WorldWideScience

Sample records for genomics visualization applications

  1. Genoviz Software Development Kit: Java tool kit for building genomics visualization applications

    Directory of Open Access Journals (Sweden)

    Chervitz Stephen A

    2009-08-01

    Full Text Available Abstract Background Visualization software can expose previously undiscovered patterns in genomic data and advance biological science. Results The Genoviz Software Development Kit (SDK is an open source, Java-based framework designed for rapid assembly of visualization software applications for genomics. The Genoviz SDK framework provides a mechanism for incorporating adaptive, dynamic zooming into applications, a desirable feature of genome viewers. Visualization capabilities of the Genoviz SDK include automated layout of features along genetic or genomic axes; support for user interactions with graphical elements (Glyphs in a map; a variety of Glyph sub-classes that promote experimentation with new ways of representing data in graphical formats; and support for adaptive, semantic zooming, whereby objects change their appearance depending on zoom level and zooming rate adapts to the current scale. Freely available demonstration and production quality applications, including the Integrated Genome Browser, illustrate Genoviz SDK capabilities. Conclusion Separation between graphics components and genomic data models makes it easy for developers to add visualization capability to pre-existing applications or build new applications using third-party data models. Source code, documentation, sample applications, and tutorials are available at http://genoviz.sourceforge.net/.

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

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    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

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

    Science.gov (United States)

    Dinov, Ivo D; Torri, Federica; Macciardi, Fabio; Petrosyan, Petros; Liu, Zhizhong; Zamanyan, Alen; Eggert, Paul; Pierce, Jonathan; Genco, Alex; Knowles, James A; Clark, Andrew P; Van Horn, John D; Ames, Joseph; Kesselman, Carl; Toga, Arthur W

    2011-07-26

    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. 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. 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 Pipeline client-server model provides computational power

  4. 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

  5. Easyfig: a genome comparison visualizer.

    Science.gov (United States)

    Sullivan, Mitchell J; Petty, Nicola K; Beatson, Scott A

    2011-04-01

    Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface. BLAST comparisons between multiple genomic regions, ranging from single genes to whole prokaryote chromosomes, can be generated, visualized and interactively coloured, enabling a rapid transition between analysis and the preparation of publication quality figures. Easyfig is freely available (under a GPL license) for download (for Mac OS X, Unix and Microsoft Windows) from the SourceForge web site: http://easyfig.sourceforge.net/.

  6. Web-based visual analysis for high-throughput genomics.

    Science.gov (United States)

    Goecks, Jeremy; Eberhard, Carl; Too, Tomithy; Nekrutenko, Anton; Taylor, James

    2013-06-13

    Visualization plays an essential role in genomics research by making it possible to observe correlations and trends in large datasets as well as communicate findings to others. Visual analysis, which combines visualization with analysis tools to enable seamless use of both approaches for scientific investigation, offers a powerful method for performing complex genomic analyses. However, there are numerous challenges that arise when creating rich, interactive Web-based visualizations/visual analysis applications for high-throughput genomics. These challenges include managing data flow from Web server to Web browser, integrating analysis tools and visualizations, and sharing visualizations with colleagues. We have created a platform simplifies the creation of Web-based visualization/visual analysis applications for high-throughput genomics. This platform provides components that make it simple to efficiently query very large datasets, draw common representations of genomic data, integrate with analysis tools, and share or publish fully interactive visualizations. Using this platform, we have created a Circos-style genome-wide viewer, a generic scatter plot for correlation analysis, an interactive phylogenetic tree, a scalable genome browser for next-generation sequencing data, and an application for systematically exploring tool parameter spaces to find good parameter values. All visualizations are interactive and fully customizable. The platform is integrated with the Galaxy (http://galaxyproject.org) genomics workbench, making it easy to integrate new visual applications into Galaxy. Visualization and visual analysis play an important role in high-throughput genomics experiments, and approaches are needed to make it easier to create applications for these activities. Our framework provides a foundation for creating Web-based visualizations and integrating them into Galaxy. Finally, the visualizations we have created using the framework are useful tools for high

  7. GenomeGraphs: integrated genomic data visualization with R

    Directory of Open Access Journals (Sweden)

    Spellman Paul T

    2009-01-01

    Full Text Available Abstract Background Biological studies involve a growing number of distinct high-throughput experiments to characterize samples of interest. There is a lack of methods to visualize these different genomic datasets in a versatile manner. In addition, genomic data analysis requires integrated visualization of experimental data along with constantly changing genomic annotation and statistical analyses. Results We developed GenomeGraphs, as an add-on software package for the statistical programming environment R, to facilitate integrated visualization of genomic datasets. GenomeGraphs uses the biomaRt package to perform on-line annotation queries to Ensembl and translates these to gene/transcript structures in viewports of the grid graphics package. This allows genomic annotation to be plotted together with experimental data. GenomeGraphs can also be used to plot custom annotation tracks in combination with different experimental data types together in one plot using the same genomic coordinate system. Conclusion GenomeGraphs is a flexible and extensible software package which can be used to visualize a multitude of genomic datasets within the statistical programming environment R.

  8. GenomeGraphs: integrated genomic data visualization with R.

    Science.gov (United States)

    Durinck, Steffen; Bullard, James; Spellman, Paul T; Dudoit, Sandrine

    2009-01-06

    Biological studies involve a growing number of distinct high-throughput experiments to characterize samples of interest. There is a lack of methods to visualize these different genomic datasets in a versatile manner. In addition, genomic data analysis requires integrated visualization of experimental data along with constantly changing genomic annotation and statistical analyses. We developed GenomeGraphs, as an add-on software package for the statistical programming environment R, to facilitate integrated visualization of genomic datasets. GenomeGraphs uses the biomaRt package to perform on-line annotation queries to Ensembl and translates these to gene/transcript structures in viewports of the grid graphics package. This allows genomic annotation to be plotted together with experimental data. GenomeGraphs can also be used to plot custom annotation tracks in combination with different experimental data types together in one plot using the same genomic coordinate system. GenomeGraphs is a flexible and extensible software package which can be used to visualize a multitude of genomic datasets within the statistical programming environment R.

  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. 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.

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

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    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.

  12. 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.

  13. JBrowse: a dynamic web platform for genome visualization and analysis.

    Science.gov (United States)

    Buels, Robert; Yao, Eric; Diesh, Colin M; Hayes, Richard D; Munoz-Torres, Monica; Helt, Gregg; Goodstein, David M; Elsik, Christine G; Lewis, Suzanna E; Stein, Lincoln; Holmes, Ian H

    2016-04-12

    JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page. Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions can readily be added using the plugin framework; most visual aspects of tracks can also be customized, along with clicks, mouseovers, menus, and popup boxes. JBrowse can also be used to browse local annotation files offline and to generate high-resolution figures for publication. JBrowse is a mature web application suitable for genome visualization and analysis.

  14. 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.

  15. 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/.

  16. 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.

  17. 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.

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

    Science.gov (United States)

    Chang, Yi-Feng; Chang, Chuan-Hsiung

    2011-01-01

    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.

  19. Future Health Applications of Genomics

    Science.gov (United States)

    McBride, Colleen M.; Bowen, Deborah; Brody, Lawrence C.; Condit, Celeste M.; Croyle, Robert T.; Gwinn, Marta; Khoury, Muin J.; Koehly, Laura M.; Korf, Bruce R.; Marteau, Theresa M.; McLeroy, Kenneth; Patrick, Kevin; Valente, Thomas W.

    2014-01-01

    Despite the quickening momentum of genomic discovery, the communication, behavioral, and social sciences research needed for translating this discovery into public health applications has lagged behind. The National Human Genome Research Institute held a 2-day workshop in October 2008 convening an interdisciplinary group of scientists to recommend forward-looking priorities for translational research. This research agenda would be designed to redress the top three risk factors (tobacco use, poor diet, and physical inactivity) that contribute to the four major chronic diseases (heart disease, type 2 diabetes, lung disease, and many cancers) and account for half of all deaths worldwide. Three priority research areas were identified: (1) improving the public’s genetic literacy in order to enhance consumer skills; (2) gauging whether genomic information improves risk communication and adoption of healthier behaviors more than current approaches; and (3) exploring whether genomic discovery in concert with emerging technologies can elucidate new behavioral intervention targets. Important crosscutting themes also were identified, including the need to: (1) anticipate directions of genomic discovery; (2) take an agnostic scientific perspective in framing research questions asking whether genomic discovery adds value to other health promotion efforts; and (3) consider multiple levels of influence and systems that contribute to important public health problems. The priorities and themes offer a framework for a variety of stakeholders, including those who develop priorities for research funding, interdisciplinary teams engaged in genomics research, and policymakers grappling with how to use the products born of genomics research to address public health challenges. PMID:20409503

  20. 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 pe...

  1. 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

  2. Application of Genomic In Situ Hybridization in Horticultural Science

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    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.

  3. 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 .

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

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    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

  5. Feature selection environment for genomic applications

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    Martins David

    2008-10-01

    Full Text Available Abstract Background Feature selection is a pattern recognition approach to choose important variables according to some criteria in order to distinguish or explain certain phenomena (i.e., for dimensionality reduction. There are many genomic and proteomic applications that rely on feature selection to answer questions such as selecting signature genes which are informative about some biological state, e.g., normal tissues and several types of cancer; or inferring a prediction network among elements such as genes, proteins and external stimuli. In these applications, a recurrent problem is the lack of samples to perform an adequate estimate of the joint probabilities between element states. A myriad of feature selection algorithms and criterion functions have been proposed, although it is difficult to point the best solution for each application. Results The intent of this work is to provide an open-source multiplataform graphical environment for bioinformatics problems, which supports many feature selection algorithms, criterion functions and graphic visualization tools such as scatterplots, parallel coordinates and graphs. A feature selection approach for growing genetic networks from seed genes (targets or predictors is also implemented in the system. Conclusion The proposed feature selection environment allows data analysis using several algorithms, criterion functions and graphic visualization tools. Our experiments have shown the software effectiveness in two distinct types of biological problems. Besides, the environment can be used in different pattern recognition applications, although the main concern regards bioinformatics tasks.

  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. 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

  8. 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 decade...... sequence information may aid mixture interpretation and will increase the statistical weight of the evidence. In this chapter, we provide an overview on conventional DNA diagnostics and the possible applications of single cell sequencing and NGS in forensic medicine....

  9. Sybil: methods and software for multiple genome comparison and visualization.

    Science.gov (United States)

    Crabtree, Jonathan; Angiuoli, Samuel V; Wortman, Jennifer R; White, Owen R

    2007-01-01

    With the successful completion of genome sequencing projects for a variety of model organisms, the selection of candidate organisms for future sequencing efforts has been guided increasingly by a desire to enable comparative genomics. This trend has both depended on and encouraged the development of software tools that can elucidate and capitalize on the similarities and differences between genomes. "Sybil," one such tool, is a primarily web-based software package whose primary goal is to facilitate the analysis and visualization of comparative genome data, with a particular emphasis on protein and gene cluster data. Herein, a two-phase protein clustering algorithm, used to generate protein clusters suitable for analysis through Sybil and a method for creating graphical displays of protein or gene clusters that span multiple genomes are described. When combined, these two relatively simple techniques provide the user of the Sybil software (The Institute for Genomic Research [TIGR] Bioinformatics Department) with a browsable graphical display of his or her "input" genomes, showing which genes are conserved based on the parameters supplied to the protein clustering algorithm. For any given protein cluster the graphical display consists of a local alignment of the genomes in which the clustered genes are located. The genomes are arranged in a vertical stack, as in a multiple alignment, and shaded areas are used to connect genes in the same cluster, thus displaying conservation at the protein level in the context of the underlying genomic sequences. The authors have found this display-and slight variants thereof-useful for a variety of annotation and comparison tasks, ranging from identifying "missed" gene models or single-exon discrepancies between orthologous genes, to finding large or small regions of conserved gene synteny, and investigating the properties of the breakpoints between such regions.

  10. 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.

  11. Genome display tool: visualizing features in complex data sets

    Directory of Open Access Journals (Sweden)

    Lu Yue

    2007-02-01

    Full Text Available Abstract Background The enormity of the information contained in large data sets makes it difficult to develop intuitive understanding. It would be useful to have software that allows visualization of possible correlations between properties that can be associated with a core data set. In the case of bacterial genomes, existing visualization tools focus on either global properties such as variations in composition or detailed local displays of the features that comprise the annotation. It is not easy to visualize other information in the context of this core information. Results A Java based software known as the Genome Display Tool (GDT, allows the user to simultaneously view the distribution of multiple attributes pertaining to genes and intragenic regions in a single bacterial genome using different colours and shapes on a single screen. The display represents each gene by small boxes that correlate with physical position in the genome. The size of the boxes is dynamically allocated based on the number of genes and a zoom feature allows close-up inspection of regions of interest. The display is interfaced with a MS-Access relational database and can display any feature in the database that can be represented by discrete values. Data is readily added to the database from an MS-Excel spread sheet. The functionality of GDT is demonstrated by comparing the results of two predictions of recent horizontal transfer events in the genome of Synechocystis PCC-6803. The resulting display allows the user to immediately see how much agreement exists between the two methods and also visualize how genes in various categories (e.g. predicted in both methods, one method etc are distributed in the genome. Conclusion The GDT software provides the user with a powerful tool that allows development of an intuitive understanding of the relative distribution of features in a large data set. As additional features are added to the data set, the number of possible

  12. Interactive data visualization foundations, techniques, and applications

    CERN Document Server

    Ward, Matthew; Keim, Daniel

    2015-01-01

    Interactive Data Visualization: Foundations, Techniques, and Applications, Second Edition provides all the theory, details, and tools necessary to build visualizations and systems involving the visualization of data. In color throughout, it explains basic terminology and concepts, algorithmic and software engineering issues, and commonly used techniques and high-level algorithms. Full source code is provided for completing implementations.

  13. Cascade: an RNA-seq visualization tool for cancer genomics.

    Science.gov (United States)

    Shifman, Aaron R; Johnson, Radia M; Wilhelm, Brian T

    2016-01-25

    Cancer genomics projects are producing ever-increasing amounts of rich and diverse data from patient samples. The ability to easily visualize this data in an integrated an intuitive way is currently limited by the current software available. As a result, users typically must use several different tools to view the different data types for their cohort, making it difficult to have a simple unified view of their data. Here we present Cascade, a novel web based tool for the intuitive 3D visualization of RNA-seq data from cancer genomics experiments. The Cascade viewer allows multiple data types (e.g. mutation, gene expression, alternative splicing frequency) to be simultaneously displayed, allowing a simplified view of the data in a way that is tuneable based on user specified parameters. The main webpage of Cascade provides a primary view of user data which is overlaid onto known biological pathways that are either predefined or added by users. A space-saving menu for data selection and parameter adjustment allows users to access an underlying MySQL database and customize the features presented in the main view. There is currently a pressing need for new software tools to allow researchers to easily explore large cancer genomics datasets and generate hypotheses. Cascade represents a simple yet intuitive interface for data visualization that is both scalable and customizable.

  14. 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.

  15. 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.

  16. Tetrahedral gray code for visualization of genome information.

    Science.gov (United States)

    Ichinose, Natsuhiro; Yada, Tetsushi; Gotoh, Osamu

    2014-01-01

    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.

  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. Reverse engineering a visual age application

    NARCIS (Netherlands)

    Sneed, Harry M.; Verhoef, Chris

    2015-01-01

    This paper is an industrial case study of how a VisualAge application system on an IBM mainframe was reverse engineered into a system reference repository. The starting point was the code fragments generated by the VisualAge interactive development tool. The results of the reverse engineering

  19. Three-Dimensional Visualizations in Teaching Genomics and Bioinformatics: Mutations in HIV Envelope Proteins and Their Consequences for Vaccine Design

    Directory of Open Access Journals (Sweden)

    Kathy Takayama

    2009-11-01

    Full Text Available This project addresses the need to provide a visual context to teach the practical applications of genome sequencing and bioinformatics. Present-day research relies on indirect visualization techniques (e.g., fluorescence-labeling of DNA in sequencing reactions and sophisticated computer analysis. Such methods are impractical and prohibitively expensive for laboratory classes. More importantly, there is a need for curriculum resources that visually demonstrate the application of genome sequence information rather than the DNA sequencing methodology itself. This project is a computer-based lesson plan that engages students in collaborative, problem-based learning. The specific example focuses on approaches to Human Immunodeficiency Virus-1 (HIV-1 vaccine design based on HIV-1 genome sequences using a case study. Students performed comparative alignments of variant HIV-1 sequences available from a public database. Students then examined the consequences of HIV-1 mutations by applying the alignments to three-dimensional images of the HIV-1 envelope protein structure, thus visualizing the implications for applications such as vaccine design. The lesson enhances problem solving through the application of one type of information (genomic or protein sequence into concrete visual conceptualizations. Assessment of student comprehension and problem-solving ability revealed marked improvement after the computer tutorial. Furthermore, contextual presentation of these concepts within a case study resulted in student responses that demonstrated higher levels of cognitive ability than was expected by the instructor.

  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. Applications of visual soil evaluation

    DEFF Research Database (Denmark)

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

    2013-01-01

    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......., 2006). Ten visual and tactile methods were used to assess soil structure on the same soil. This stimulated significant ongoing cooperation between participants and several authors have since modified and developed their procedures (Mueller et al., 2009 and Shepherd, 2009). Cooperation also led...... 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...

  2. [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.

  3. Genomic and personalized medicine: foundations and applications.

    Science.gov (United States)

    Ginsburg, Geoffrey S; Willard, Huntington F

    2009-12-01

    application of genomic and personalized medicine in health care will require dramatic changes in regulatory and reimbursement policies as well as legislative protections for privacy for system-wide adoption. Thus, there are challenges from both a scientific and a policy perspective to personalized health care; however, they will be confronted and solved with the certainty that the science behind genomic medicine is sound and the practice of medicine that it informs is evidence based.

  4. 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

    of regions. Additional information can be added to these plots, and as an example we have added circles showing the probability of the DNA helix opening up under superhelical tension. The tool is SOAP compliant and WSDL (web services description language) files are located on our website: (http......://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...

  5. Agricultural applications of insect ecological genomics.

    Science.gov (United States)

    Poelchau, Monica F; Coates, Brad S; Childers, Christopher P; Peréz de León, Adalberto A; Evans, Jay D; Hackett, Kevin; Shoemaker, DeWayne

    2016-02-01

    Agricultural entomology is poised to benefit from the application of ecological genomics, particularly the fields of biofuels generation and pest control. Metagenomic methods can characterize microbial communities of termites, wood-boring beetles and livestock pests, and transcriptomic approaches reveal molecular bases behind wood-digesting capabilities of these insects, leading to potential mechanisms for biofuel generation. Genome sequences are being exploited to develop new pest control methods, identify candidate antigens to vaccinate livestock, and discover RNAi target sequences and potential non-target effects in other insects. Gene content analyses of pest genome sequences and their endosymbionts suggest metabolic interdependencies between organisms, exposing potential gene targets for insect control. Finally, genome-wide association studies and genotyping by high-throughput sequencing promise to improve management of pesticide resistance. Published by Elsevier Inc.

  6. Volume visualization of multiple alignment of large genomicDNA

    Energy Technology Data Exchange (ETDEWEB)

    Shah, Nameeta; Dillard, Scott E.; Weber, Gunther H.; Hamann, Bernd

    2005-07-25

    Genomes of hundreds of species have been sequenced to date, and many more are being sequenced. As more and more sequence data sets become available, and as the challenge of comparing these massive ''billion basepair DNA sequences'' becomes substantial, so does the need for more powerful tools supporting the exploration of these data sets. Similarity score data used to compare aligned DNA sequences is inherently one-dimensional. One-dimensional (1D) representations of these data sets do not effectively utilize screen real estate. As a result, tools using 1D representations are incapable of providing informatory overview for extremely large data sets. We present a technique to arrange 1D data in 3D space to allow us to apply state-of-the-art interactive volume visualization techniques for data exploration. We demonstrate our technique using multi-millions-basepair-long aligned DNA sequence data and compare it with traditional 1D line plots. The results show that our technique is superior in providing an overview of entire data sets. Our technique, coupled with 1D line plots, results in effective multi-resolution visualization of very large aligned sequence data sets.

  7. 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.

