscopic technologies. We present here results of stereoscopic visualization of clinical data, as well as an atlas of whole-brain functional connectivity. In comparison with traditional 3D rendering techniques, we demonstrate the utility of stereoscopic visualizations to provide an intuitive description of the exact location and the relative sizes of various brain landmarks, structures and lesions. In the case of resting state fMRI, stereoscopic 3D visualization facilitated comprehension of the anatomical position of complex large-scale functional connectivity patterns. Overall, stereoscopic visualization improves the intuitive visual comprehension of image contents, and brings increased dimensionality to visualization of traditional MRI data, as well as patterns of functional connectivity.

  13. Application of the inter-line PCR for the analyse of genomic rearrangements in radiation-transformed mammalian cell lines

    International Nuclear Information System (INIS)

    Leibhard, S.; Smida, J.

    1996-01-01

    Repetitive DNA sequences of the LINE-family (long interspersed elements) that are widely distributed among the mammalian genome can be activated or altered by the exposure to ionizing radiation [1]. By the integration at new sites in the genome alterations in the expression of genes that are involved in cell transformation and/or carcinogenesis may occur [2, 3]. A new technique -the inter-LINE PCR - has been developed in order to detect and analyse such genomic rearrangements in radiation-transformed cell lines. From the sites of transformation- or tumour-specific changes in the genome it might be possible to develop new tumour markers for diagnostic purpose. (orig.) [de

  14. Flow visualization

    International Nuclear Information System (INIS)

    Weinstein, L.M.

    1991-01-01

    Flow visualization techniques are reviewed, with particular attention given to those applicable to liquid helium flows. Three techniques capable of obtaining qualitative and quantitative measurements of complex 3D flow fields are discussed including focusing schlieren, particle image volocimetry, and holocinematography (HCV). It is concluded that the HCV appears to be uniquely capable of obtaining full time-varying, 3D velocity field data, but is limited to the low speeds typical of liquid helium facilities. 8 refs

  15. Integrative Sparse K-Means With Overlapping Group Lasso in Genomic Applications for Disease Subtype Discovery.

    Science.gov (United States)

    Huo, Zhiguang; Tseng, George

    2017-06-01

    Cancer subtypes discovery is the first step to deliver personalized medicine to cancer patients. With the accumulation of massive multi-level omics datasets and established biological knowledge databases, omics data integration with incorporation of rich existing biological knowledge is essential for deciphering a biological mechanism behind the complex diseases. In this manuscript, we propose an integrative sparse K -means (is- K means) approach to discover disease subtypes with the guidance of prior biological knowledge via sparse overlapping group lasso. An algorithm using an alternating direction method of multiplier (ADMM) will be applied for fast optimization. Simulation and three real applications in breast cancer and leukemia will be used to compare is- K means with existing methods and demonstrate its superior clustering accuracy, feature selection, functional annotation of detected molecular features and computing efficiency.

  16. Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing.

    Directory of Open Access Journals (Sweden)

    Alexander William Eastman

    2015-01-01

    Full Text Available Advances in sequencing technology have drastically increased the depth and feasibility of bacterial genome sequencing. However, little information is available that details the specific techniques and procedures employed during genome sequencing despite the large numbers of published genomes. Shotgun approaches employed by second-generation sequencing platforms has necessitated the development of robust bioinformatics tools for in silico assembly, and complete assembly is limited by the presence of repetitive DNA sequences and multi-copy operons. Typically, re-sequencing with multiple platforms and laborious, targeted Sanger sequencing are employed to finish a draft bacterial genome. Here we describe a novel strategy based on the identification and targeted sequencing of repetitive rDNA operons to expedite bacterial genome assembly and finishing. Our strategy was validated by finishing the genome of Paenibacillus polymyxa strain CR1, a bacterium with potential in sustainable agriculture and bio-based processes. An analysis of the 38 contigs contained in the P. polymyxa strain CR1 draft genome revealed 12 repetitive rDNA operons with varied intragenic and flanking regions of variable length, unanimously located at contig boundaries and within contig gaps. These highly similar but not identical rDNA operons were experimentally verified and sequenced simultaneously with multiple, specially designed primer sets. This approach also identified and corrected significant sequence rearrangement generated during the initial in silico assembly of sequencing reads. Our approach reduces the required effort associated with blind primer walking for contig assembly, increasing both the speed and feasibility of genome finishing. Our study further reinforces the notion that repetitive DNA elements are major limiting factors for genome finishing. Moreover, we provided a step-by-step workflow for genome finishing, which may guide future bacterial genome finishing