  8. Genome editing in fishes and their applications.

    Science.gov (United States)

    Zhu, Bo; Ge, Wei

    2018-02-01

    There have been revolutionary progresses in genome engineering in the past few years. The newly-emerged genome editing technologies including zinc-finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats associated with Cas9 (CRISPR/Cas9) have enabled biological scientists to perform efficient and precise targeted genome editing in different species. Fish represent the largest group of vertebrates with many species having values for both scientific research and aquaculture industry. Genome editing technologies have found extensive applications in different fish species for basic functional studies as well asapplied research in such fields as disease modeling and aquaculture. This mini-review focuses on recent advancements and applications of the new generation of genome editing technologies in fish species, with particular emphasis on their applications in understanding reproductive functions because the reproductive axis has been most systematically and best studied among others and its function has been difficult to address with reverse genetics approach. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. 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.

  10. 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.

  11. solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database

    Directory of Open Access Journals (Sweden)

    van der Knaap Esther

    2010-10-01

    Full Text Available Abstract Background A common approach to understanding the genetic basis of complex traits is through identification of associated quantitative trait loci (QTL. Fine mapping QTLs requires several generations of backcrosses and analysis of large populations, which is time-consuming and costly effort. Furthermore, as entire genomes are being sequenced and an increasing amount of genetic and expression data are being generated, a challenge remains: linking phenotypic variation to the underlying genomic variation. To identify candidate genes and understand the molecular basis underlying the phenotypic variation of traits, bioinformatic approaches are needed to exploit information such as genetic map, expression and whole genome sequence data of organisms in biological databases. Description The Sol Genomics Network (SGN, http://solgenomics.net is a primary repository for phenotypic, genetic, genomic, expression and metabolic data for the Solanaceae family and other related Asterids species and houses a variety of bioinformatics tools. SGN has implemented a new approach to QTL data organization, storage, analysis, and cross-links with other relevant data in internal and external databases. The new QTL module, solQTL, http://solgenomics.net/qtl/, employs a user-friendly web interface for uploading raw phenotype and genotype data to the database, R/QTL mapping software for on-the-fly QTL analysis and algorithms for online visualization and cross-referencing of QTLs to relevant datasets and tools such as the SGN Comparative Map Viewer and Genome Browser. Here, we describe the development of the solQTL module and demonstrate its application. Conclusions solQTL allows Solanaceae researchers to upload raw genotype and phenotype data to SGN, perform QTL analysis and dynamically cross-link to relevant genetic, expression and genome annotations. Exploration and synthesis of the relevant data is expected to help facilitate identification of candidate genes

  12. 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…

  13. 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.

  14. 8th International Conference on Information Visualization Theory and Applications

    CERN Document Server

    2017-01-01

    The International Conference on Information Visualization Theory and Applications aims at becoming a major point of contact between researchers, engineers and practitioners in Information Visualization. The conference will be structured along several topics related to Information Visualization.

  15. 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.

  16. Application of visualization technique in computational science

    International Nuclear Information System (INIS)

    Watanabe, Tadashi

    1996-01-01

    At the center for promotion of computational science and engineering in JAERI, complex phenomena in nuclear application fields such as heat conduction and fluid dynamics are studied through computer simulations based on first-principle models and equations. This research project is divided into three parts according to objectives and methodologies: continuum-system simulation, particle-system simulation, and large scale numerical simulation technique. Application of visualization technique is studied for the large scale numerical simulation technique. In the course of establishing a distributed processing environment, an animation processing system has been developed, in which simulation results are consecutively visualized on a server workstation for image processing and automatically recorded on a video tape. In this report, the animation processing system is described using examples in the particle-system simulation. (author)

  17. 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.

  18. 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.

  19. SeqPlots - Interactive software for exploratory data analyses, pattern discovery and visualization in genomics.

    Science.gov (United States)

    Stempor, Przemyslaw; Ahringer, Julie

    2016-01-01

    Experiments involving high-throughput sequencing are widely used for analyses of chromatin function and gene expression. Common examples are the use of chromatin immunoprecipitation for the analysis of chromatin modifications or factor binding, enzymatic digestions for chromatin structure assays, and RNA sequencing to assess gene expression changes after biological perturbations. To investigate the pattern and abundance of coverage signals across regions of interest, data are often visualized as profile plots of average signal or stacked rows of signal in the form of heatmaps. We found that available plotting software was either slow and laborious or difficult to use by investigators with little computational training, which inhibited wide data exploration. To address this need, we developed SeqPlots, a user-friendly exploratory data analysis (EDA) and visualization software for genomics. After choosing groups of signal and feature files and defining plotting parameters, users can generate profile plots of average signal or heatmaps clustered using different algorithms in a matter of seconds through the graphical user interface (GUI) controls. SeqPlots accepts all major genomic file formats as input and can also generate and plot user defined motif densities. Profile plots and heatmaps are highly configurable and batch operations can be used to generate a large number of plots at once. SeqPlots is available as a GUI application for Mac or Windows and Linux, or as an R/Bioconductor package. It can also be deployed on a server for remote and collaborative usage. The analysis features and ease of use of SeqPlots encourages wide data exploration, which should aid the discovery of novel genomic associations.

  20. 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

  1. 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

  2. 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.

  3. Mining, visualizing and comparing multidimensional biomolecular data using the Genomics Data Miner (GMine) Web-Server.

    Science.gov (United States)

    Proietti, Carla; Zakrzewski, Martha; Watkins, Thomas S; Berger, Bernard; Hasan, Shihab; Ratnatunga, Champa N; Brion, Marie-Jo; Crompton, Peter D; Miles, John J; Doolan, Denise L; Krause, Lutz

    2016-12-06

    Genomics Data Miner (GMine) is a user-friendly online software that allows non-experts to mine, cluster and compare multidimensional biomolecular datasets. Various powerful visualization techniques are provided, generating high quality figures that can be directly incorporated into scientific publications. Robust and comprehensive analyses are provided via a broad range of data-mining techniques, including univariate and multivariate statistical analysis, supervised learning, correlation networks, clustering and multivariable regression. The software has a focus on multivariate techniques, which can attribute variance in the measurements to multiple explanatory variables and confounders. Various normalization methods are provided. Extensive help pages and a tutorial are available via a wiki server. Using GMine we reanalyzed proteome microarray data of host antibody response against Plasmodium falciparum. Our results support the hypothesis that immunity to malaria is a higher-order phenomenon related to a pattern of responses and not attributable to any single antigen. We also analyzed gene expression across resting and activated T cells, identifying many immune-related genes with differential expression. This highlights both the plasticity of T cells and the operation of a hardwired activation program. These application examples demonstrate that GMine facilitates an accurate and in-depth analysis of complex molecular datasets, including genomics, transcriptomics and proteomics data.

  4. 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

  5. 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...

  6. 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.

  7. Applicability of Visual Analytics to Defence and Security Operations

    Science.gov (United States)

    2011-06-01

    The Gestalt laws of organization describe how people perceive visual components as organized patterns or wholes, instead of many different parts...IEEE. Koffka, K. (1935), Principles of Gestalt Psychology, Harcourt Brace, New York. Kohlhammer, J. and Keim, D. (2007), Visual Analytics in...Applicability of Visual Analytics to Defence and Security Operations Primary Topic: Primary Topic: 4 - Information and Knowledge Exploitation Alternate

  8. 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…

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

    Directory of Open Access Journals (Sweden)

    Fei Gu

    Full Text Available 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

  10. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

    Science.gov (United States)

    Raney, Brian J.; Dreszer, Timothy R.; Barber, Galt P.; Clawson, Hiram; Fujita, Pauline A.; Wang, Ting; Nguyen, Ngan; Paten, Benedict; Zweig, Ann S.; Karolchik, Donna; Kent, W. James

    2014-01-01

    Summary: Track data hubs provide an efficient mechanism for visualizing remotely hosted Internet-accessible collections of genome annotations. Hub datasets can be organized, configured and fully integrated into the University of California Santa Cruz (UCSC) Genome Browser and accessed through the familiar browser interface. For the first time, individuals can use the complete browser feature set to view custom datasets without the overhead of setting up and maintaining a mirror. Availability and implementation: Source code for the BigWig, BigBed and Genome Browser software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/. Binary Alignment/Map (BAM) and Variant Call Format (VCF)/tabix utilities are available from http://samtools.sourceforge.net/ and http://vcftools.sourceforge.net/. The UCSC Genome Browser is publicly accessible at http://genome.ucsc.edu. Contact: donnak@soe.ucsc.edu PMID:24227676

  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. 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...

  13. 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.

  14. [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.

  15. 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

  16. Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps.

    Science.gov (United States)

    Kumar, Rajendra; Sobhy, Haitham; Stenberg, Per; Lizana, Ludvig

    2017-09-29

    Hi-C experiments generate data in form of large genome contact maps (Hi-C maps). These show that chromosomes are arranged in a hierarchy of three-dimensional compartments. But to understand how these compartments form and by how much they affect genetic processes such as gene regulation, biologists and bioinformaticians need efficient tools to visualize and analyze Hi-C data. However, this is technically challenging because these maps are big. In this paper, we remedied this problem, partly by implementing an efficient file format and developed the genome contact map explorer platform. Apart from tools to process Hi-C data, such as normalization methods and a programmable interface, we made a graphical interface that let users browse, scroll and zoom Hi-C maps to visually search for patterns in the Hi-C data. In the software, it is also possible to browse several maps simultaneously and plot related genomic data. The software is openly accessible to the scientific community. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. 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 can......IP)-in conjunction with metabolite-and reaction-oriented data types (e.g. metabolomics, fluxomics). Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each...... of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools....

  18. iPiG: integrating peptide spectrum matches into genome browser visualizations.

    Directory of Open Access Journals (Sweden)

    Mathias Kuhring

    Full Text Available Proteogenomic approaches have gained increasing popularity, however it is still difficult to integrate mass spectrometry identifications with genomic data due to differing data formats. To address this difficulty, we introduce iPiG as a tool for the integration of peptide identifications from mass spectrometry experiments into existing genome browser visualizations. Thereby, the concurrent analysis of proteomic and genomic data is simplified and proteomic results can directly be compared to genomic data. iPiG is freely available from https://sourceforge.net/projects/ipig/. It is implemented in Java and can be run as a stand-alone tool with a graphical user-interface or integrated into existing workflows. Supplementary data are available at PLOS ONE online.

  19. 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

  20. Data management for genomic mapping applications: A case study

    Energy Technology Data Exchange (ETDEWEB)

    Markowitz, V.M.; Lewis, S.; McCarthy, J.; Olken, F.; Zorn, M.

    1992-05-01

    In this paper we describe a new approach to the construction of data management systems for genomic mapping applications in molecular biology, genetics, and plant breeding. We discuss the architecture of such systems and propose an incremental approach to the development of such systems. We illustrate the proposed approach and architecture with a case study of a prototype data management system for genomic maps.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. Visual basic application in computer hardware control and data ...

    African Journals Online (AJOL)

    ... hardware device control and data acquisition is experimented using Visual Basic and the Speech Application Programming Interface (SAPI) Software Development Kit. To control hardware using Visual Basic, all hardware requests were designed to go through Windows via the printer parallel ports which is accessed and ...

  7. 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.

  8. Genome constraint through sexual reproduction: application of 4D-Genomics in reproductive biology.

    Science.gov (United States)

    Horne, Steven D; Abdallah, Batoul Y; Stevens, Joshua B; Liu, Guo; Ye, Karen J; Bremer, Steven W; Heng, Henry H Q

    2013-06-01

    Assisted reproductive technologies have been used to achieve pregnancies since the first successful test tube baby was born in 1978. Infertile couples are at an increased risk for multiple miscarriages and the application of current protocols are associated with high first-trimester miscarriage rates. Among the contributing factors of these higher rates is a high incidence of fetal aneuploidy. Numerous studies support that protocols including ovulation-induction, sperm cryostorage, density-gradient centrifugation, and embryo culture can induce genome instability, but the general mechanism is less clear. Application of the genome theory and 4D-Genomics recently led to the establishment of a new paradigm for sexual reproduction; sex primarily constrains genome integrity that defines the biological system rather than just providing genetic diversity at the gene level. We therefore propose that application of assisted reproductive technologies can bypass this sexual reproduction filter as well as potentially induce additional system instability. We have previously demonstrated that a single-cell resolution genomic approach, such as spectral karyotyping to trace stochastic genome level alterations, is effective for pre- and post-natal analysis. We propose that monitoring overall genome alteration at the karyotype level alongside the application of assisted reproductive technologies will improve the efficacy of the techniques while limiting stress-induced genome instability. The development of more single-cell based cytogenomic technologies are needed in order to better understand the system dynamics associated with infertility and the potential impact that assisted reproductive technologies have on genome instability. Importantly, this approach will be useful in studying the potential for diseases to arise as a result of bypassing the filter of sexual reproduction.

  9. 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.

  10. Application of photogrammetry to surface flow visualization

    Energy Technology Data Exchange (ETDEWEB)

    Karthikeyan, N.; Venkatakrishnan, L. [Council of Scientific and Industrial Research, Experimental Aerodynamics Division, National Aerospace Laboratories, Delhi (India)

    2011-03-15

    The construction of three-dimensional surface flow fields is an extremely difficult task owing largely to the fragmented information available in the form of 2D images. Here, the method of photogrammetric resection based on a comprehensive camera model has been used to map oil flow visualization images on to the surface grid of the model. The data exported in the VRML format allow for user interaction in a manner not possible with 2D images. The technique is demonstrated here using the surface oil flow visualization images of a simplified landing gear model at low speed in a conventional wind tunnel without any specialized rigs for photogrammetry. The results are not limited to low-speed regimes and show that this technique can have significant impact on understanding the flow physics associated with the surface flow topology of highly three-dimensional separated flows on complex models. (orig.)

  11. Application of photogrammetry to surface flow visualization

    Science.gov (United States)

    Karthikeyan, N.; Venkatakrishnan, L.

    2011-03-01

    The construction of three-dimensional surface flow fields is an extremely difficult task owing largely to the fragmented information available in the form of 2D images. Here, the method of photogrammetric resection based on a comprehensive camera model has been used to map oil flow visualization images on to the surface grid of the model. The data exported in the VRML format allow for user interaction in a manner not possible with 2D images. The technique is demonstrated here using the surface oil flow visualization images of a simplified landing gear model at low speed in a conventional wind tunnel without any specialized rigs for photogrammetry. The results are not limited to low-speed regimes and show that this technique can have significant impact on understanding the flow physics associated with the surface flow topology of highly three-dimensional separated flows on complex models.

  12. 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

  13. Data management tools for genomic applications: A progress report

    Energy Technology Data Exchange (ETDEWEB)

    Markowitz, V.M.; Chen, I-Min A.

    1993-09-01

    We report in this paper on the development of data management tools that allow scientist to construct and manipulate genomic data bases in terms of application-specific objects and protocols. We are developing tools for specifying genomic database structures, as well as for entering, changing, maintaining, browsing and querying data in genomic data bases. These tools are based on the Object-protocol Model (OPM) developed by us and target commercial relational database management systems which are widely used in molecular biology laboratories. OPM allows scientists to interact with genomic databases in terms of their own frame or reference, namely genomic objects and protocols. Databases developed using the data management tools are easier to use, manage, and adapt.

  14. 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.

  15. Visualizing and Measuring Enterprise Application Architecture: An Exploratory Telecom Case

    OpenAIRE

    Lagerstroem, Robert; Baldwin, Carliss Y.; MacCormack, Alan D.; Aier, Stephan

    2014-01-01

    We test a method for visualizing and measuring enterprise application architectures. The method was designed and previously used to reveal the hidden internal architectural structure of software applications. The focus of this paper is to test if it can also uncover new facts about the applications and their relationships in an enterprise architecture, i.e., if the method can reveal the hidden external structure between software applications. Our test uses data from a large international tele...

  16. Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.

    Science.gov (United States)

    Pavlopoulos, Georgios A; Malliarakis, Dimitris; Papanikolaou, Nikolas; Theodosiou, Theodosis; Enright, Anton J; Iliopoulos, Ioannis

    2015-01-01

    "Α picture is worth a thousand words." This widely used adage sums up in a few words the notion that a successful visual representation of a concept should enable easy and rapid absorption of large amounts of information. Although, in general, the notion of capturing complex ideas using images is very appealing, would 1000 words be enough to describe the unknown in a research field such as the life sciences? Life sciences is one of the biggest generators of enormous datasets, mainly as a result of recent and rapid technological advances; their complexity can make these datasets incomprehensible without effective visualization methods. Here we discuss the past, present and future of genomic and systems biology visualization. We briefly comment on many visualization and analysis tools and the purposes that they serve. We focus on the latest libraries and programming languages that enable more effective, efficient and faster approaches for visualizing biological concepts, and also comment on the future human-computer interaction trends that would enable for enhancing visualization further.

  17. Information-theoretic identification of predictive SNPs and supervised visualization of genome-wide association studies

    Science.gov (United States)

    Bhasi, Kavitha; Zhang, Li; Brazeau, Daniel; Zhang, Aidong; Ramanathan, Murali

    2006-01-01

    The size, dimensionality and the limited range of the data values makes visualization of single nucleotide polymorphism (SNP) datasets challenging. The purpose of this study is to evaluate the usefulness of 3D VizStruct, a novel multi-dimensional data visualization technique for SNP datasets capable of identifying informative SNPs in genome-wide association studies. VizStruct is an interactive visualization technique that reduces multi-dimensional data to three dimensions using a combination of the discrete Fourier transform and the Kullback–Leibler divergence. The performance of 3D VizStruct was challenged with several diverse, biologically relevant published datasets including the human lipoprotein lipase (LPL) gene locus, the human Y-chromosome in several populations and a multi-locus genotype dataset of coral samples from four populations. In every case, the SNPs and or polymorphic markers identified by the 3D VizStruct mapping were predictive of the underlying biology. PMID:16899448

  18. 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.

  19. GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization.

    Science.gov (United States)

    Liao, Yu-Chieh; Tsai, Ming-Hsin; Chen, Feng-Chi; Hsiung, Chao A

    2012-07-01

    Genome-scale metabolic network models have become an indispensable part of the increasingly important field of systems biology. Metabolic systems biology studies usually include three major components-network model construction, objective- and experiment-guided model editing and visualization, and simulation studies based mainly on flux balance analyses. Bioinformatics tools are required to facilitate these complicated analyses. Although some of the required functions have been served separately by existing tools, a free software resource that simultaneously serves the needs of the three major components is not yet available. Here we present a software platform, GEMSiRV (GEnome-scale Metabolic model Simulation, Reconstruction and Visualization), to provide functionalities of easy metabolic network drafting and editing, amenable network visualization for experimental data integration and flux balance analysis tools for simulation studies. GEMSiRV comes with downloadable, ready-to-use public-domain metabolic models, reference metabolite/reaction databases and metabolic network maps, all of which can be input into GEMSiRV as the starting materials for network construction or simulation analyses. Furthermore, all of the GEMSiRV-generated metabolic models and analysis results, including projects in progress, can be easily exchanged in the research community. GEMSiRV is a powerful integrative resource that may facilitate the development of systems biology studies. The software is freely available on the web at http://sb.nhri.org.tw/GEMSiRV.

  20. Emerging genomic applications in coronary artery disease.

    Science.gov (United States)

    Damani, Samir B; Topol, Eric J

    2011-05-01

    Over the last 4 years, an unprecedented number of studies illuminating the genomic underpinnings of common "polygenic" diseases including coronary artery disease have been published. Notably, these studies have established numerous deoxyribonucleic acid (DNA) variants within or near chromosome 9p21.3, the LPA, CXADR, and APOE genes, to name a few, as key coronary artery disease and sudden cardiac death susceptibility markers. Most importantly, many of these DNA variants confer over a 2-fold increase in risk for coronary artery disease, myocardial infarction, and ventricular fibrillation. Additionally, loss-of-function variants in the hepatic cytochrome 2C19 system have now been found to be the predominant genetic mediators of clopidogrel antiplatelet response, with variant carriers having a >3-fold increase in risk for stent thrombosis. In the near future, many additional rare polymorphisms, structural variants, and tissue-specific epigenetic features of the human genome including DNA methylation, histone modifications, and chromatin state will emerge as significant contributors to disease pathogenesis and drug response. In aggregate, these findings will have the potential to radically change the practice of cardiovascular medicine. However, only the individual clinician can ultimately enable the translation of these important discoveries to systematic implementation in clinical practice. Copyright © 2011 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

  1. 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.

  2. 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.

  3. Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy.

    Science.gov (United States)

    Garmann, Rees F; Gopal, Ajaykumar; Athavale, Shreyas S; Knobler, Charles M; Gelbart, William M; Harvey, Stephen C

    2015-05-01

    The lifecycle, and therefore the virulence, of single-stranded (ss)-RNA viruses is regulated not only by their particular protein gene products, but also by the secondary and tertiary structure of their genomes. The secondary structure of the entire genomic RNA of satellite tobacco mosaic virus (STMV) was recently determined by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). The SHAPE analysis suggested a single highly extended secondary structure with much less branching than occurs in the ensemble of structures predicted by purely thermodynamic algorithms. Here we examine the solution-equilibrated STMV genome by direct visualization with cryo-electron microscopy (cryo-EM), using an RNA of similar length transcribed from the yeast genome as a control. The cryo-EM data reveal an ensemble of branching patterns that are collectively consistent with the SHAPE-derived secondary structure model. Thus, our results both elucidate the statistical nature of the secondary structure of large ss-RNAs and give visual support for modern RNA structure determination methods. Additionally, this work introduces cryo-EM as a means to distinguish between competing secondary structure models if the models differ significantly in terms of the number and/or length of branches. Furthermore, with the latest advances in cryo-EM technology, we suggest the possibility of developing methods that incorporate restraints from cryo-EM into the next generation of algorithms for the determination of RNA secondary and tertiary structures. © 2015 Garmann et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  4. Application of 3D stereoscopic visualization technology in casting aspect

    Directory of Open Access Journals (Sweden)

    Kang Jinwu

    2014-07-01

    Full Text Available 3D stereoscopic visualization technology is coming into more and more common use in the field of entertainment, and this technology is also beginning to cut a striking figure in casting industry and scientific research. The history, fundamental principle, and devices of 3D stereoscopic visualization technology are reviewed in this paper. The authors’ research achievements on the 3D stereoscopic visualization technology in the modeling and simulation of the casting process are presented. This technology can be used for the observation of complex 3D solid models of castings and the simulated results of solidification processes such as temperature, fluid flow, displacement, stress strain and microstructure, as well as the predicted defects such as shrinkage/porosity, cracks, and deformation. It can also be used for other areas relating to 3D models, such as assembling of dies, cores, etc. Several cases are given to compare the illustration of simulated results by traditional images and red-blue 3D stereoscopic images. The spatial shape is observed better by the new method. The prospect of 3D stereoscopic visualization in the casting aspect is discussed as well. The need for aided-viewing devices is still the most prominent problem of 3D stereoscopic visualization technology. However, 3D stereoscopic visualization represents the tendency of visualization technology in the future; and as the problem is solved in the years ahead, great breakthroughs will certainly be made for its application in casting design and modeling and simulation of the casting processes.

  5. [3D visualization and information interaction in biomedical applications].

    Science.gov (United States)

    Pu, F; Fan, Y; Jiang, W; Zhang, M; Mak, A F; Chen, J

    2001-06-01

    3D visualization and virtual reality are important trend in the development of modern science and technology, and as well in the studies on biomedical engineering. This paper presents a computer procedure developed for 3D visualization in biomedical applications. The biomedical models are constructed in slice sequences based on polygon cells and information interaction is realized on the basis of OpenGL selection mode in particular consideration of the specialties in this field such as irregularity in geometry and complexity in material etc. The software developed has functions of 3D model construction and visualization, real-time modeling transformation, information interaction and so on. It could serve as useful platform for 3D visualization in biomedical engineering research.

  6. 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.

  7. Genome Modification Technologies and Their Applications in Avian Species

    Directory of Open Access Journals (Sweden)

    Hong Jo Lee

    2017-10-01

    Full Text Available The rapid development of genome modification technology has provided many great benefits in diverse areas of research and industry. Genome modification technologies have also been actively used in a variety of research areas and fields of industry in avian species. Transgenic technologies such as lentiviral systems and piggyBac transposition have been used to produce transgenic birds for diverse purposes. In recent years, newly developed programmable genome editing tools such as transcription activator-like effector nuclease (TALEN and clustered regularly interspaced short palindromic repeats (CRISPR/CRISPR-associated protein 9 (CRISPR/Cas9 have also been successfully adopted in avian systems with primordial germ cell (PGC-mediated genome modification. These genome modification technologies are expected to be applied to practical uses beyond system development itself. The technologies could be used to enhance economic traits in poultry such as acquiring a disease resistance or producing functional proteins in eggs. Furthermore, novel avian models of human diseases or embryonic development could also be established for research purposes. In this review, we discuss diverse genome modification technologies used in avian species, and future applications of avian biotechnology.

  8. 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...

  9. The clinical applications of genome editing in HIV.

    Science.gov (United States)

    Wang, Cathy X; Cannon, Paula M

    2016-05-26

    HIV/AIDS has long been at the forefront of the development of gene- and cell-based therapies. Although conventional gene therapy approaches typically involve the addition of anti-HIV genes to cells using semirandomly integrating viral vectors, newer genome editing technologies based on engineered nucleases are now allowing more precise genetic manipulations. The possible outcomes of genome editing include gene disruption, which has been most notably applied to the CCR5 coreceptor gene, or the introduction of small mutations or larger whole gene cassette insertions at a targeted locus. Disruption of CCR5 using zinc finger nucleases was the first-in-human application of genome editing and remains the most clinically advanced platform, with 7 completed or ongoing clinical trials in T cells and hematopoietic stem/progenitor cells (HSPCs). Here we review the laboratory and clinical findings of CCR5 editing in T cells and HSPCs for HIV therapy and summarize other promising genome editing approaches for future clinical development. In particular, recent advances in the delivery of genome editing reagents and the demonstration of highly efficient homology-directed editing in both T cells and HSPCs are expected to spur the development of even more sophisticated applications of this technology for HIV therapy. © 2016 by The American Society of Hematology.

  10. 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.

  11. 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.

  12. HYBRIDCHECK: software for the rapid detection, visualization and dating of recombinant regions in genome sequence data.

    Science.gov (United States)

    Ward, Ben J; van Oosterhout, Cock

    2016-03-01

    HYBRIDCHECK is a software package to visualize the recombination signal in large DNA sequence data set, and it can be used to analyse recombination, genetic introgression, hybridization and horizontal gene transfer. It can scan large (multiple kb) contigs and whole-genome sequences of three or more individuals. HYBRIDCHECK is written in the r software for OS X, Linux and Windows operating systems, and it has a simple graphical user interface. In addition, the r code can be readily incorporated in scripts and analysis pipelines. HYBRIDCHECK implements several ABBA-BABA tests and visualizes the effects of hybridization and the resulting mosaic-like genome structure in high-density graphics. The package also reports the following: (i) the breakpoint positions, (ii) the number of mutations in each introgressed block, (iii) the probability that the identified region is not caused by recombination and (iv) the estimated age of each recombination event. The divergence times between the donor and recombinant sequence are calculated using a JC, K80, F81, HKY or GTR correction, and the dating algorithm is exceedingly fast. By estimating the coalescence time of introgressed blocks, it is possible to distinguish between hybridization and incomplete lineage sorting. HYBRIDCHECK is libré software and it and its manual are free to download from http://ward9250.github.io/HybridCheck/. © 2015 John Wiley & Sons Ltd.

  13. Microarray comparative genomic hybridisation analysis incorporating genomic organisation, and application to enterobacterial plant pathogens.

    Directory of Open Access Journals (Sweden)

    Leighton Pritchard

    2009-08-01

    Full Text Available Microarray comparative genomic hybridisation (aCGH provides an estimate of the relative abundance of genomic DNA (gDNA taken from comparator and reference organisms by hybridisation to a microarray containing probes that represent sequences from the reference organism. The experimental method is used in a number of biological applications, including the detection of human chromosomal aberrations, and in comparative genomic analysis of bacterial strains, but optimisation of the analysis is desirable in each problem domain.We present a method for analysis of bacterial aCGH data that encodes spatial information from the reference genome in a hidden Markov model. This technique is the first such method to be validated in comparisons of sequenced bacteria that diverge at the strain and at the genus level: Pectobacterium atrosepticum SCRI1043 (Pba1043 and Dickeya dadantii 3937 (Dda3937; and Lactococcus lactis subsp. lactis IL1403 and L. lactis subsp. cremoris MG1363. In all cases our method is found to outperform common and widely used aCGH analysis methods that do not incorporate spatial information. This analysis is applied to comparisons between commercially important plant pathogenic soft-rotting enterobacteria (SRE Pba1043, P. atrosepticum SCRI1039, P. carotovorum 193, and Dda3937.Our analysis indicates that it should not be assumed that hybridisation strength is a reliable proxy for sequence identity in aCGH experiments, and robustly extends the applicability of aCGH to bacterial comparisons at the genus level. Our results in the SRE further provide evidence for a dynamic, plastic 'accessory' genome, revealing major genomic islands encoding gene products that provide insight into, and may play a direct role in determining, variation amongst the SRE in terms of their environmental survival, host range and aetiology, such as phytotoxin synthesis, multidrug resistance, and nitrogen fixation.

  14. 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.

  15. Professional Application Lifecycle Management with Visual Studio 2010

    CERN Document Server

    Gousset, Mickey; Krishnamoorthy, Ajoy

    2010-01-01

    Get up to speed on Application Lifecycle Management (ALM) with Visual Studio 2010 through a combination of hands-on instruction and deep-dives. Microsoft has packed a lot of brand new testing and modeling tools into Visual Studio 2010, tools that previously were available only to Microsoft internal development teams. Developers will appreciate the focus on practical implementation techniques and best practices. A team of Microsoft insiders provides a nuts-and-bolts approach. This Wrox guide is designed as both a step-by-step guide and a reference for modeling, designing, and coordinating softw

  16. 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)

  17. ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation.

    Directory of Open Access Journals (Sweden)

    Tom Sante

    Full Text Available Structural genomic variations play an important role in human disease and phenotypic diversity. With the rise of high-throughput sequencing tools, mate-pair/paired-end/single-read sequencing has become an important technique for the detection and exploration of structural variation. Several analysis tools exist to handle different parts and aspects of such sequencing based structural variation analyses pipelines. A comprehensive analysis platform to handle all steps, from processing the sequencing data, to the discovery and visualization of structural variants, is missing. The ViVar platform is built to handle the discovery of structural variants, from Depth Of Coverage analysis, aberrant read pair clustering to split read analysis. ViVar provides you with powerful visualization options, enables easy reporting of results and better usability and data management. The platform facilitates the processing, analysis and visualization, of structural variation based on massive parallel sequencing data, enabling the rapid identification of disease loci or genes. ViVar allows you to scale your analysis with your work load over multiple (cloud servers, has user access control to keep your data safe and is easy expandable as analysis techniques advance. URL: https://www.cmgg.be/vivar/

  18. 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.

  19. 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....

  20. Genome Editing and Its Applications in Model Organisms

    Directory of Open Access Journals (Sweden)

    Dongyuan Ma

    2015-12-01

    Full Text Available Technological advances are important for innovative biological research. Development of molecular tools for DNA manipulation, such as zinc finger nucleases (ZFNs, transcription activator-like effector nucleases (TALENs, and the clustered regularly-interspaced short palindromic repeat (CRISPR/CRISPR-associated (Cas, has revolutionized genome editing. These approaches can be used to develop potential therapeutic strategies to effectively treat heritable diseases. In the last few years, substantial progress has been made in CRISPR/Cas technology, including technical improvements and wide application in many model systems. This review describes recent advancements in genome editing with a particular focus on CRISPR/Cas, covering the underlying principles, technological optimization, and its application in zebrafish and other model organisms, disease modeling, and gene therapy used for personalized medicine.

  1. Genome Editing and Its Applications in Model Organisms.

    Science.gov (United States)

    Ma, Dongyuan; Liu, Feng

    2015-12-01

    Technological advances are important for innovative biological research. Development of molecular tools for DNA manipulation, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regularly-interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas), has revolutionized genome editing. These approaches can be used to develop potential therapeutic strategies to effectively treat heritable diseases. In the last few years, substantial progress has been made in CRISPR/Cas technology, including technical improvements and wide application in many model systems. This review describes recent advancements in genome editing with a particular focus on CRISPR/Cas, covering the underlying principles, technological optimization, and its application in zebrafish and other model organisms, disease modeling, and gene therapy used for personalized medicine. Copyright © 2016 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

  2. 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

  3. Medical visualization based on VRML technology and its application

    Science.gov (United States)

    Yin, Meng; Luo, Qingming; Lu, Qiang; Sheng, Rongbing; Liu, Yafeng

    2003-07-01

    Current high-performance computers and advanced image processing capabilities have made the application of three dimensional visualization objects in biomedical images facilitate the researches on biomedical engineering greatly. Trying to cooperate with the update technology using Internet, where 3-D data are typically stored and processed on powerful servers accessible by using TCP/IP, we held the results of the isosurface be applied in medical visualization generally. So in this system we use the 3-D file format VRML2.0, which is used through the Web interface for manipulating 3-D models. In this program we implemented to generate and modify triangular isosurface meshes by marching cubes algorithm, using OpenGL and MFC techniques to render the isosurface and manipulate voxel data. This software is more adequate visualization of volumetric data. The drawbacks are that 3-D image processing on personal computers is rather slow and the set of tools for 3-D visualization is limited. However, these limitations have not affected the applicability of this platform for all the tasks needed in elementary experiments in laboratory or data preprocessed. With the help of OCT and MPE scanning image system, applying these techniques to the visualization of rabbit brain, constructing data sets of hierarchical subdivisions of the cerebral information, we can establish a virtual environment on the World Wide Web for the rabbit brain research from its gross anatomy to its tissue and cellular levels of detail, providng graphical modeling and information management of both the outer and the inner space of the rabbit brain.

  4. Visual genome-wide RNAi screening to identify human host factors required for Trypanosoma cruzi infection.

    Directory of Open Access Journals (Sweden)

    Auguste Genovesio

    Full Text Available The protozoan parasite Trypanosoma cruzi is the etiologic agent of Chagas disease, a neglected tropical infection that affects millions of people in the Americas. Current chemotherapy relies on only two drugs that have limited efficacy and considerable side effects. Therefore, the development of new and more effective drugs is of paramount importance. Although some host cellular factors that play a role in T. cruzi infection have been uncovered, the molecular requirements for intracellular parasite growth and persistence are still not well understood. To further study these host-parasite interactions and identify human host factors required for T. cruzi infection, we performed a genome-wide RNAi screen using cellular microarrays of a printed siRNA library that spanned the whole human genome. The screening was reproduced 6 times and a customized algorithm was used to select as hits those genes whose silencing visually impaired parasite infection. The 162 strongest hits were subjected to a secondary screening and subsequently validated in two different cell lines. Among the fourteen hits confirmed, we recognized some cellular membrane proteins that might function as cell receptors for parasite entry and others that may be related to calcium release triggered by parasites during cell invasion. In addition, two of the hits are related to the TGF-beta signaling pathway, whose inhibition is already known to diminish levels of T. cruzi infection. This study represents a significant step toward unveiling the key molecular requirements for host cell invasion and revealing new potential targets for antiparasitic therapy.

  5. 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.

  6. The application of genome editing in studying hearing loss.

    Science.gov (United States)

    Zou, Bing; Mittal, Rahul; Grati, M'hamed; Lu, Zhongmin; Shu, Yilai; Tao, Yong; Feng, Youg; Xie, Dinghua; Kong, Weijia; Yang, Shiming; Chen, Zheng-Yi; Liu, Xuezhong

    2015-09-01

    Targeted genome editing mediated by clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9) technology has emerged as one of the most powerful tools to study gene functions, and with potential to treat genetic disorders. Hearing loss is one of the most common sensory disorders, affecting approximately 1 in 500 newborns with no treatment. Mutations of inner ear genes contribute to the largest portion of genetic deafness. The simplicity and robustness of CRISPR/Cas9-directed genome editing in human cells and model organisms such as zebrafish, mice and primates make it a promising technology in hearing research. With CRISPR/Cas9 technology, functions of inner ear genes can be studied efficiently by the disruption of normal gene alleles through non-homologous-end-joining (NHEJ) mechanism. For genetic hearing loss, CRISPR/Cas9 has potential to repair gene mutations by homology-directed-repair (HDR) or to disrupt dominant mutations by NHEJ, which could restore hearing. Our recent work has shown CRISPR/Cas9-mediated genome editing can be efficiently performed in the mammalian inner ear in vivo. Thus, application of CRISPR/Cas9 in hearing research will open up new avenues for understanding the pathology of genetic hearing loss and provide new routes in the development of treatment to restore hearing. In this review, we describe major methodologies currently used for genome editing. We will highlight applications of these technologies in studies of genetic disorders and discuss issues pertaining to applications of CRISPR/Cas9 in auditory systems implicated in genetic hearing loss. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Therapeutic applications of CRISPR RNA-guided genome editing.

    Science.gov (United States)

    Koo, Taeyoung; Kim, Jin-Soo

    2017-01-01

    The rapid development of programmable nuclease-based genome editing technologies has enabled targeted gene disruption and correction both in vitro and in vivo This revolution opens up the possibility of precise genome editing at target genomic sites to modulate gene function in animals and plants. Among several programmable nucleases, the type II clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated nuclease 9 (Cas9) system has progressed remarkably in recent years, leading to its widespread use in research, medicine and biotechnology. In particular, CRISPR-Cas9 shows highly efficient gene editing activity for therapeutic purposes in systems ranging from patient stem cells to animal models. However, the development of therapeutic approaches and delivery methods remains a great challenge for biomedical applications. Herein, we review therapeutic applications that use the CRISPR-Cas9 system and discuss the possibilities and challenges ahead. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

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

    Directory of Open Access Journals (Sweden)

    Li Minn Ang

    2017-05-01

    Full Text Available 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.

  9. 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.

  10. Visual Servoing for a Quadrotor UAV in Target Tracking Applications

    Science.gov (United States)

    Popova, Marinela Georgieva

    This research study investigates the design and implementation of position-based and image-based visual servoing techniques for controlling the motion of quadrotor unmanned aerial vehicles (UAVs). The primary applications considered are tracking stationary and moving targets. A novel position-based tracking law is developed and integrated with inner loop proportional-integral-derivative control algorithm. A theoretical proof for the stability of the proposed method is provided and numerical simulations are performed to validate the performance of the closed-loop system. A classical image-based visual servoing technique is also implemented and a modification of the classical method is suggested to reduce the undesirable effects due to the underactuated quadrotor system. Finally, the case when the quadrotor loses sight of the target is investigated and several solutions are proposed to help maintain the view of the target.

  11. 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

  12. 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

    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. 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. 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. With this approach, we significantly reduced the amount of time needed to perform clonal analysis from NGS data in acute myeloid leukemia.

  13. 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.

  14. 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.

  15. MOBILE VISUAL ACUITY ASSESSMENT APPLICATION: AcuMob

    OpenAIRE

    AKBULUT, Akhan; AYDIN, Muhammed Ali; ZAİM, Abdül Halim

    2018-01-01

    This paper presents a mobile healthcare (mHealth) system for estimation of visual impairment that provides easiness by specifying the degree of an eye as orthoscopes. Our proposed system called AcuMob which is an Android based mobile application aimed to be used by patients who have myopia. In the crowd society, our proposed app will be implemented faster than the traditional ophthalmologic examination treatments as an alternative. Because AcuMob can be used in everywhere in any time slot, it...

  16. Optimized application of penalized regression methods to diverse genomic data.

    Science.gov (United States)

    Waldron, Levi; Pintilie, Melania; Tsao, Ming-Sound; Shepherd, Frances A; Huttenhower, Curtis; Jurisica, Igor

    2011-12-15

    Penalized regression methods have been adopted widely for high-dimensional feature selection and prediction in many bioinformatic and biostatistical contexts. While their theoretical properties are well-understood, specific methodology for their optimal application to genomic data has not been determined. Through simulation of contrasting scenarios of correlated high-dimensional survival data, we compared the LASSO, Ridge and Elastic Net penalties for prediction and variable selection. We found that a 2D tuning of the Elastic Net penalties was necessary to avoid mimicking the performance of LASSO or Ridge regression. Furthermore, we found that in a simulated scenario favoring the LASSO penalty, a univariate pre-filter made the Elastic Net behave more like Ridge regression, which was detrimental to prediction performance. We demonstrate the real-life application of these methods to predicting the survival of cancer patients from microarray data, and to classification of obese and lean individuals from metagenomic data. Based on these results, we provide an optimized set of guidelines for the application of penalized regression for reproducible class comparison and prediction with genomic data. A parallelized implementation of the methods presented for regression and for simulation of synthetic data is provided as the pensim R package, available at http://cran.r-project.org/web/packages/pensim/index.html. chuttenh@hsph.harvard.edu; juris@ai.utoronto.ca Supplementary data are available at Bioinformatics online.

  17. 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.