  17. Method for the visualization of landform by mapping using low altitude UAV application

    Science.gov (United States)

    Sharan Kumar, N.; Ashraf Mohamad Ismail, Mohd; Sukor, Nur Sabahiah Abdul; Cheang, William

    2018-05-01

    Unmanned Aerial Vehicle (UAV) and Digital Photogrammetry are evolving drastically in mapping technology. The significance and necessity for digital landform mapping are developing with years. In this study, a mapping workflow is applied to obtain two different input data sets which are the orthophoto and DSM. A fine flying technology is used to capture Low Altitude Aerial Photography (LAAP). Low altitude UAV (Drone) with the fixed advanced camera was utilized for imagery while computerized photogrammetry handling using Photo Scan was applied for cartographic information accumulation. The data processing through photogrammetry and orthomosaic processes is the main applications. High imagery quality is essential for the effectiveness and nature of normal mapping output such as 3D model, Digital Elevation Model (DEM), Digital Surface Model (DSM) and Ortho Images. The exactitude of Ground Control Points (GCP), flight altitude and the resolution of the camera are essential for good quality DEM and Orthophoto.

  18. A xylanase gene directly cloned from the genomic DNA of alkaline wastewater sludge showing application potential in the paper industry.

    Science.gov (United States)

    Zhao, Yanyu; Luo, Huiying; Meng, Kun; Shi, Pengjun; Wang, Guozeng; Yang, Peilong; Yuan, Tiezheng; Yao, Bin

    2011-09-01

    A xylanase gene, aws-2x, was directly cloned from the genomic DNA of the alkaline wastewater sludge using degenerated PCR and modified TAIL-PCR. The deduced amino acid sequence of AWS-2x shared the highest identity (60%) with the xylanase from Chryseobacterium gleum belonging to the glycosyl hydrolase GH family 10. Recombinant AWS-2x was expressed in Escherichia coli BL21 (DE3) and purified to electrophoretic homogeneity. The enzyme showed maximal activity at pH 7.5 and 55 °C, maintained more than 50% of maximal activity when assayed at pH 9.0, and was stable over a wide pH range from 4.0 to 11.0. The specific activity of AWS-2x towards hardwood xylan (beechwood and birchwood xylan) was significantly higher than that to cereal xylan (oat spelt xylan and wheat arabinoxylan). These properties make AWS-2x a potential candidate for application in the pulp and paper industry.

  19. The Need for Clinical Decision Support Integrated with the Electronic Health Record for the Clinical Application of Whole Genome Sequencing Information

    Directory of Open Access Journals (Sweden)

    Brandon M. Welch

    2013-12-01

    Full Text Available Whole genome sequencing (WGS is rapidly approaching widespread clinical application. Technology advancements over the past decade, since the first human genome was decoded, have made it feasible to use WGS for clinical care. Future advancements will likely drive down the price to the point wherein WGS is routinely available for care. However, were this to happen today, most of the genetic information available to guide clinical care would go unused due to the complexity of genetics, limited physician proficiency in genetics, and lack of genetics professionals in the clinical workforce. Furthermore, these limitations are unlikely to change in the future. As such, the use of clinical decision support (CDS to guide genome-guided clinical decision-making is imperative. In this manuscript, we describe the barriers to widespread clinical application of WGS information, describe how CDS can be an important tool for overcoming these barriers, and provide clinical examples of how genome-enabled CDS can be used in the clinical setting.

  20. Human genome I

    International Nuclear Information System (INIS)

    Anon.

    1989-01-01

    An international conference, Human Genome I, was held Oct. 2-4, 1989 in San Diego, Calif. Selected speakers discussed: Current Status of the Genome Project; Technique Innovations; Interesting regions; Applications; and Organization - Different Views of Current and Future Science and Procedures. Posters, consisting of 119 presentations, were displayed during the sessions. 119 were indexed for inclusion to the Energy Data Base