  18. Study of a direct visualization display tool for space applications

    Science.gov (United States)

    Pereira do Carmo, J.; Gordo, P. R.; Martins, M.; Rodrigues, F.; Teodoro, P.

    2017-11-01

    The study of a Direct Visualization Display Tool (DVDT) for space applications is reported. The review of novel technologies for a compact display tool is described. Several applications for this tool have been identified with the support of ESA astronauts and are presented. A baseline design is proposed. It consists mainly of OLEDs as image source; a specially designed optical prism as relay optics; a Personal Digital Assistant (PDA), with data acquisition card, as control unit; and voice control and simplified keyboard as interfaces. Optical analysis and the final estimated performance are reported. The system is able to display information (text, pictures or/and video) with SVGA resolution directly to the astronaut using a Field of View (FOV) of 20x14.5 degrees. The image delivery system is a monocular Head Mounted Display (HMD) that weights less than 100g. The HMD optical system has an eye pupil of 7mm and an eye relief distance of 30mm.

  19. The AIRS Applications Pipeline, from Identification to Visualization to Distribution

    Science.gov (United States)

    Ray, S. E.; Pagano, T. S.; Fetzer, E. J.; Lambrigtsen, B.; Teixeira, J.

    2014-12-01

    The Atmospheric Infrared Sounder (AIRS) on NASA's Aqua spacecraft has been returning daily global observations of Earth's atmospheric constituents and properties since 2002. AIRS provides observations of temperature and water vapor along the atmospheric column and is sensitive to many atmospheric constituents in the mid-troposphere, including carbon monoxide, carbon dioxide and ozone. With a 12-year data record and daily, global observations in near real-time, we are finding that AIRS data can play a role in applications that fall under most of the NASA Applied Sciences focus areas. Currently in development are temperature inversion maps that can potentially correlate to respiratory health problems, dengue fever and West Nile virus outbreak prediction maps, maps that can be used to make assessments of air quality, and maps of volcanic ash burden. This poster will communicate the Project's approach and efforts to date of its applications pipeline, which includes identifying applications, utilizing science expertise, hiring outside experts to assist with development and dissemination, visualization along application themes, and leveraging existing NASA data frameworks and organizations to facilitate archiving and distribution. In addition, a new web-based browse tool being developed by the AIRS Project for easy access to application product imagery will also be described.

  20. 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.

  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. Application of genomic technologies to the breeding of trees

    Directory of Open Access Journals (Sweden)

    Maria Luisa Badenes

    2016-11-01

    Full Text Available 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

  3. LEGER: knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species.

    Science.gov (United States)

    Dieterich, Guido; Kärst, Uwe; Fischer, Elmar; Wehland, Jürgen; Jänsch, Lothar

    2006-01-01

    Listeria species are ubiquitous in the environment and often contaminate foods because they grow under conditions used for food preservation. Listeria monocytogenes, the human and animal pathogen, causes Listeriosis, an infection with a high mortality rate in risk groups such as immune-compromised individuals. Furthermore, L.monocytogenes is a model organism for the study of intracellular bacterial pathogens. The publication of its genome sequence and that of the non-pathogenic species Listeria innocua initiated numerous comparative studies and efforts to sequence all species comprising the genus. The Proteome database LEGER (http://leger2.gbf.de/cgi-bin/expLeger.pl) was developed to support functional genome analyses by combining information obtained by applying bioinformatics methods and from public databases to improve the original annotations. LEGER offers three unique key features: (i) it is the first comprehensive information system focusing on the functional assignment of genes and proteins; (ii) integrated visualization tools, KEGG pathway and Genome Viewer, alleviate the functional exploration of complex data; and (iii) LEGER presents results of systematic post-genome studies, thus facilitating analyses combining computational and experimental results. Moreover, LEGER provides an unpublished membrane proteome analysis of L.innocua and in total visualizes experimentally validated information about the subcellular localizations of 789 different listerial proteins.

  4. 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.

  5. Genotyping-by-Sequencing and Its Application to Oat Genomic Research.

    Science.gov (United States)

    Fu, Yong-Bi; Yang, Mo-Hua

    2017-01-01

    Genotyping-by-sequencing (GBS) has emerged as a useful genomic approach for sampling genome-wide genetic variation, performing genome-wide association mapping, and conducting genomic selection. It is a combined one-step process of SNP marker discovery and genotyping through genome reduction with restriction enzymes and SNP calling with or without a sequenced genome. This approach has the advantage of being rapid, high throughput, cost effective, and applicable to organisms without sequenced genomes. It has been increasingly applied to generate SNP genotype data for plant genetic and genomic studies. To facilitate a wider GBS application, particularly in oat genetic and genomic research, we describe the GBS approach, review the current applications of GBS in plant species, and highlight some applications of GBS to oat research. We also discuss issues in various applications of GBS and provide some perspectives in GBS research. Recent developments of bioinformatics pipelines in high-quality SNP discovery for polyploid crops will enhance the application of GBS to oat genetic and genomic research.

  6. 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.

  7. Improving Pre-Service Teachers’ Visual Literacy through Online Photo-Sharing Applications

    Directory of Open Access Journals (Sweden)

    Alaa Sadik

    2011-03-01

    Full Text Available This study aims to investigate how pre-service teachers' visual literacy skills are affected by their use of online photo management and sharing applications like Flickr. Two approaches are used to develop the visual literacy skills of pre-service teachers through Flickr. The first is to help them decode visuals through practicing analysis techniques, and interpreting and creating meaning from visual stimuli. The second is to help them encode visuals as a tool for communication. Visual literacy tests, participants' logs, photograph evaluation instruments, and interviews are used to assess the improvement in the participants' visual literacy skills. The results of the analysis revealed that the pre-service teachers' skills in interpreting, understanding, and appreciating the meaning of visual messages were enhanced through online exchange and interaction by means of photo management and sharing applications. They were able to communicate more effectively through applying the basic principles and concepts of visual design.

  8. Application of genomics to forage crop breeding for quality traits

    DEFF Research Database (Denmark)

    Lübberstedt, Thomas

    2007-01-01

    Forage quality depends on the digestibility of fodder, and can be directly measured by the intake and metabolic conversion in animal trials. However, animal trials are time-consuming, laborious, and thus expensive. It is not possible to study thousands of plant genotypes, as required in breeding...... selection ultimately without need of field trials, and being environment independent. In addition, once identified relevant genes controlling forage quality are targets for transgenic approaches. Substantial progress has recently been achieved in the development and application of genomic tools both...... studied in detail and sequence motifs with likely effect on forage quality have been identified by association studies. Moreover, transgenic approaches substantiated the effect of several of these genes on forage quality. Perspectives and limitations of these findings for forage crop breeding...

  9. 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.

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

    OpenAIRE

    Allison Silverstein; Rachita Sood; Ainhoa Costas-Chavarri

    2016-01-01

    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 ...

  11. 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. ...

  12. Ontology-based information visualization : Toward semantic web applications

    NARCIS (Netherlands)

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

    2006-01-01

    This chapter has demonstrated an elegant way to visually represent ontological data. We have described how the Cluster Map visualization can use ontologies to create expressive information visualizations, with the attractive property that classes and objects that are semantically related are also

  13. Genomics Analogy Model for Educators (GAME): Fuzzy DNA Model to Enable the Learning of Gene Sequencing by Visually-Impaired and Blind Students

    Science.gov (United States)

    Butler, Charles; Bello, Julia; York, Alan; Orvis, Kathryn; Pittendrigh, Barry R.

    2008-01-01

    Much of the general population is aware of terms such as biotechnology, genetic engineering, and genomics. However, there is a lack of understanding concerning these fields among many secondary school students. Few teaching models exist to explain concepts behind genomics and even less are available for teaching the visually impaired and blind.…

  14. 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…

  15. [Genome editing technology and its application in forage legumes].

    Science.gov (United States)

    Liu, Huan; Meng, Yingying; Niu, Lifang; Lin, Hao

    2017-10-25

    Genome editing is a novel targeted genome modification biotechnology, which could successfully mutate specific loci as well as generate gene replacement and insertion in various organisms. So far, genome editing technology has been widely applied in investigating gene function and developing valuable traits in both model plants and major crops. In this review, we briefly survey the historical development of genome editing technology, summarize recent progress using the CRISPR/Cas9 system for plant genome editing and explore the potential of the CRISPR/Cas technology in improving forage legumes.

  16. 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

  17. 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

  18. Current status of potential applications of repurposed Cas9 for structural and functional genomics of plants.

    Science.gov (United States)

    Seth, Kunal; Harish

    2016-11-25

    Redesigned Cas9 has emerged as a tool with various applications like gene editing, gene regulation, epigenetic modification and chromosomal imaging. Target specific single guide RNA (sgRNA) can be used with Cas9 for precise gene editing with high efficiency than previously known methods. Further, nuclease-deactivated Cas9 (dCas9) can be fused with activator or repressor for activation (CRISPRa) and repression (CRISPRi) of gene expression, respectively. dCas9 fused with epigenetic modifier like methylase or acetylase further expand the scope of this technique. Fluorescent probes can be tagged to dCas9 to visualize the chromosome. Due to its wide-spread application, simplicity, accessibility, efficacy and universality, this technique is expanding the structural and functional genomic studies of plant and developing CRISPR crops. The present review focuses on current status of using repurposed Cas9 system in these various areas, with major focus on application in plants. Major challenges, concerns and future directions of using this technique are discussed in brief. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. 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.

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

    DEFF Research Database (Denmark)

    Lukjancenko, Oksana

    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...... typing; and Paper VIII represents the application of PanFunPro approach for in silico taxonomy prediction. In summary, this thesis presents three projects that have contributed to identification and characterization of microbial organisms, and open new possibilities for comparative genomics...

  1. [The application of genome editing in identification of plant gene function and crop breeding].

    Science.gov (United States)

    Zhou, Xiang-chun; Xing, Yong-zhong

    2016-03-01

    Plant genome can be modified via current biotechnology with high specificity and excellent efficiency. Zinc finger nucleases (ZFN), transcription activator-like effector nucleases (TALEN) and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system are the key engineered nucleases used in the genome editing. Genome editing techniques enable gene targeted mutagenesis, gene knock-out, gene insertion or replacement at the target sites during the endogenous DNA repair process, including non-homologous end joining (NHEJ) and homologous recombination (HR), triggered by the induction of DNA double-strand break (DSB). Genome editing has been successfully applied in the genome modification of diverse plant species, such as Arabidopsis thaliana, Oryza sativa, and Nicotiana tabacum. In this review, we summarize the application of genome editing in identification of plant gene function and crop breeding. Moreover, we also discuss the improving points of genome editing in crop precision genetic improvement for further study.

  2. 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.

  3. 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.

  4. 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...

  5. 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.

  6. 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.

  7. Gnome View: A tool for visual representation of human genome data

    Energy Technology Data Exchange (ETDEWEB)

    Pelkey, J.E.; Thomas, G.S.; Thurman, D.A.; Lortz, V.B.; Douthart, R.J.

    1993-02-01

    GnomeView is a tool for exploring data generated by the Human Gemone Project. GnomeView provides both graphical and textural styles of data presentation: employs an intuitive window-based graphical query interface: and integrates its underlying genome databases in such a way that the user can navigate smoothly across databases and between different levels of data. This paper describes GnomeView and discusses how it addresses various genome informatics issues.

  8. Genomics applications in food preservation and safety research

    NARCIS (Netherlands)

    Brul, S.; Keijser, B.J.F.; Spek, H. van der; Oomes, S.J.C.M.; Montijn, R.

    2005-01-01

    Genomes are being sequenced at an ever-increasing pace. Also genomes of many of the microorganisms of concern to food safety are now known. The next step is of course how to exploit this information in an effective way. This article briefly introduces the issues in the food processing industry as

  9. 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

  10. Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data.

    Science.gov (United States)

    Bolser, Dan; Staines, Daniel M; Pritchard, Emily; Kersey, Paul

    2016-01-01

    Ensembl Plants ( http://plants.ensembl.org ) is an integrative resource presenting genome-scale information for a growing number of sequenced plant species (currently 33). Data provided includes genome sequence, gene models, functional annotation, and polymorphic loci. Various additional information are provided for variation data, including population structure, individual genotypes, linkage, and phenotype data. In each release, comparative analyses are performed on whole genome and protein sequences, and genome alignments and gene trees are made available that show the implied evolutionary history of each gene family. Access to the data is provided through a genome browser incorporating many specialist interfaces for different data types, and through a variety of additional methods for programmatic access and data mining. These access routes are consistent with those offered through the Ensembl interface for the genomes of non-plant species, including those of plant pathogens, pests, and pollinators.Ensembl Plants is updated 4-5 times a year and is developed in collaboration with our international partners in the Gramene ( http://www.gramene.org ) and transPLANT projects ( http://www.transplantdb.org ).

  11. 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.

  12. 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.

  13. Development and Applications of CRISPR-Cas9 for Genome Engineering

    Science.gov (United States)

    Hsu, Patrick D.; Lander, Eric S.; Zhang, Feng

    2015-01-01

    Recent advances in genome engineering technologies based on the CRISPR-associated RNA-guided endonuclease Cas9 are enabling the systematic interrogation of mammalian genome function. Analogous to the search function in modern word processors, Cas9 can be guided to specific locations within complex genomes by a short RNA search string. Using this system, DNA sequences within the endogenous genome and their functional outputs are now easily edited or modulated in virtually any organism of choice. Cas9-mediated genetic perturbation is simple and scalable, empowering researchers to elucidate the functional organization of the genome at the systems level and establish causal linkages between genetic variations and biological phenotypes. In this Review, we describe the development and applications of Cas9 for a variety of research or translational applications while highlighting challenges as well as future directions. Derived from a remarkable microbial defense system, Cas9 is driving innovative applications from basic biology to biotechnology and medicine. PMID:24906146

  14. 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.

  15. Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomic Data.

    Science.gov (United States)

    Bolser, Dan M; Staines, Daniel M; Perry, Emily; Kersey, Paul J

    2017-01-01

    Ensembl Plants ( http://plants.ensembl.org ) is an integrative resource presenting genome-scale information for 39 sequenced plant species. Available data includes genome sequence, gene models, functional annotation, and polymorphic loci; for the latter, additional information including population structure, individual genotypes, linkage, and phenotype data is available for some species. Comparative data is also available, including genomic alignments and "gene trees," which show the inferred evolutionary history of each gene family represented in the resource. Access to the data is provided through a genome browser, which incorporates many specialist interfaces for different data types, through a variety of programmatic interfaces, and via a specialist data mining tool supporting rapid filtering and retrieval of bulk data. Genomic data from many non-plant species, including those of plant pathogens, pests, and pollinators, is also available via the same interfaces through other divisions of Ensembl.Ensembl Plants is updated 4-6 times a year and is developed in collaboration with our international partners in the Gramene ( http://www.gramene.org ) and transPLANT projects ( http://www.transplantdb.eu ).

  16. [The application of CRISPR/Cas9 genome editing technology in cancer research].

    Science.gov (United States)

    Wang, Da-yong; Ma, Ning; Hui, Yang; Gao, Xu

    2016-01-01

    The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein-9 nuclease) genome editing technology has become more and more popular in gene editing because of its simple design and easy operation. Using the CRISPR/Cas9 system, researchers can perform site-directed genome modification at the base level. Moreover, it has been widely used in genome editing in multiple species and related cancer research. In this review, we summarize the application of the CRISPR/Cas9 system in cancer research based on the latest research progresses as well as our understanding of cancer research and genome editing techniques.

  17. 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...

  18. Clinical application of visual evoked potential in orbital cellulitis of infants

    Directory of Open Access Journals (Sweden)

    Xiao-Juan Jing

    2014-07-01

    Full Text Available AIM: To explore the visual evoked potential in infantile orbital cellulitis' clinical applications by monitoring the visual evoked potential changes in infantile orbital cellulitis before, during and after treatment.METHODS: Twenty-three cases of CT diagnosed single orbital cellulitis were examined by the visual evoked potentials. The affected eyes as observation group, and healthy eyes as control group. Comparative observation of visual evoked potential changes in amplitude and incubation period before, during and after the treatment. RESULTS: Compared with the control group, the observation group's visual evoked potential changes included reduced amplitude, extended incubation period. With the treatment progress, the observation group had gradual increase in amplitude, gradual reduction in incubation period. CONCLUSION: In infantile orbital cellulitis, the use of visual evoked potentials is a simple, feasible and effective method to monitoring the visual function during the treatment.

  19. Applications of genome editing by programmable nucleases to the metabolic engineering of secondary metabolites.

    Science.gov (United States)

    Leitão, Ana Lúcia; Costa, Marina C; Enguita, Francisco J

    2017-01-10

    Genome engineering is a branch of modern biotechnology composed of a cohort of protocols designed to construct and modify a genotype with the main objective of giving rise to a desired phenotype. Conceptually, genome engineering is based on the so called genome editing technologies, a group of genetic techniques that allow either to delete or to insert genetic information in a particular genomic locus. Ten years ago, genome editing tools were limited to virus-driven integration and homologous DNA recombination. However, nowadays the uprising of programmable nucleases is rapidly changing this paradigm. There are two main families of modern tools for genome editing depending on the molecule that controls the specificity of the system and drives the editor machinery to its place of action. Enzymes such as Zn-finger and TALEN nucleases are protein-driven genome editors; while CRISPR system is a nucleic acid-guided editing system. Genome editing techniques are still not widely applied for the design of new compounds with pharmacological activity, but they are starting to be considered as promising tools for rational genome manipulation in biotechnology applications. In this review we will discuss the potential applications of programmable nucleases for the metabolic engineering of secondary metabolites with biological activity. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. 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.

  1. Progress in Genome Editing Technology and Its Application in Plants

    OpenAIRE

    Zhang, Kai; Raboanatahiry, Nadia; Zhu, Bin; Li, Maoteng

    2017-01-01

    Genome editing technology (GET) is a versatile approach that has progressed rapidly as a mechanism to alter the genotype and phenotype of organisms. However, conventional genome modification using GET cannot satisfy current demand for high-efficiency and site-directed mutagenesis, retrofitting of artificial nucleases has developed into a new avenue within this field. Based on mechanisms to recognize target genes, newly-developed GETs can generally be subdivided into three cleavage systems, pr...

  2. Application of the GRADE Approach in the Development of Guidelines and Recommendations in Genomic Medicine

    Science.gov (United States)

    Rafiq, Muhammad; Boccia, Stefania

    2018-01-01

    A great deal of ambiguity exists in the development of guidelines for genomic applications used in clinical practice. The GRADE (Grading of Recommendations Assessment, Development and Evaluation) approach has the potential to be applied in the guidelines and recommendations development process in genomics. Here, we discuss whether and how GRADE can be applied to address the challenges posed by the evidence-based guidelines and recommendations development process in genomics. To see how GRADE can complement to the current guidelines development in genomics, we compare and contrast GRADE with other approaches. GRADE differed from other methods by incorporating patient values and preferences and balance of consequences. We conclude that the groups trying to implement genomics into practice may gleam more information from applying the GRADE framework. However, it is not clear yet whether GRADE can address the issue of timeliness in terms of the differences between the time required for guidelines development and the rapid pace of genomics. PMID:29410601

  3. Genomic risk prediction of complex human disease and its clinical application.

    Science.gov (United States)

    Abraham, Gad; Inouye, Michael

    2015-08-01

    Recent advances in genome-wide association studies have stimulated interest in the genomic prediction of disease risk, potentially enabling individual-level risk estimates for early intervention and improved diagnostic procedures. Here, we review recent findings and approaches to genomic prediction model construction and performance, then contrast the potential benefits of such models in two complex human diseases, aiding diagnosis in celiac disease and prospective risk prediction for cardiovascular disease. Early indications are that optimal application of genomic risk scores will differ substantially for each disease depending on underlying genetic architecture as well as current clinical and public health practice. As costs decline, genomic profiles become common, and popular understanding of risk and its communication improves, genomic risk will become increasingly useful for the individual and the clinician. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  4. From Gene Targeting to Genome Editing: Transgenic animals applications and beyond.

    Science.gov (United States)

    Rocha-Martins, Maurício; Cavalheiro, Gabriel R; Matos-Rodrigues, Gabriel E; Martins, Rodrigo A P

    2015-08-01

    Genome modification technologies are powerful tools for molecular biology and related areas. Advances in animal transgenesis and genome editing technologies during the past three decades allowed systematic interrogation of gene function that can help model how the genome influences cellular physiology. Genetic engineering via homologous recombination (HR) has been the standard method to modify genomic sequences. Nevertheless, nuclease-guided genome editing methods that were developed recently, such as ZFN, TALEN and CRISPR/Cas, opened new perspectives for biomedical research. Here, we present a brief historical perspective of genome modification methods, focusing on transgenic mice models. Moreover, we describe how new techniques were discovered and improved, present the paradigm shifts and discuss their limitations and applications for biomedical research as well as possible future directions.

  5. 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.

  6. 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.

  7. 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,

  8. Populations of latent Mycobacterium tuberculosis lack a cell wall: Isolation, visualization, and whole-genome characterization

    Directory of Open Access Journals (Sweden)

    Ali Akbar Velayati

    2016-01-01

    Conclusion: Here, we show cell-wall free cells of MTB bacilli in their latent state, and the biological adaptation of these cells was more phenotypic in nature than genomic. These cell-wall free cells represent a good model for understanding the nature of TB latency.

  9. 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.

  10. 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

  11. 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

  12. Perception of Visual Variables on Tiled Wall-Sized Displays for Information Visualization Applications.

    Science.gov (United States)

    Bezerianos, A; Isenberg, P

    2012-12-01

    We present the results of two user studies on the perception of visual variables on tiled high-resolution wall-sized displays. We contribute an understanding of, and indicators predicting how, large variations in viewing distances and viewing angles affect the accurate perception of angles, areas, and lengths. Our work, thus, helps visualization researchers with design considerations on how to create effective visualizations for these spaces. The first study showed that perception accuracy was impacted most when viewers were close to the wall but differently for each variable (Angle, Area, Length). Our second study examined the effect of perception when participants could move freely compared to when they had a static viewpoint. We found that a far but static viewpoint was as accurate but less time consuming than one that included free motion. Based on our findings, we recommend encouraging viewers to stand further back from the display when conducting perception estimation tasks. If tasks need to be conducted close to the wall display, important information should be placed directly in front of the viewer or above, and viewers should be provided with an estimation of the distortion effects predicted by our work-or encouraged to physically navigate the wall in specific ways to reduce judgement error.

  13. 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

  14. 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...

  15. The application of genomics to emerging zoonotic viral diseases.

    Directory of Open Access Journals (Sweden)

    Bart L Haagmans

    2009-10-01

    Full Text Available Interspecies transmission of pathogens may result in the emergence of new infectious diseases in humans as well as in domestic and wild animals. Genomics tools such as high-throughput sequencing, mRNA expression profiling, and microarray-based analysis of single nucleotide polymorphisms are providing unprecedented ways to analyze the diversity of the genomes of emerging pathogens as well as the molecular basis of the host response to them. By comparing and contrasting the outcomes of an emerging infection with those of closely related pathogens in different but related host species, we can further delineate the various host pathways determining the outcome of zoonotic transmission and adaptation to the newly invaded species. The ultimate challenge is to link pathogen and host genomics data with biological outcomes of zoonotic transmission and to translate the integrated data into novel intervention strategies that eventually will allow the effective control of newly emerging infectious diseases.

  16. 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

  17. 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.

  18. 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.

  19. Application of genome editing technologies to the study and treatment of hematological disease.

    Science.gov (United States)

    Pellagatti, Andrea; Dolatshad, Hamid; Yip, Bon Ham; Valletta, Simona; Boultwood, Jacqueline

    2016-01-01

    Genome editing technologies have advanced significantly over the past few years, providing a fast and effective tool to precisely manipulate the genome at specific locations. The three commonly used genome editing technologies are Zinc Finger Nucleases (ZFNs), Transcription Activator-Like Effector Nucleases (TALENs), and the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Cas9 (CRISPR/Cas9) system. ZFNs and TALENs consist of endonucleases fused to a DNA-binding domain, while the CRISPR/Cas9 system uses guide RNAs to target the bacterial Cas9 endonuclease to the desired genomic location. The double-strand breaks made by these endonucleases are repaired in the cells either by non-homologous end joining, resulting in the introduction of insertions/deletions, or, if a repair template is provided, by homology directed repair. The ZFNs, TALENs and CRISPR/Cas9 systems take advantage of these repair mechanisms for targeted genome modification and have been successfully used to manipulate the genome in human cells. These genome editing tools can be used to investigate gene function, to discover new therapeutic targets, and to develop disease models. Moreover, these genome editing technologies have great potential in gene therapy. Here, we review the latest advances in the application of genome editing technology to the study and treatment of hematological disorders. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Histogram-based DNA analysis for the visualization of chromosome, genome and species information.

    Science.gov (United States)

    Costa, António M; Machado, José T; Quelhas, Maria D

    2011-05-01

    We describe a novel approach to explore DNA nucleotide sequence data, aiming to produce high-level categorical and structural information about the underlying chromosomes, genomes and species. The article starts by analyzing chromosomal data through histograms using fixed length DNA sequences. After creating the DNA-related histograms, a correlation between pairs of histograms is computed, producing a global correlation matrix. These data are then used as input to several data processing methods for information extraction and tabular/graphical output generation. A set of 18 species is processed and the extensive results reveal that the proposed method is able to generate significant and diversified outputs, in good accordance with current scientific knowledge in domains such as genomics and phylogenetics. Source code freely available for download at http://www4.dei.isep.ipp.pt/etc/dnapaper2010, implemented in Free Pascal and UNIX scripting tools. Study input data available online for download at University of California at Santa Cruz Genome Bioinformatics, http://hgdownload.cse.ucsc.edu/downloads.html.

  1. 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

  2. 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...

  3. QTL map meets population genomics: an application to rice.

    Directory of Open Access Journals (Sweden)

    Jeffrey A Fawcett

    Full Text Available Genes involved in the transition from wild to cultivated crop species should be of great agronomic importance. Population genomic approaches utilizing genome resequencing data have been recently applied for this purpose, although it only reports a large list of candidate genes with no biological information. Here, by resequencing more than 30 genomes altogether of wild rice Oryza rufipogon and cultivated rice O. sativa, we identified a number of regions with clear footprints of selection during the domestication process. We then focused on identifying candidate domestication genes in these regions by utilizing the wealth of QTL information in rice. We were able to identify a number of interesting candidates such as transcription factors that should control key domestication traits such as shattering, awn length, and seed dormancy. Other candidates include those that might have been related to the improvement of grain quality and those that might have been involved in the local adaptation to dry conditions and colder environments. Our study shows that population genomic approaches and QTL mapping information can be used together to identify genes that might be of agronomic importance.

  4. Clinical Applications of Genome Editing to HIV Cure.

    Science.gov (United States)

    Wang, Cathy X; Cannon, Paula M

    2016-12-01

    Despite significant advances in HIV drug treatment regimens, which grant near-normal life expectancies to infected individuals who have good virological control, HIV infection itself remains incurable. In recent years, novel gene- and cell-based therapies have gained increasing attention due to their potential to provide a functional or even sterilizing cure for HIV infection with a one-shot treatment. A functional cure would keep the infection in check and prevent progression to AIDS, while a sterilizing cure would eradicate all HIV viruses from the patient. Genome editing is the most precise form of gene therapy, able to achieve permanent genetic disruption, modification, or insertion at a predesignated genetic locus. The most well-studied candidate for anti-HIV genome editing is CCR5, an essential coreceptor for the majority of HIV strains, and the lack of which confers HIV resistance in naturally occurring homozygous individuals. Genetic disruption of CCR5 to treat HIV has undergone clinical testing, with seven completed or ongoing trials in T cells and hematopoietic stem and progenitor cells, and has shown promising safety and potential efficacy profiles. Here we summarize clinical findings of CCR5 editing for HIV therapy, as well as other genome editing-based approaches under pre-clinical development. The anticipated development of more sophisticated genome editing technologies should continue to benefit HIV cure efforts.

  5. 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.

  6. 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.

  7. Mixed Light Modulation Mode Application for 3D Visualization System

    OpenAIRE

    Osmanis, K; Misāns, P

    2015-01-01

    3D visualization system consists of a multilayer optical shutter screen and a projection system. High-frame rate projector projects images on shutter screen. Projector is based on spatial light modulator (for example, Texas Instruments Digital Micromirror Device), that consists of a number of micromirrors, displaying a binary image. To achieve image with desired color depth, several light modulation methods can be used – binary pulse width modulation, light source intensity mod...

  8. APPLICATION FOR DESIGN OF STRUCTURAL ELEMENT USING VISUAL BASIC CODING

    OpenAIRE

    T. Thenmozhi; K. Nithya; M. Arun Kumar; M. Ravichandran

    2017-01-01

    The increasing reliance of engineers on computer software in the performance of their tasks requires engineers, the future professional engineers, must be knowledgeable of sound engineering concepts, updated on the latest computer technology used in the industry and aware of the limitations and capabilities of the computer in solving engineering problems. Computer Methods in Civil Engineering to developed structural design program for design of structural element using Visual Basic. By creati...

  9. 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...

  10. 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.

  11. From Gene Targeting to Genome Editing: Transgenic animals applications and beyond

    Directory of Open Access Journals (Sweden)

    MAURÍCIO ROCHA-MARTINS

    2015-08-01

    Full Text Available ABSTRACTGenome modification technologies are powerful tools for molecular biology and related areas. Advances in animal transgenesis and genome editing technologies during the past three decades allowed systematic interrogation of gene function that can help model how the genome influences cellular physiology. Genetic engineering via homologous recombination (HR has been the standard method to modify genomic sequences. Nevertheless, nuclease-guided genome editing methods that were developed recently, such as ZFN, TALEN and CRISPR/Cas, opened new perspectives for biomedical research. Here, we present a brief historical perspective of genome modification methods, focusing on transgenic mice models. Moreover, we describe how new techniques were discovered and improved, present the paradigm shifts and discuss their limitations and applications for biomedical research as well as possible future directions.

  12. 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....

  13. Future health applications of genomics: priorities for communication, behavioral, and social sciences research.

    Science.gov (United States)

    McBride, Colleen M; Bowen, Deborah; Brody, Lawrence C; Condit, Celeste M; Croyle, Robert T; Gwinn, Marta; Khoury, Muin J; Koehly, Laura M; Korf, Bruce R; Marteau, Theresa M; McLeroy, Kenneth; Patrick, Kevin; Valente, Thomas W

    2010-05-01

    Despite the quickening momentum of genomic discovery, the communication, behavioral, and social sciences research needed for translating this discovery into public health applications has lagged behind. The National Human Genome Research Institute held a 2-day workshop in October 2008 convening an interdisciplinary group of scientists to recommend forward-looking priorities for translational research. This research agenda would be designed to redress the top three risk factors (tobacco use, poor diet, and physical inactivity) that contribute to the four major chronic diseases (heart disease, type 2 diabetes, lung disease, and many cancers) and account for half of all deaths worldwide. Three priority research areas were identified: (1) improving the public's genetic literacy in order to enhance consumer skills; (2) gauging whether genomic information improves risk communication and adoption of healthier behaviors more than current approaches; and (3) exploring whether genomic discovery in concert with emerging technologies can elucidate new behavioral intervention targets. Important crosscutting themes also were identified, including the need to: (1) anticipate directions of genomic discovery; (2) take an agnostic scientific perspective in framing research questions asking whether genomic discovery adds value to other health promotion efforts; and (3) consider multiple levels of influence and systems that contribute to important public health problems. The priorities and themes offer a framework for a variety of stakeholders, including those who develop priorities for research funding, interdisciplinary teams engaged in genomics research, and policymakers grappling with how to use the products born of genomics research to address public health challenges. 2010. Published by Elsevier Inc.

  14. 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

    2013-01-01

    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. PMID:23748955

  15. 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.

  16. 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...

  17. Survey of the Applications of NGS to Whole-Genome Sequencing and Expression Profiling

    Directory of Open Access Journals (Sweden)

    Jong-Sung Lim

    2012-03-01

    Full Text Available Recently, the technologies of DNA sequence variation and gene expression profiling have been used widely as approaches in the expertise of genome biology and genetics. The application to genome study has been particularly developed with the introduction of the next-generation DNA sequencer (NGS Roche/454 and Illumina/Solexa systems, along with bioinformation analysis technologies of whole-genome de novo assembly, expression profiling, DNA variation discovery, and genotyping. Both massive whole-genome shotgun paired-end sequencing and mate paired-end sequencing data are important steps for constructing de novo assembly of novel genome sequencing data. It is necessary to have DNA sequence information from a multiplatform NGS with at least 2× and 30× depth sequence of genome coverage using Roche/454 and Illumina/Solexa, respectively, for effective an way of de novo assembly. Massive short-length reading data from the Illumina/Solexa system is enough to discover DNA variation, resulting in reducing the cost of DNA sequencing. Whole-genome expression profile data are useful to approach genome system biology with quantification of expressed RNAs from a whole-genome transcriptome, depending on the tissue samples. The hybrid mRNA sequences from Rohce/454 and Illumina/Solexa are more powerful to find novel genes through de novo assembly in any whole-genome sequenced species. The 20× and 50× coverage of the estimated transcriptome sequences using Roche/454 and Illumina/Solexa, respectively, is effective to create novel expressed reference sequences. However, only an average 30× coverage of a transcriptome with short read sequences of Illumina/Solexa is enough to check expression quantification, compared to the reference expressed sequence tag sequence.

  18. 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.

  19. 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.

  20. Fluorescent signaling based on sulfoxide profluorophores: application to the visual detection of the explosive TATP.

    Science.gov (United States)

    Malashikhin, Sergey; Finney, Nathaniel S

    2008-10-01

    The first visual fluorescence-based assay for the peroxide explosive triacetone triperoxide (TATP) is described. The assay is based on a conceptually new fluorescence signaling mechanism, in which nonemissive pyrenyl sulfoxide profluorophores are oxidized to visibly emissive pyrenyl sulfones. Although not without limitations, these first-generation fluorescent probes can provide a visual response to ca. 100 nmol of TATP. In addition, the success of this assay suggests the potential for broader application of aryl sulfoxides in fluorescent chemosensing.

  1. 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)

  2. Web-based interactive visualization in a Grid-enabled neuroimaging application using HTML5.

    Science.gov (United States)

    Siewert, René; Specovius, Svenja; Wu, Jie; Krefting, Dagmar

    2012-01-01

    Interactive visualization and correction of intermediate results are required in many medical image analysis pipelines. To allow certain interaction in the remote execution of compute- and data-intensive applications, new features of HTML5 are used. They allow for transparent integration of user interaction into Grid- or Cloud-enabled scientific workflows. Both 2D and 3D visualization and data manipulation can be performed through a scientific gateway without the need to install specific software or web browser plugins. The possibilities of web-based visualization are presented along the FreeSurfer-pipeline, a popular compute- and data-intensive software tool for quantitative neuroimaging.

  3. 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

  4. 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.

  5. Progress in Genome Editing Technology and Its Application in Plants.

    Science.gov (United States)

    Zhang, Kai; Raboanatahiry, Nadia; Zhu, Bin; Li, Maoteng

    2017-01-01

    Genome editing technology (GET) is a versatile approach that has progressed rapidly as a mechanism to alter the genotype and phenotype of organisms. However, conventional genome modification using GET cannot satisfy current demand for high-efficiency and site-directed mutagenesis, retrofitting of artificial nucleases has developed into a new avenue within this field. Based on mechanisms to recognize target genes, newly-developed GETs can generally be subdivided into three cleavage systems, protein-dependent DNA cleavage systems (i.e., zinc-finger nucleases, ZFN, and transcription activator-like effector nucleases, TALEN), RNA-dependent DNA cleavage systems (i.e., clustered regularly interspaced short palindromic repeats-CRISPR associated proteins, CRISPR-Cas9, CRISPR-Cpf1, and CRISPR-C2c1), and RNA-dependent RNA cleavage systems (i.e., RNA interference, RNAi, and CRISPR-C2c2). All these techniques can lead to double-stranded (DSB) or single-stranded breaks (SSB), and result in either random mutations via non-homologous end-joining (NHEJ) or targeted mutation via homologous recombination (HR). Thus, site-directed mutagenesis can be induced via targeted gene knock-out, knock-in, or replacement to modify specific characteristics including morphology-modification, resistance-enhancement, and physiological mechanism-improvement along with plant growth and development. In this paper, an non-comprehensive review on the development of different GETs as applied to plants is presented.

  6. Progress in Genome Editing Technology and Its Application in Plants

    Science.gov (United States)

    Zhang, Kai; Raboanatahiry, Nadia; Zhu, Bin; Li, Maoteng

    2017-01-01

    Genome editing technology (GET) is a versatile approach that has progressed rapidly as a mechanism to alter the genotype and phenotype of organisms. However, conventional genome modification using GET cannot satisfy current demand for high-efficiency and site-directed mutagenesis, retrofitting of artificial nucleases has developed into a new avenue within this field. Based on mechanisms to recognize target genes, newly-developed GETs can generally be subdivided into three cleavage systems, protein-dependent DNA cleavage systems (i.e., zinc-finger nucleases, ZFN, and transcription activator-like effector nucleases, TALEN), RNA-dependent DNA cleavage systems (i.e., clustered regularly interspaced short palindromic repeats-CRISPR associated proteins, CRISPR-Cas9, CRISPR-Cpf1, and CRISPR-C2c1), and RNA-dependent RNA cleavage systems (i.e., RNA interference, RNAi, and CRISPR-C2c2). All these techniques can lead to double-stranded (DSB) or single-stranded breaks (SSB), and result in either random mutations via non-homologous end-joining (NHEJ) or targeted mutation via homologous recombination (HR). Thus, site-directed mutagenesis can be induced via targeted gene knock-out, knock-in, or replacement to modify specific characteristics including morphology-modification, resistance-enhancement, and physiological mechanism-improvement along with plant growth and development. In this paper, an non-comprehensive review on the development of different GETs as applied to plants is presented. PMID:28261237

  7. Development of genomics-based genotyping platforms and their applications in rice breeding.

    Science.gov (United States)

    Chen, Haodong; He, Hang; Zhou, Fasong; Yu, Huihui; Deng, Xing Wang

    2013-05-01

    Breeding by design has been an aspiration of researchers in the plant sciences for a decade. With the rapid development of genomics-based genotyping platforms and available of hundreds of functional genes/alleles in related to important traits, however, it may now be possible to turn this enduring ambition into a practical reality. Rice has a relatively simple genome comparing to other crops, and its genome composition and genetic behavior have been extensively investigated. Recently, rice has been taken as a model crop to perform breeding by design. The essential process of breeding by design is to integrate functional genes/alleles in an ideal genetic background, which requires high throughput genotyping platforms to screen for expected genotypes. With large amount of genome resequencing data and high-throughput genotyping technologies available, quite a number of genomics-based genotyping platforms have been developed. These platforms are widely used in genetic mapping, integration of target traits via marker-assisted backcrossing (MABC), pyramiding, recurrent selection (MARS) or genomic selection (GS). Here, we summarize and discuss recent exciting development of rice genomics-based genotyping platforms and their applications in molecular breeding. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. 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

  9. 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

  10. 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.

  11. 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....

  12. OPPORTUNITIES OF ELECTRO-OPTIC VISUALIZATION PRACTICAL APPLICATIONS ON BOARD THE AIRCRAFT

    Directory of Open Access Journals (Sweden)

    Sergey B. Stukalov

    2017-01-01

    Full Text Available The article covers the following issues: the development and practical application of airborne electro-optic systems in the civil aviation aircraft. They provide flight visual information for the pilot day and night in visual and instrument weather conditions. The legal documents establishing the requirements for the application of this type of electro-optic systems in aircraft are presented. The classification of airborne electro-optic systems, commonly named as electronic visualization systems is analyzed. The ways of implementing the recommendations in their construction are considered. There have been analyzed the possibilities of systems of different classes: enhanced vision systems (EVS, synthetic vision systems (SVS, combine vision systems (CVS and on-board vision systems with advanced visualization features, Enhanced Flight Vision Systems (EFVS. It is determined that nowadays EVS systems are considered to be the potential application systems. In order to analyze the possibilities of practical application of such systems in the issues of flight safety at low altitude and landing, flight experiments of the system installed on a light helicopter were conducted. The research introduces the results of flight experiments on the practical work of television and infrared (IR viewing channels of a promising typical system in simple and complex observation conditions. Based on the results of flight experiments, a conclusion can be made about the relevance of practical application of electronic visualization systems on board the aircraft to ensure flight safety. It is determined that the systems can be used in flight both for land observation tasks and ensuring a safe flight. When flying the helicopter at low altitude and landing procedures the pilot should use visual information from the rear hemisphere of the lower tail unit by electro-optical visualization system. It was elicited that in the infrared (IR channel and the fast rotation of

  13. 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.

  14. A touch typing application for blind and visually impaired users

    OpenAIRE

    Blažič , Veronika

    2015-01-01

    Fast typing is nowadays one of the most important skills needed to efficiently use a computer. As a part of this thesis, we have developed an application, that guides its user towards mastering touch typing, which can significantly increase one's typing speed. We collaborated with the Association for the Blind and Partially Sighted Youth in Ljubljana, which is also an educational institution, and adapted our solution to suit their student's needs by creating a customizable interface that can ...

  15. New Applications for the Testing and Visualization of Wireless Networks

    Science.gov (United States)

    2005-03-01

    networks. • Assist with pointing directional antennas in complex network architectures. These applications are capable of reporting wireless network...mechanism for clean shutdown of the iperf client as dictated by the user’s interaction with the GPSIPerf executable were a little more complex . A...distributed computing frameworks created by the Object Management Group (ref. 9). Mico (ref. 10) is an open source implementation of the CORBA

  16. 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.

  17. 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....

  18. 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.

  19. An Application Tool for Visualizing Research Work on Landslides

    OpenAIRE

    Lepp, Katarina

    2014-01-01

    This report describes the process of organizing the research material of a PhD thesis into a database, and the development of an application in order to access the information. The thesis relates to rainfall-induced landslides in the capital of Honduras: The data are a collection of press-based information related to these landslides over a period of 26 years and stored in several Excel files. The task has been to analyze the data and organize them into a conceptual database model. After proc...

  20. 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.

  1. 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.

  2. CRISPR/Cas 9 genome editing and its applications in organoids

    NARCIS (Netherlands)

    Driehuis, Else; Clevers, Hans

    2017-01-01

    Organoids are three-dimensional (3D) structures derived from adult or embryonic stem cells that maintain many structural and functional features of their respective organ. Recently, genome editing based on the bacterial defense mechanism CRISPR/Cas9 has emerged as an easily applicable and reliable

  3. 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.

  4. Pyramidal Normalization Filter: Visual Model With Applications To Image Understanding

    Science.gov (United States)

    Schenker, P. S.; Unangst, D. R.; Knaak, T. F.; Huntley, D. T.; Patterson, W. R.

    1982-12-01

    This paper introduces a new nonlinear filter model which has applications in low-level machine vision. We show that this model, which we designate the normalization filter, is the basis for non-directional, multiple spatial frequency channel resolved detection of image edge structure. We show that the results obtained in this procedure are in close correspondence to the zero-crossing sets of the Marr-Hildreth edge detector.6 By comparison to their model, ours has the additional feature of constant-contrast thresholding, viz., it is spatially brightness adaptive. We describe a highly efficient and flexible realization of the normalization filter based on Burt's algorithm for pyramidal filtering.18 We present illustrative experimental results that we have obtained with a computer implementation of this filter design.

  5. The CRISPR/Cas Genome-Editing Tool: Application in Improvement of Crops

    Science.gov (United States)

    Khatodia, Surender; Bhatotia, Kirti; Passricha, Nishat; Khurana, S. M. P.; Tuteja, Narendra

    2016-01-01

    The Clustered Regularly Interspaced Short Palindromic Repeats associated Cas9/sgRNA system is a novel targeted genome-editing technique derived from bacterial immune system. It is an inexpensive, easy, most user friendly and rapidly adopted genome editing tool transforming to revolutionary paradigm. This technique enables precise genomic modifications in many different organisms and tissues. 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 a changing climate. The emerging areas of research for the genome editing in plants include interrogating gene function, rewiring the regulatory signaling networks and sgRNA library for high-throughput loss-of-function screening. In this review, we have described 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 described. With this powerful and innovative technique the designer GE non-GM plants could further advance climate resilient and sustainable agriculture in the future and maximizing yield by combating abiotic and biotic stresses. PMID:27148329

  6. The CRISPR/Cas Genome-Editing Tool: Application in Improvement of Crops.

    Science.gov (United States)

    Khatodia, Surender; Bhatotia, Kirti; Passricha, Nishat; Khurana, S M P; Tuteja, Narendra

    2016-01-01

    The Clustered Regularly Interspaced Short Palindromic Repeats associated Cas9/sgRNA system is a novel targeted genome-editing technique derived from bacterial immune system. It is an inexpensive, easy, most user friendly and rapidly adopted genome editing tool transforming to revolutionary paradigm. This technique enables precise genomic modifications in many different organisms and tissues. 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 a changing climate. The emerging areas of research for the genome editing in plants include interrogating gene function, rewiring the regulatory signaling networks and sgRNA library for high-throughput loss-of-function screening. In this review, we have described 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 described. With this powerful and innovative technique the designer GE non-GM plants could further advance climate resilient and sustainable agriculture in the future and maximizing yield by combating abiotic and biotic stresses.

  7. [The research advances and applications of genome editing in hereditary eye diseases].

    Science.gov (United States)

    Cai, S W; Zhang, Y; Hou, M Z; Liu, Y; Li, X R

    2017-05-11

    Genome editing is a cutting-edge technology that generates DNA double strand breaks at the specific genomic DNA sequence through nuclease recognition and cleavage, and then achieves insertion, replacement, or deletion of the target gene via endogenous DNA repair mechanisms, such as non-homologous end joining, homology directed repair, and homologous recombination. So far, more than 600 human hereditary eye diseases and systemic hereditary diseases with ocular phenotypes have been found. However, most of these diseases are of incompletely elucidated pathogenesis and without effective therapies. Genome editing technology can precisely target and alter the genomes of animals, establish animal models of the hereditary diseases, and elucidate the relationship between the target gene and the disease phenotype, thereby providing a powerful approach to studying the pathogenic mechanisms underlying the hereditary eye diseases. In addition, correction of gene mutations by the genome editing brings a new hope to gene therapy for the hereditary eye diseases. This review introduces the molecular characteristics of 4 major enzymes used in the genome editing, including homing endonucleases, zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated protein 9 (Cas9), and summarizes the current applications of this technology in investigating the pathogenic mechanisms underlying the hereditary eye diseases. (Chin J Ophthalmol, 2017, 53: 386-371 ) .

  8. Plastid genomics in horticultural species: Importance and applications for plant diversity, evolution and biotechnology

    Directory of Open Access Journals (Sweden)

    Marcelo eRogalski

    2015-07-01

    Full Text Available During the evolution of the eukaryotic cell, plastids and mitochondria arose from an endosymbiotic process, which determined the presence of three genetic compartments into the incipient plant cell. After that, these three genetic materials from host and symbiont suffered several rearrangements, bringing on a complex interaction between nuclear and organellar gene products. Nowadays, plastids harbor a small genome with ~130 genes in a 100-220 kb sequence in higher plants. Plastid genes are mostly highly conserved between plant species, being useful for phylogenetic analysis in higher taxa. However, intergenic spacers have a relatively higher mutation rate and are important markers to study genetic diversity and divergence within natural plant populations. The predominant uniparental inheritance of plastids is like a highly desirable feature for phylogeny studies. Moreover, the gene content and genome rearrangements are efficient tools to capture and understand evolutionary events between different plant species. Currently, genetic engineering of the plastid genome (plastome offers a number of attractive advantages as high-level of foreign protein expression, marker-gene excision, gene expression in operon and transgene containment because of maternal inheritance of plastid genome in most crops. Therefore, plastid genome can be used for adding new characteristics related to synthesis of metabolic compounds, biopharmaceutical and tolerance to biotic and abiotic stresses. Here, we describe the importance and applications of plastid genome as tools for genetic and evolutionary studies, and plastid transformation focusing on increasing the performance of horticultural species in the field.

  9. 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.

  10. 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

  11. 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.

  12. The Handy Eye Check: a mobile medical application to test visual acuity in children.

    Science.gov (United States)

    Toner, Keri N; Lynn, Michael J; Candy, T Rowan; Hutchinson, Amy K

    2014-06-01

    To compare visual acuity results obtained with the Handy Eye Chart to results obtained using the Handy Eye Check, a mobile medical application that electronically presents isolated Handy Eye Chart optotypes according the Amblyopia Treatment Study (ATS) protocol. Consecutive patients 6-18 years of age presenting for eye examinations between May 30, 2012, and June 26, 2012, were invited to participate. Monocular visual acuity testing was performed on the subject's poorer-seeing eye using both the Handy Eye Check and the Handy Eye Chart under the same conditions. Visual acuity was first tested using the mobile application, then using the chart, followed by repeated application testing. Patients were excluded if they were unable to undergo the required visual acuity testing or if visual acuity in the worse-seeing eye was less than 20/200 (for validity testing, but not reliability testing). There was a strong linear correlation (r = 0.92) and a mean difference in acuity of -0.005 logMAR, or less than one letter (95% CI, -0.03 to 0.02), between the two tests. The 95% limits of agreement were ± 2 lines. Test-retest reliability was high, with 81% of retest scores within 0.1 logMAR (5 letters) and 100% within 0.2 logMAR (10 letters), an intraclass correlation coefficient of 0.93, and a standard error of measurement of 0.08. The Handy Eye Check mobile application compares similarly to the Handy Eye Chart as a valid and reliable test of visual acuity in children age 6-18 years. Published by Mosby, Inc.

  13. 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…

  14. Approaches to Visual Communication Media Criticism and Their Application to Television Genres.

    Science.gov (United States)

    Metallinos, Nikos

    Several schools of thought regarding media criticism, derived from diverse disciplines and literary sources, have emerged during the last decade. To examine their application to the visual communication media arts such as film and television, this paper: (1) reviews the literature of media criticism; (2) discusses various approaches to visual…

  15. 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…

  16. 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…

  17. 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...

  18. 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.

  19. 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.

  20. The Application of the Montage Image Mosaic Engine To The Visualization Of Astronomical Images

    Science.gov (United States)

    Berriman, G. Bruce; Good, J. C.

    2017-05-01

    The Montage Image Mosaic Engine was designed as a scalable toolkit, written in C for performance and portability across *nix platforms, that assembles FITS images into mosaics. This code is freely available and has been widely used in the astronomy and IT communities for research, product generation, and for developing next-generation cyber-infrastructure. Recently, it has begun finding applicability in the field of visualization. This development has come about because the toolkit design allows easy integration into scalable systems that process data for subsequent visualization in a browser or client. The toolkit it includes a visualization tool suitable for automation and for integration into Python: mViewer creates, with a single command, complex multi-color images overlaid with coordinate displays, labels, and observation footprints, and includes an adaptive image histogram equalization method that preserves the structure of a stretched image over its dynamic range. The Montage toolkit contains functionality originally developed to support the creation and management of mosaics, but which also offers value to visualization: a background rectification algorithm that reveals the faint structure in an image; and tools for creating cutout and downsampled versions of large images. Version 5 of Montage offers support for visualizing data written in HEALPix sky-tessellation scheme, and functionality for processing and organizing images to comply with the TOAST sky-tessellation scheme required for consumption by the World Wide Telescope (WWT). Four online tutorials allow readers to reproduce and extend all the visualizations presented in this paper.

  1. 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.

  2. 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…

  3. Using the transcriptome to annotate the genome revisited: application of massively parallel signature sequencing (MPSS).

    Science.gov (United States)

    Shah, Trushar; de Villiers, Etienne; Nene, Vishvanath; Hass, Brian; Taracha, Evans; Gardner, Malcolm J; Sansom, Clare; Pelle, Roger; Bishop, Richard

    2006-01-17

    Transcriptome analysis can provide useful data for refining genome sequence annotation. Application of massively parallel signature sequencing (MPSS) revealed reproducible transcription, in multiple MPSS cycles, from 73% of computationally predicted genes in the Theileria parva schizont lifecycle stage. Signatures spanning consecutive exons confirmed 142 predicted introns. MPSS identified 83 putative genes, >100 codons overlooked by annotation software, and 139 potentially incorrect gene models (with either truncated ORFs or overlooked exons) by interfacing signature locations with stop codon maps. Twenty representative models were confirmed as likely to be incorrect using reverse transcription PCR amplification from independent schizont cDNA preparations. More than 50% of the 60 putative single copy genes in T. parva that were absent from the genome of the closely related T. annulata had MPSS signatures. This study illustrates the utility of MPSS for improving annotation of small, gene-rich microbial eukaryotic genomes.

  4. [Research Progress on Application of CRISPR/Cas Genome Editing Technology in Hematological Diseases -Review].

    Science.gov (United States)

    Xin, Liu-Yan; Liu, Ai-Fei; Zhong, Si-Si; Chen, Yi-Jian

    2016-08-01

    CRISPR/Cas genome editing technology is a newly developed powerful tool for genetic manipulation, which can be used to manipulate the genome at specific locations precisely, to restore the function of genetic defect cells, and to develop various disease models. In recentl years, with the advances of precise genome manipulation, CRISPR/Cas technology has been applied to many aspects of diseases research and becomes an unique tool to investigate gene function and discover new therapeutic targets for genetic diseases. Nowadays, CRISPR/Cas technology has been a hot research point in agriculture, graziery, biotechnology and medicine. This review focuses on the recent advances in CRISPR/Cas technology and its application in hematological diseases.

  5. 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

    In food industry due to the high variety of the object including the shape, size and structure the involvement of real time robotic system is limited compared to the applications of robotic systems in automotive industry. For completing operations within food industry it is generally necessary...... 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...

  6. 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.

  7. 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

  8. A dictionary based informational genome analysis

    Directory of Open Access Journals (Sweden)

    Castellini Alberto

    2012-09-01

    Full Text Available Abstract Background In the post-genomic era several methods of computational genomics are emerging to understand how the whole information is structured within genomes. Literature of last five years accounts for several alignment-free methods, arisen as alternative metrics for dissimilarity of biological sequences. Among the others, recent approaches are based on empirical frequencies of DNA k-mers in whole genomes. Results Any set of words (factors occurring in a genome provides a genomic dictionary. About sixty genomes were analyzed by means of informational indexes based on genomic dictionaries, where a systemic view replaces a local sequence analysis. A software prototype applying a methodology here outlined carried out some computations on genomic data. We computed informational indexes, built the genomic dictionaries with different sizes, along with frequency distributions. The software performed three main tasks: computation of informational indexes, storage of these in a database, index analysis and visualization. The validation was done by investigating genomes of various organisms. A systematic analysis of genomic repeats of several lengths, which is of vivid interest in biology (for example to compute excessively represented functional sequences, such as promoters, was discussed, and suggested a method to define synthetic genetic networks. Conclusions We introduced a methodology based on dictionaries, and an efficient motif-finding software application for comparative genomics. This approach could be extended along many investigation lines, namely exported in other contexts of computational genomics, as a basis for discrimination of genomic pathologies.

  9. A survey of application: genomics and genetic programming, a new frontier.

    Science.gov (United States)

    Khan, Mohammad Wahab; Alam, Mansaf

    2012-08-01

    The aim of this paper is to provide an introduction to the rapidly developing field of genetic programming (GP). Particular emphasis is placed on the application of GP to genomics. First, the basic methodology of GP is introduced. This is followed by a review of applications in the areas of gene network inference, gene expression data analysis, SNP analysis, epistasis analysis and gene annotation. Finally this paper concluded by suggesting potential avenues of possible future research on genetic programming, opportunities to extend the technique, and areas for possible practical applications. Copyright © 2012 Elsevier Inc. All rights reserved.

  10. 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.

  11. 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.

  12. 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)

  13. The UCSC Cancer Genomics Browser: update 2015.

    Science.gov (United States)

    Goldman, Mary; Craft, Brian; Swatloski, Teresa; Cline, Melissa; Morozova, Olena; Diekhans, Mark; Haussler, David; Zhu, Jingchun

    2015-01-01

    The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a web-based application that integrates relevant data, analysis and visualization, allowing users to easily discover and share their research observations. Users can explore the relationship between genomic alterations and phenotypes by visualizing various -omic data alongside clinical and phenotypic features, such as age, subtype classifications and genomic biomarkers. The Cancer Genomics Browser currently hosts 575 public datasets from genome-wide analyses of over 227,000 samples, including datasets from TCGA, CCLE, Connectivity Map and TARGET. Users can download and upload clinical data, generate Kaplan-Meier plots dynamically, export data directly to Galaxy for analysis, plus generate URL bookmarks of specific views of the data to share with others. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Basics of genome editing technology and its application in livestock species.

    Science.gov (United States)

    Petersen, Bjoern

    2017-08-01

    In the last decade, the research community has witnessed a blooming of targeted genome editing tools and applications. Novel programmable DNA nucleases such as zinc finger nucleases (ZFNs), transcription activator-like endonucleases (TALENs) and the clustered regularly interspaced short palindromic repeats/Cas9 system (CRISPR/Cas9) possess long recognition sites and are capable of cutting DNA in a very specific manner. These DNA nucleases mediate targeted genetic alterations by enhancing the DNA mutation rate via induction of double-strand breaks at a predetermined genomic site. Compared to conventional homologous recombination-based gene targeting, DNA nucleases, also referred to as Genome Editors (GEs), can increase the targeting rate around 10,000- to 100,000-fold. The successful application of different GEs has been shown in a myriad of different organisms, including insects, amphibians, plants, nematodes and several mammalian species, including human cells and embryos. In contrast to all other DNA nucleases, that rely on protein-DNA binding, CRISPR/Cas9 uses RNA to establish a specific binding of its DNA nuclease. Besides its capability to facilitate multiplexed genomic modifications in one shot, the CRISPR/Cas is much easier to design compared to all other DNA nucleases. Current results indicate that any DNA nuclease can be successfully employed in a broad range of organisms which renders them useful for improving the understanding of complex physiological systems such as reproduction, producing transgenic animals, including creating large animal models for human diseases, creating specific cell lines, and plants, and even for treating human genetic diseases. This review provides an update on DNA nucleases, their underlying mechanism and focuses on their application to edit the genome of livestock species. © 2017 Blackwell Verlag GmbH.

  15. The application of CRISPR-Cas9 genome editing in Caenorhabditis elegans.

    Science.gov (United States)

    Xu, Suhong

    2015-08-20

    Genome editing using the Cas9 endonuclease of Streptococcus pyogenes has demonstrated unparalleled efficacy and facility for modifying genomes in a wide variety of organisms. Caenorhabditis elegans is one of the most convenient multicellular organisms for genetic analysis, and the application of this novel genome editing technique to this organism promises to revolutionize analysis of gene function in the future. CRISPR-Cas9 has been successfully used to generate imprecise insertions and deletions via non-homologous end-joining mechanisms and to create precise mutations by homology-directed repair from donor templates. Key variables are the methods used to deliver the Cas9 endonuclease and the efficiency of the single guide RNAs. CRISPR-Cas9-mediated editing appears to be highly specific in C. elegans, with no reported off-target effects. In this review, I briefly summarize recent progress in CRISPR-Cas9-based genome editing in C. elegans, highlighting technical improvements in mutagenesis and mutation detection, and discuss potential future applications of this technique. Copyright © 2015 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

  16. 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.

  17. 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.

  18. Auditory-visual interaction: from fundamental research in cognitive psychology to (possible) applications

    Science.gov (United States)

    Kohlrausch, Armin; van de Par, Steven

    1999-05-01

    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 even have a fixed temporal relation when reaching the observer. In speech, for example, visible lip movements and audible utterances occur in close synchrony which contributes to the improvement of speech intelligibility under adverse acoustic conditions. Research into multi- sensory perception is currently being performed in a great variety of experimental contexts. This paper attempts to give an overview of the typical research areas dealing with audio-visual interaction and integration, bridging the range from cognitive psychology to applied research for multimedia applications. Issues of interest are the sensitivity to asynchrony between audio and video signals, the interaction between audio-visual stimuli with discrepant spatial and temporal rate information, crossmodal effects in attention, audio-visual interactions in speech perception and the combined perceived quality of audio-visual stimuli.

  19. 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.

  20. 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

  1. Integrative Systems Biology Visualization with MAYDAY

    Directory of Open Access Journals (Sweden)

    Symonsy Stephan

    2010-12-01

    Full Text Available Visualization is pivotal for gaining insight in systems biology data. As the size and complexity of datasets and supplemental information increases, an efficient, integrated framework for general and specialized views is necessary. MAYDAY is an application for analysis and visualization of general ‘omics’ data. It follows a trifold approach for data visualization, consisting of flexible data preprocessing, highly customizable data perspective plots for general purpose visualization and systems based plots. Here, we introduce two new systems biology visualization tools for MAYDAY. Efficiently implemented genomic viewers allow the display of variables associated with genomic locations. Multiple variables can be viewed using our new track-based ChromeTracks tool. A functional perspective is provided by visualizing metabolic pathways either in KEGG or BioPax format. Multiple options of displaying pathway components are available, including Systems Biology Graphical Notation (SBGN glyphs. Furthermore, pathways can be viewed together with gene expression data either as heatmaps or profiles.

  2. 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

  3. 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

  4. Inferring genome-wide recombination landscapes from advanced intercross lines: application to yeast crosses.

    Directory of Open Access Journals (Sweden)

    Christopher J R Illingworth

    Full Text Available Accurate estimates of recombination rates are of great importance for understanding evolution. In an experimental genetic cross, recombination breaks apart and rejoins genetic material, such that the genomes of the resulting isolates are comprised of distinct blocks of differing parental origin. We here describe a method exploiting this fact to infer genome-wide recombination profiles from sequenced isolates from an advanced intercross line (AIL. We verified the accuracy of the method against simulated data. Next, we sequenced 192 isolates from a twelve-generation cross between West African and North American yeast Saccharomyces cerevisiae strains and inferred the underlying recombination landscape at a fine genomic resolution (mean segregating site distance 0.22 kb. Comparison was made with landscapes inferred for a similar cross between four yeast strains, and with a previous single-generation, intra-strain cross (Mancera et al., Nature 2008. Moderate congruence was identified between landscapes (correlation 0.58-0.77 at 5 kb resolution, albeit with variance between mean genome-wide recombination rates. The multiple generations of mating undergone in the AILs gave more precise inference of recombination rates than could be achieved from a single-generation cross, in particular in identifying recombination cold-spots. The recombination landscapes we describe have particular utility; both AILs are part of a resource to study complex yeast traits (see e.g. Parts et al., Genome Res 2011. Our results will enable future applications of this resource to take better account of local linkage structure heterogeneities. Our method has general applicability to other crossing experiments, including a variety of experimental designs.

  5. SocialTrends: a Web Application for Monitoring and Visualizing Users in Social Media

    OpenAIRE

    Tesconi, Maurizio; Gazz?, Davide; Lo Duca, Angelica

    2012-01-01

    Nowadays social media trends are becoming very importantto describe the variation of popularity, activity and influence of an entity.In this paper we define an abstract model which can be used on differentsocial media to compare metrics with the same meaning. In particularwe describe three classes of metrics: popularity, activity and influence.We also present SocialTrends, a web application (http://www.social-trends.it/) which collects, elaborates and visualizes social media data.Finally, we ...

  6. 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...

  7. 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.

  8. Program Aplikasi Perhitungan Premi Asuransi Jiwa Dengan Macro Dan Excel Visual Basic for Application (Vba)

    OpenAIRE

    Nuryanto, Khamdan; Zaki, Solichin

    2012-01-01

    Microsoft Excel merupakan software yang salah satu fungsinya adalah sebagai basis data. Di dalam Microsoft Excel terdapat Macro yang dapat mengotomatisasi operator atau fungsi yang ada pada Microsoft Excel. Selain itu, di dalam Microsoft Excel juga terdapat Excel Visual Basic for Application (VBA) yang dapat digunakan untuk membuat program aplikasi. Tabel mortalitas yang digunakan untuk menghitung premi asuransi jiwa dibuat menjadi database pada Microsoft Excel, kemudian rumus-rumus yang digu...

  9. 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.

  10. 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.

  11. HaploForge: a comprehensive pedigree drawing and haplotype visualization web application.

    Science.gov (United States)

    Tekman, Mehmet; Medlar, Alan; Mozere, Monika; Kleta, Robert; Stanescu, Horia

    2017-12-15

    Haplotype reconstruction is an important tool for understanding the aetiology of human disease. Haplotyping infers the most likely phase of observed genotypes conditional on constraints imposed by the genotypes of other pedigree members. The results of haplotype reconstruction, when visualized appropriately, show which alleles are identical by descent despite the presence of untyped individuals. When used in concert with linkage analysis, haplotyping can help delineate a locus of interest and provide a succinct explanation for the transmission of the trait locus. Unfortunately, the design choices made by existing haplotype visualization programs do not scale to large numbers of markers. Indeed, following haplotypes from generation to generation requires excessive scrolling back and forth. In addition, the most widely used program for haplotype visualization produces inconsistent recombination artefacts for the X chromosome. To resolve these issues, we developed HaploForge, a novel web application for haplotype visualization and pedigree drawing. HaploForge takes advantage of HTML5 to be fast, portable and avoid the need for local installation. It can accurately visualize autosomal and X-linked haplotypes from both outbred and consanguineous pedigrees. Haplotypes are coloured based on identity by descent using a novel A* search algorithm and we provide a flexible viewing mode to aid visual inspection. HaploForge can currently process haplotype reconstruction output from Allegro, GeneHunter, Merlin and Simwalk. HaploForge is licensed under GPLv3 and is hosted and maintained via GitHub. https://github.com/mtekman/haploforge. r.kleta@ucl.ac.uk. 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

  12. 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

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

    Science.gov (United States)

    Simple sequence repeats (SSR) or microsatellite markers are one of the most informative and versatile DNA-based markers. The use of next-generation sequencing technologies allow whole genome sequencing and make it possible to develop large numbers of SSRs through bioinformatic analysis of genome da...

  15. 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.

  16. 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

  17. 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.

  18. Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics

    Directory of Open Access Journals (Sweden)

    Brunham Robert C

    2004-07-01

    Full Text Available Abstract Background We establish that the occurrence of protein folds among genomes can be accurately described with a Weibull function. Systems which exhibit Weibull character can be interpreted with reliability theory commonly used in engineering analysis. For instance, Weibull distributions are widely used in reliability, maintainability and safety work to model time-to-failure of mechanical devices, mechanisms, building constructions and equipment. Results We have found that the Weibull function describes protein fold distribution within and among genomes more accurately than conventional power functions which have been used in a number of structural genomic studies reported to date. It has also been found that the Weibull reliability parameter β for protein fold distributions varies between genomes and may reflect differences in rates of gene duplication in evolutionary history of organisms. Conclusions The results of this work demonstrate that reliability analysis can provide useful insights and testable predictions in the fields of comparative and structural genomics.

  19. 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...

  20. Application of Visual Cues on 3D Dynamic Visualizations for Engineering Technology Students and Effects on Spatial Visualization Ability: A Quasi-Experimental Study

    Science.gov (United States)

    Katsioloudis, Petros; Jovanovic, Vukica; Jones, Mildred

    2016-01-01

    Several theorists believe that different types of visual cues influence cognition and behavior through learned associations; however, research provides inconsistent results. Considering this, a quasi-experimental study was done to determine if there are significant positive effects of visual cues (color blue) and to identify if a positive increase…

  1. 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

  2. CircularLogo: A lightweight web application to visualize intra-motif dependencies.

    Science.gov (United States)

    Ye, Zhenqing; Ma, Tao; Kalmbach, Michael T; Dasari, Surendra; Kocher, Jean-Pierre A; Wang, Liguo

    2017-05-22

    The sequence logo has been widely used to represent DNA or RNA motifs for more than three decades. Despite its intelligibility and intuitiveness, the traditional sequence logo is unable to display the intra-motif dependencies and therefore is insufficient to fully characterize nucleotide motifs. Many methods have been developed to quantify the intra-motif dependencies, but fewer tools are available for visualization. We developed CircularLogo, a web-based interactive application, which is able to not only visualize the position-specific nucleotide consensus and diversity but also display the intra-motif dependencies. Applying CircularLogo to HNF6 binding sites and tRNA sequences demonstrated its ability to show intra-motif dependencies and intuitively reveal biomolecular structure. CircularLogo is implemented in JavaScript and Python based on the Django web framework. The program's source code and user's manual are freely available at http://circularlogo.sourceforge.net . CircularLogo web server can be accessed from http://bioinformaticstools.mayo.edu/circularlogo/index.html . CircularLogo is an innovative web application that is specifically designed to visualize and interactively explore intra-motif dependencies.

  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. 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.

  5. Recent developments in olive (Olea europaea L.) genetics and genomics: applications in taxonomy, varietal identification, traceability and breeding.

    Science.gov (United States)

    Sebastiani, L; Busconi, M

    2017-09-01

    The latest results in DNA markers application and genomic studies in olive. Olive (Olea europaea L.) is among the most ancient tree crops worldwide and the source of oil beneficial for human health. Despite this, few data on olive genetics are available in comparison with other cultivated plant species. Molecular information is mainly linked to molecular markers and their application to the study of DNA variation in the Olea europaea complex. In terms of genomic research, efforts have been made in sequencing, heralding the era of olive genomic. The present paper represents an update of a previous review work published in this journal in 2011. The review is again mainly focused on DNA markers, whose application still constitutes a relevant percentage of the most recently published researches. Since the olive genomic era has recently started, the latest results in this field are also being discussed.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

    Functional annotation of the genome is important to understand the phenotypic complexity of various species. The road toward functional annotation involves several challenges ranging from experiments on individual molecules to large-scale analysis of high-throughput sequencing (HTS) data. HTS dat...... 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....

  13. Application of the genome editing tool CRISPR/Cas9 in non-human primates.

    Science.gov (United States)

    Luo, Xin; Li, Min; Su, Bing

    2016-07-18

    In the past three years, RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system has been used to facilitate efficient genome editing in many model and non-model animals. However, its application in nonhuman primates is still at the early stage, though in view of the similarities in anatomy, physiology, behavior and genetics, closely related nonhuman primates serve as optimal models for human biology and disease studies. In this review, we summarize the current proceedings of gene editing using CRISPR/Cas9 in nonhuman primates.

  14. Application and study of 3D visualization model on nuclear power plant construction

    Science.gov (United States)

    Guo, Depeng; Pu, Chenghao; Li, Maolin; Zhang, Wenguang; Zhao, Jing; Arlia, Laura Alejandra

    2017-04-01

    3-D visualization model is an advanced tool which addresses a digital expression to the project entity and functional characteristics by integrating the relative engineering data. Construction units lead this technique in the equipment installation activities of the first unit of AP1000 Nuclear Power Plant Project in the world. 3-D technique proved its advantages in construction scheme preparation, second design, collision simulation, construction logic, etc. Through the introduction of the main characteristics and superiority of this technique, the solution and suggestions for some project insufficiencies have been proposed. This will represent a benefit for its application in the future.

  15. Iq Test Program Application for Senior High School Level Using Microsoft Visual Basic 6.0

    OpenAIRE

    Deni Kurniawan; Sahni Damerianta,SKom, MMSI

    2003-01-01

    Scientific writing contains a description of the IQ test programs, which are measuring the level of intelligence, psychological aspects, and the direction of interest in accordance with the ability of a student who was still in high school and sat dibangku second class who later IQ tests would also determine the direction will get students at third grade, using Microsoft Visual Basic 6.0.As for the first time that must be filled in this application is the biodata of students, such as: Number ...

  16. Background Oriented Schlieren (BOS) and other Flow Visualization Developments and Applications at GRC

    Science.gov (United States)

    Clem, Michelle; Woike, Mark

    2013-01-01

    This is a presentation to be given at an internal NASA Advanced Schlieren Working Group Meeting. The presentation will cover the recent developments and applications of flow visualization methods at GRC. The topics being discussed will include the use of Background Oriented Schlieren (BOS) in the study of screech and its associated shock spacing as well as in the investigation of broadband shock noise reduction in the Jet-Surface Interaction Tests. In addition, other flow visualiztion methods will be discussed in an on-going study comparing schlieren, shadowgraph, BOS, and focusing schlieren.

  17. 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)

  18. Efficient Data Reduction Techniques for Remote Applications of a Wireless Visual Sensor Network

    Directory of Open Access Journals (Sweden)

    Khursheed Khursheed

    2013-05-01

    Full Text Available Abstract A Wireless Visual Sensor Network (WVSN is formed by deploying many Visual Sensor Nodes (VSNs in the field. After acquiring an image of the area of interest, the VSN performs local processing on it and transmits the result using an embedded wireless transceiver. Wireless data transmission consumes a great deal of energy, where energy consumption is mainly dependent on the amount of information being transmitted. The image captured by the VSN contains a huge amount of data. For certain applications, segmentation can be performed on the captured images. The amount of information in the segmented images can be reduced by applying efficient bi-level image compression methods. In this way, the communication energy consumption of each of the VSNs can be reduced. However, the data reduction capability of bi-level image compression standards is fixed and is limited by the used compression algorithm. For applications attributing few changes in adjacent frames, change coding can be applied for further data reduction. Detecting and compressing only the Regions of Interest (ROIs in the change frame is another possibility for further data reduction. In a communication system, where both the sender and the receiver know the employed compression standard, there is a possibility for further data reduction by not including the header information in the compressed bit stream of the sender. This paper summarizes different information reduction techniques such as image coding, change coding and ROI coding. The main contribution is the investigation of the combined effect of all these coding methods and their application to a few representative real life applications. This paper is intended to be a resource for researchers interested in techniques for information reduction in energy constrained embedded applications.

  19. GridMol: a grid application for molecular modeling and visualization

    Science.gov (United States)

    Sun, Yanhua; Shen, Bin; Lu, Zhonghua; Jin, Zhong; Chi, Xuebin

    2008-02-01

    In this paper we present GridMol, an extensible tool for building a high performance computational chemistry platform in the grid environment. GridMol provides computational chemists one-stop service for molecular modeling, scientific computing and molecular information visualization. GridMol is not only a visualization and modeling tool but also simplifies control of remote Grid software that can access high performance computing resources. GridMol has been successfully integrated into China National Grid, the most powerful Chinese Grid Computing platform. In Section "Grid computing" of this paper, a computing example is given to show the availability and efficiency of GridMol. GridMol is coded using Java and Java3D for portability and cross-platform compatibility (Windows, Linux, MacOS X and UNIX). GridMol can run not only as a stand-alone application, but also as an applet through web browsers. In this paper, we will present the techniques for molecular visualization, molecular modeling and grid computing. GridMol is available free of charge under the GNU Public License (GPL) from our website: http://www.sccas.cn/ syh/GridMol/index.html.

  20. 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.

  1. 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.

  2. 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.

  3. MEA Viewer: A high-performance interactive application for visualizing electrophysiological data.

    Science.gov (United States)

    Bridges, Daniel C; Tovar, Kenneth R; Wu, Bian; Hansma, Paul K; Kosik, Kenneth S

    2018-01-01

    Action potentials can be recorded extracellularly from hundreds of neurons simultaneously with multi-electrode arrays. These can typically have as many as 120 or more electrodes. The brief duration of action potentials requires a high sampling frequency to reliably capture each waveform. The resulting raw data files are therefore large and difficult to visualize with traditional plotting tools. Common approaches to deal with the difficulties of data display, such as extracting spike times and performing spike train analysis, are useful in many contexts but they also significantly reduce data dimensionality. The use of tools which minimize data processing enable the development of heuristic perspective of experimental results. Here we introduce MEA Viewer, a high-performance open source application for the direct visualization of multi-channel electrophysiological data. MEA Viewer includes several high-performance visualizations, including an easily navigable overview of recorded extracellular action potentials from all data channels overlaid with spike timestamp data and an interactive raster plot. MEA Viewer can also display the two dimensional extent of action potential propagation in single neurons by signal averaging extracellular action potentials (eAPs) from single neurons detected on multiple electrodes. This view extracts and displays eAP timing information and eAP waveforms that are otherwise below the spike detection threshold. This entirely new method of using MEAs opens up novel research applications for medium density arrays. MEA Viewer is licensed under the General Public License version 3, GPLv3, and is available at http://github.com/dbridges/mea-tools.

  4. MEA Viewer: A high-performance interactive application for visualizing electrophysiological data.

    Directory of Open Access Journals (Sweden)

    Daniel C Bridges

    Full Text Available Action potentials can be recorded extracellularly from hundreds of neurons simultaneously with multi-electrode arrays. These can typically have as many as 120 or more electrodes. The brief duration of action potentials requires a high sampling frequency to reliably capture each waveform. The resulting raw data files are therefore large and difficult to visualize with traditional plotting tools. Common approaches to deal with the difficulties of data display, such as extracting spike times and performing spike train analysis, are useful in many contexts but they also significantly reduce data dimensionality. The use of tools which minimize data processing enable the development of heuristic perspective of experimental results. Here we introduce MEA Viewer, a high-performance open source application for the direct visualization of multi-channel electrophysiological data. MEA Viewer includes several high-performance visualizations, including an easily navigable overview of recorded extracellular action potentials from all data channels overlaid with spike timestamp data and an interactive raster plot. MEA Viewer can also display the two dimensional extent of action potential propagation in single neurons by signal averaging extracellular action potentials (eAPs from single neurons detected on multiple electrodes. This view extracts and displays eAP timing information and eAP waveforms that are otherwise below the spike detection threshold. This entirely new method of using MEAs opens up novel research applications for medium density arrays. MEA Viewer is licensed under the General Public License version 3, GPLv3, and is available at http://github.com/dbridges/mea-tools.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. A versatile data-visualization application for the Norwegian flood forecasting service

    Science.gov (United States)

    Kobierska, Florian; Langsholt, Elin G.; Hamududu, Byman H.; Engeland, Kolbjørn

    2017-04-01

    - General motivation A graphical user interface has been developed to visualize multi-model hydrological forecasts at the flood forecasting service of the Norwegian water and energy directorate. It is based on the R 'shiny' package, with which interactive web applications can quickly be prototyped. The app queries multiple data sources, building a comprehensive infographics dashboard for the decision maker. - Main features of the app The visualization application comprises several tabs, each built with different functionality and focus. A map of forecast stations gives a rapid insight of the flood situation and serves, concurrently, as a map station selection (based on the 'leaflet' package). The map selection is linked to multi-panel forecast plots which can present input, state or runoff parameters. Another tab focuses on past model performance and calibration runs. - Software design choices The application was programmed with a focus on flexibility regarding data-sources. The parsing of text-based model results was explicitly separated from the app (in the separate R package 'NVEDATA'), so that it only loads standardized RData binary files. We focused on allowing re-usability in other contexts by structuring the app into specific 'shiny' modules. The code was bundled into an R package, which is available on GitHub. - Documentation efforts A documentation website is under development. For easier collaboration, we chose to host it on the 'GitHub Pages' branch of the repository and build it automatically with a continuous integration service. The aim is to gather all information about the flood forecasting methodology at NVE in one location. This encompasses details on each hydrological model used as well as the documentation of the data-visualization application. - Outlook for further development The ability to select a group of stations by filtering a table (i.e. past performance, past major flood events, catchment parameters) and exporting it to the forecast tab

  12. Information Visualization Techniques in Bioinformatics during the Postgenomic Era

    Science.gov (United States)

    Tao, Ying; Liu, Yang; Friedman, Carol

    2010-01-01

    Information visualization techniques, which take advantage of the bandwidth of human vision, are powerful tools for organizing and analyzing a large amount of data. In the postgenomic era, information visualization tools are indispensable for biomedical research. This paper aims to present an overview of current applications of information visualization techniques in bioinformatics for visualizing different types of biological data, such as from genomics, proteomics, expression profiling and structural studies. Finally, we discuss the challenges of information visualization in bioinformatics related to dealing with more complex biological information in the emerging fields of systems biology and systems medicine. PMID:20976032

  13. LEGER: knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species

    OpenAIRE

    Dieterich, Guido; Kärst, Uwe; Fischer, Elmar; Wehland, Jürgen; Jänsch, Lothar

    2005-01-01

    Listeria species are ubiquitous in the environment and often contaminate foods because they grow under conditions used for food preservation. Listeria monocytogenes, the human and animal pathogen, causes Listeriosis, an infection with a high mortality rate in risk groups such as immune-compromised individuals. Furthermore, L.monocytogenes is a model organism for the study of intracellular bacterial pathogens. The publication of its genome sequence and that of the non-pathogenic species Lister...

  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. Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics.

    Science.gov (United States)

    Ren, Jie; Song, Kai; Deng, Minghua; Reinert, Gesine; Cannon, Charles H; Sun, Fengzhu

    2016-04-01

    Next-generation sequencing (NGS) technologies generate large amounts of short read data for many different organisms. The fact that NGS reads are generally short makes it challenging to assemble the reads and reconstruct the original genome sequence. For clustering genomes using such NGS data, word-count based alignment-free sequence comparison is a promising approach, but for this approach, the underlying expected word counts are essential.A plausible model for this underlying distribution of word counts is given through modeling the DNA sequence as a Markov chain (MC). For single long sequences, efficient statistics are available to estimate the order of MCs and the transition probability matrix for the sequences. As NGS data do not provide a single long sequence, inference methods on Markovian properties of sequences based on single long sequences cannot be directly used for NGS short read data. Here we derive a normal approximation for such word counts. We also show that the traditional Chi-square statistic has an approximate gamma distribution ,: using the Lander-Waterman model for physical mapping. We propose several methods to estimate the order of the MC based on NGS reads and evaluate those using simulations. We illustrate the applications of our results by clustering genomic sequences of several vertebrate and tree species based on NGS reads using alignment-free sequence dissimilarity measures. We find that the estimated order of the MC has a considerable effect on the clustering results ,: and that the clustering results that use a N: MC of the estimated order give a plausible clustering of the species. Our implementation of the statistics developed here is available as R package 'NGS.MC' at http://www-rcf.usc.edu/∼fsun/Programs/NGS-MC/NGS-MC.html fsun@usc.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  16. Fractal Dimension Analysis of Transient Visual Evoked Potentials: Optimisation and Applications.

    Science.gov (United States)

    Boon, Mei Ying; Henry, Bruce Ian; Chu, Byoung Sun; Basahi, Nour; Suttle, Catherine May; Luu, Chi; Leung, Harry; Hing, Stephen

    2016-01-01

    The visual evoked potential (VEP) provides a time series signal response to an external visual stimulus at the location of the visual cortex. The major VEP signal components, peak latency and amplitude, may be affected by disease processes. Additionally, the VEP contains fine detailed and non-periodic structure, of presently unclear relevance to normal function, which may be quantified using the fractal dimension. The purpose of this study is to provide a systematic investigation of the key parameters in the measurement of the fractal dimension of VEPs, to develop an optimal analysis protocol for application. VEP time series were mathematically transformed using delay time, τ, and embedding dimension, m, parameters. The fractal dimension of the transformed data was obtained from a scaling analysis based on straight line fits to the numbers of pairs of points with separation less than r versus log(r) in the transformed space. Optimal τ, m, and scaling analysis were obtained by comparing the consistency of results using different sampling frequencies. The optimised method was then piloted on samples of normal and abnormal VEPs. Consistent fractal dimension estimates were obtained using τ = 4 ms, designating the fractal dimension = D2 of the time series based on embedding dimension m = 7 (for 3606 Hz and 5000 Hz), m = 6 (for 1803 Hz) and m = 5 (for 1000Hz), and estimating D2 for each embedding dimension as the steepest slope of the linear scaling region in the plot of log(C(r)) vs log(r) provided the scaling region occurred within the middle third of the plot. Piloting revealed that fractal dimensions were higher from the sampled abnormal than normal achromatic VEPs in adults (p = 0.02). Variances of fractal dimension were higher from the abnormal than normal chromatic VEPs in children (p = 0.01). A useful analysis protocol to assess the fractal dimension of transformed VEPs has been developed.

  17. 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.

  18. 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.

  19. RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome.

    Science.gov (United States)

    Thongjuea, Supat; Ruanjaichon, Vinitchan; Bruskiewich, Richard; Vanavichit, Apichart

    2009-01-01

    RiceGeneThresher is a public online resource for mining genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome. It is a compendium of rice genomic resources consisting of genetic markers, genome annotation, expressed sequence tags (ESTs), protein domains, gene ontology, plant stress-responsive genes, metabolic pathways and prediction of protein-protein interactions. RiceGeneThresher system integrates these diverse data sources and provides powerful web-based applications, and flexible tools for delivering customized set of biological data on rice. Its system supports whole-genome gene mining for QTL by querying using DNA marker intervals or genomic loci. RiceGeneThresher provides biologically supported evidences that are essential for targeting groups or networks of genes involved in controlling traits underlying QTL. Users can use it to discover and to assign the most promising candidate genes in preparation for the further gene function validation analysis. The web-based application is freely available at http://rice.kps.ku.ac.th.

  20. Application of visually based, computerised diagnostic decision support system in dermatological medical education: a pilot study.

    Science.gov (United States)

    Chou, Wan-Yi; Tien, Peng-Tai; Lin, Fang-Yu; Chiu, Pin-Chi

    2017-05-01

    Medical education has shifted from memory-based practice to evidence-based decisions. The question arises: how can we ensure that all students get correct and systematic information? Visually based, computerised diagnostic decision support system (VCDDSS, VisualDx) may just fit our needs. A pilot study was conducted to investigate its role in medical education and clinical practice. This was a prospective study, including one consultant dermatologist, 51 medical students and 13 dermatology residents, conducted in the dermatology teaching clinic at China Medical University Hospital from 30 December 2014 to 21 April 2015. Clinical diagnoses of 13 patients were made before and after using VCDDSS. Questionnaires were filled out at the end. The consultant dermatologist's diagnosis was defined as the standard answer; the Sign test was used to analyse diagnostic accuracy and the Fisher exact test to analyse questionnaires. There was an 18.75% increase in diagnostic accuracy after use of VCDDSS (62.5-81.25%; p value system in clinical practice, medical education, residency training, and patient education in the future. Further large-scale studies should be planned to confirm its application. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  1. The Five W's for Information Visualization with Application to Healthcare Informatics.

    Science.gov (United States)

    Zhang, Zhiyuan; Wang, Bing; Ahmed, Faisal; Ramakrishnan, Iv; Zhao, Rong; Viccellio, Asa; Mueller, Klaus

    2013-06-03

    The Five W's is a popular concept for information gathering in journalistic reporting. It captures all aspects of a story or incidence: who, when, what, where, and why. We propose a framework composed of a suite of cooperating visual information displays to represent the Five W's and demonstrate its use within a healthcare informatics application. Here, the who is the patient, the where is the patient's body, and the when, what, why is a reasoning chain which can be interactively sorted and brushed. The patient is represented as a radial sunburst visualization integrated with a stylized body map. This display captures all health conditions of the past and present to serve as a quick overview to the interrogating physician. The reasoning chain is represented as a multi-stage flow chart, composed of date, symptom, data, diagnosis, treatment, and outcome. Our system seeks to improve the usability of information captured in the electronic medical record (EMR) and makes ample use of popular hierarchical medical codes, such as ICD9 and CPT, for information organization. We show via multiple examples that our framework can significantly lower the time and effort needed to access the medical patient information required to arrive at a diagnostic conclusion.

  2. The five Ws for information visualization with application to healthcare informatics.

    Science.gov (United States)

    Zhang, Zhiyuan; Wang, Bing; Ahmed, Faisal; Ramakrishnan, I V; Zhao, Rong; Viccellio, Asa; Mueller, Klaus

    2013-11-01

    The Five Ws is a popular concept for information gathering in journalistic reporting. It captures all aspects of a story or incidence: who, when, what, where, and why. We propose a framework composed of a suite of cooperating visual information displays to represent the Five Ws and demonstrate its use within a healthcare informatics application. Here, the who is the patient, the where is the patient's body, and the when, what, why is a reasoning chain which can be interactively sorted and brushed. The patient is represented as a radial sunburst visualization integrated with a stylized body map. This display captures all health conditions of the past and present to serve as a quick overview to the interrogating physician. The reasoning chain is represented as a multistage flow chart, composed of date, symptom, data, diagnosis, treatment, and outcome. Our system seeks to improve the usability of information captured in the electronic medical record (EMR) and we show via multiple examples that our framework can significantly lower the time and effort needed to access the medical patient information required to arrive at a diagnostic conclusion.

  3. 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.

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

    Directory of Open Access Journals (Sweden)

    Sachin ePundhir

    2015-05-01

    Full Text Available Functional annotation of the genome in various species is important to understand their phenotypic complexity. The road towards functional annotation involves several challenges ranging from experiments on individual molecules to large-scale analysis of high-throughput sequencing (HTS data. HTS data 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 are essential for the 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 regions such as enhancers and promoters. We also discuss the biological rationale behind their formation.

  5. Development and Testing of Functionally Operative and Visually Appealing Remote Firing Room Displays and Applications

    Science.gov (United States)

    Quaranto, Kristy

    2014-01-01

    This internship provided an opportunity for an intern to work with NASA's Ground Support Equipment (GSE) for the Spaceport Command and Control System (SCCS) at Kennedy Space Center as a remote display developer, under NASA technical mentor Kurt Leucht. The main focus was on creating remote displays and applications for the hypergolic and high pressure helium subsystem team to help control the filling of the respective tanks. As a remote display and application developer for the GSE hypergolic and high pressure helium subsystem team the intern was responsible for creating and testing graphical remote displays and applications to be used in the Launch Control Center (LCC) on the Firing Room's computers. To become more familiar with the subsystem, the individual attended multiple project meetings and acquired their specific requirements regarding what needed to be included in the software. After receiving the requirements for the displays, the next step was to create displays that had both visual appeal and logical order using the Display Editor, on the Virtual Machine (VM). In doing so, all Compact Unique Identifiers (CUI), which are associated with specific components within the subsystem, were need to be included in each respective display for the system to run properly. Then, once the display was created it was to be tested to ensure that the display runs as intended by using the Test Driver, also found on the VM. This Test Driver is a specific application that checks to make sure all the CUIs in the display are running properly and returning the correct form of information. After creating and locally testing the display it needed to go through further testing and evaluation before deemed suitable for actual use. For the remote applications the intern was responsible for creating a project that focused on channelizing each component included in each display. The core of the application code was created by setting up spreadsheets and having an auto test generator

  6. Three-dimensional computer visualization of field screening information: Examples and applications

    Energy Technology Data Exchange (ETDEWEB)

    Baker, L.A. [Automated Sciences Group, Oliver Springs, TN (United States); Hammons, W. [Analysas Corp., Oak Ridge, TN (United States)

    1995-12-31

    The first step in conducting environmental investigations is the development of a conceptual model of the area to be investigated, including the probable distribution of contaminants. Sampling locations are based on this conceptual model. Field screening techniques allow the investigator to confirm or revise the conceptual model as the investigation is being conducted and provides the investigator with real-time information about groundwater contamination at discrete depth intervals. This information enhances accurate well screen placement and optimization of subsequent well locations. The obvious benefits of field screening are reducing the time and cost associated with field investigations and defining the nature and extent of contamination in one field effort. Groundwater field screening techniques also provide a profusion of information that is essential in interpreting contaminant fate and transport, selecting remedial alternatives, and designing remediation systems. This paper will give an overview of the screened hollow-stem auger field screening technique and its application in conducting groundwater investigations at a major National Priorities List (NPL) site. The three-dimensional visualization of the field screening information collected will be discussed and applications of the three-dimensional modeling will be presented to discuss the points mentioned above. Future applications of three-dimensional modeling will be examined.

  7. Pengembangan Modul Pembelajaran Digital Berbasis Visual Basic for Application (VBA PowerPoint

    Directory of Open Access Journals (Sweden)

    Sholichatun Aisyah Rahmawati

    2017-04-01

    Full Text Available Tujuan penelitian ini untuk mengembangkan dan mengetahui keefektifan penggunaan modul digital VBA (Visual Basic for Application PowerPoint pada hasil belajar siswa SMP Kebon Dalem Semarang. Penelitian menggunakan model research and development (R&D. Subjek penelitian adalah ahli materi, ahli media, dan siswa kelas VII. Teknik pengumpulan data berupa wawancara, observasi, angket, dan tes. Hasil penelitian menunjukkan (1 pengembangan modul digital dilakukan dengan: identifkasi potensi dan masalah, pengumpulan data, desain produk, validasi produk, revisi desain, uji coba skala kecil, revisi produk tahap I, uji coba skala luas, revisi produk tahap II, produk fnal dengan penilaian dari ahli materi dan ahli media adalah sangat baik dan layak diujicobakan dan dengan tanggapan dari guru dan siswa adalah sangat baik dan baik. dan (2 modul digital efektif digunakan dengan peningkatan hasil belajar sebesar 72,3%.

  8. 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

  9. Complex for monitoring visual acuity and its application for evaluation of human psycho-physiological state

    Science.gov (United States)

    Sorokoumov, P. S.; Khabibullin, T. R.; Tolstaya, A. M.

    2017-01-01

    The existing psychological theories associate the movement of a human eye with its reactions to external change: what we see, hear and feel. By analyzing the glance, we can compare the external human response (which shows the behavior of a person), and the natural reaction (that they actually feels). This article describes the complex for detection of visual activity and its application for evaluation of the psycho-physiological state of a person. The glasses with a camera capture all the movements of the human eye in real time. The data recorded by the camera are transmitted to the computer for processing implemented with the help of the software developed by the authors. The result is given in an informative and an understandable report, which can be used for further analysis. The complex shows a high efficiency and stable operation and can be used both, for the pedagogic personnel recruitment and for testing students during the educational process.

  10. 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.

  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. 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

  13. 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.

  14. 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.

  15. 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.

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

    Science.gov (United States)

    Covell, David G

    2015-01-01

    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. From Gene Targeting to Genome Editing: Transgenic animals applications and beyond

    OpenAIRE

    ROCHA-MARTINS,MAURÍCIO; CAVALHEIRO,GABRIEL R.; MATOS-RODRIGUES,GABRIEL E.; MARTINS,RODRIGO A.P.

    2015-01-01

    ABSTRACTGenome modification technologies are powerful tools for molecular biology and related areas. Advances in animal transgenesis and genome editing technologies during the past three decades allowed systematic interrogation of gene function that can help model how the genome influences cellular physiology. Genetic engineering via homologous recombination (HR) has been the standard method to modify genomic sequences. Nevertheless, nuclease-guided genome editing methods that were developed ...

  18. 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.

  19. Application of single step genomic BLUP under different uncertain paternity scenarios using simulated data.

    Directory of Open Access Journals (Sweden)

    Rafael Lara Tonussi

    Full Text Available The objective of this study was to investigate the application of BLUP and single step genomic BLUP (ssGBLUP models in different scenarios of paternity uncertainty with different strategies of scaling the G matrix to match the A22 matrix, using simulated data for beef cattle. Genotypes, pedigree, and phenotypes for age at first calving (AFC and weight at 550 days (W550 were simulated using heritabilities based on real data (0.12 for AFC and 0.34 for W550. Paternity uncertainty scenarios using 0, 25, 50, 75, and 100% of multiple sires (MS were studied. The simulated genome had a total length of 2,333 cM, containing 735,293 biallelic markers and 7,000 QTLs randomly distributed over the 29 BTA. It was assumed that QTLs explained 100% of the genetic variance. For QTL, the amount of alleles per loci randomly ranged from two to four. The BLUP model that considers phenotypic and pedigree data, and the ssGBLUP model that combines phenotypic, pedigree and genomic information were used for genetic evaluations. Four ways of scaling the mean of the genomic matrix (G to match to the mean of the pedigree relationship matrix among genotyped animals (A22 were tested. Accuracy, bias, and inflation were investigated for five groups of animals: ALL = all animals; BULL = only bulls; GEN = genotyped animals; FEM = females; and YOUNG = young males. With the BLUP model, the accuracies of genetic evaluations decreased for both traits as the proportion of unknown sires in the population increased. The EBV accuracy reduction was higher for GEN and YOUNG groups. By analyzing the scenarios for YOUNG (from 0 to 100% of MS, the decrease was 87.8 and 86% for AFC and W550, respectively. When applying the ssGBLUP model, the accuracies of genetic evaluation also decreased as the MS in the pedigree for both traits increased. However, the accuracy reduction was less than those observed for BLUP model. Using the same comparison (scenario 0 to 100% of MS, the accuracies reductions

  20. 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.

  1. 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

  2. Complete chloroplast genome sequences of Solanum commersonii and its application to chloroplast genotype in somatic hybrids with Solanum tuberosum.

    Science.gov (United States)

    Cho, Kwang-Soo; Cheon, Kyeong-Sik; Hong, Su-Young; Cho, Ji-Hong; Im, Ju-Seong; Mekapogu, Manjulatha; Yu, Yei-Soo; Park, Tae-Ho

    2016-10-01

    Chloroplast genome of Solanum commersonii and S olanum tuberosum were completely sequenced, and Indel markers were successfully applied to distinguish chlorotypes demonstrating the chloroplast genome was randomly distributed during protoplast fusion. Somatic hybridization has been widely employed for the introgression of resistance to several diseases from wild Solanum species to overcome sexual barriers in potato breeding. Solanum commersonii is a major resource used as a parent line in somatic hybridization to improve bacterial wilt resistance in interspecies transfer to cultivated potato (S. tuberosum). Here, we sequenced the complete chloroplast genomes of Lz3.2 (S. commersonii) and S. tuberosum (PT56), which were used to develop fusion products, then compared them with those of five members of the Solanaceae family, S. tuberosum, Capsicum annum, S. lycopersicum, S. bulbocastanum and S. nigrum and Coffea arabica as an out-group. We then developed Indel markers for application in chloroplast genotyping. The complete chloroplast genome of Lz3.2 is composed of 155,525 bp, which is larger than the PT56 genome with 155,296 bp. Gene content, order and orientation of the S. commersonii chloroplast genome were highly conserved with those of other Solanaceae species, and the phylogenetic tree revealed that S. commersonii is located within the same node of S. tuberosum. However, sequence alignment revealed nine Indels between S. commersonii and S. tuberosum in their chloroplast genomes, allowing two Indel markers to be developed. The markers could distinguish the two species and were successfully applied to chloroplast genotyping (chlorotype) in somatic hybrids and their progenies. The results obtained in this study confirmed the random distribution of the chloroplast genome during protoplast fusion and its maternal inheritance and can be applied to select proper plastid genotypes in potato breeding program.

  3. 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(R) (MATrix LABoratory) is a numerical computation and simulation tool that is used by thousands Scientists and Engineers in many cou ntries. MatLab does purely numerical calculations, which can be used as a glorified calculator or interpreter programming language; its re al strength is in matrix manipulations. Computer algebra functionalities are achieved within the MatLab environment using "symbolic" toolbo x. This feature is similar to computer algebra programs, provided by Maple or Mathematica to calculate with mathematical equations using s ymbolic operations. MatLab in its interpreter programming language fo rm (command interface) is similar with well known programming languag es such as C/C++, support data structures and cell arrays to define c lasses in object oriented programming. As such, MatLab is equipped with most ofthe essential constructs of a higher programming language. M atLab is packaged with an editor and debugging functionality useful t o perform analysis of large MatLab programs and find errors. We belie ve there are many ways to approach real-world problems; prescribed methods to ensure foregoing solutions are incorporated in design and ana lysis 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 applicati ons. Specifically, it will discuss methods and techniques to perform intermediate-level data processing covering engineering and scientifi c 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 tabu lar format, exporting data to be used by other software programs such as Microsoft Excel, data presentation and visualization will be discussed. The presentation will emphasize creating

  4. Electrostatic melting in a single-molecule field-effect transistor with applications in genomic identification

    Science.gov (United States)

    Vernick, Sefi; Trocchia, Scott M.; Warren, Steven B.; Young, Erik F.; Bouilly, Delphine; Gonzalez, Ruben L.; Nuckolls, Colin; Shepard, Kenneth L.

    2017-05-01

    The study of biomolecular interactions at the single-molecule level holds great potential for both basic science and biotechnology applications. Single-molecule studies often rely on fluorescence-based reporting, with signal levels limited by photon emission from single optical reporters. The point-functionalized carbon nanotube transistor, known as the single-molecule field-effect transistor, is a bioelectronics alternative based on intrinsic molecular charge that offers significantly higher signal levels for detection. Such devices are effective for characterizing DNA hybridization kinetics and thermodynamics and enabling emerging applications in genomic identification. In this work, we show that hybridization kinetics can be directly controlled by electrostatic bias applied between the device and the surrounding electrolyte. We perform the first single-molecule experiments demonstrating the use of electrostatics to control molecular binding. Using bias as a proxy for temperature, we demonstrate the feasibility of detecting various concentrations of 20-nt target sequences from the Ebolavirus nucleoprotein gene in a constant-temperature environment.

  5. 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.

  6. 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

  7. A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog.

    Science.gov (United States)

    Morales, Joannella; Welter, Danielle; Bowler, Emily H; Cerezo, Maria; Harris, Laura W; McMahon, Aoife C; Hall, Peggy; Junkins, Heather A; Milano, Annalisa; Hastings, Emma; Malangone, Cinzia; Buniello, Annalisa; Burdett, Tony; Flicek, Paul; Parkinson, Helen; Cunningham, Fiona; Hindorff, Lucia A; MacArthur, Jacqueline A L

    2018-02-15

    The accurate description of ancestry is essential to interpret, access, and integrate human genomics data, and to ensure that these benefit individuals from all ancestral backgrounds. However, there are no established guidelines for the representation of ancestry information. Here we describe a framework for the accurate and standardized description of sample ancestry, and validate it by application to the NHGRI-EBI GWAS Catalog. We confirm known biases and gaps in diversity, and find that African and Hispanic or Latin American ancestry populations contribute a disproportionately high number of associations. It is our hope that widespread adoption of this framework will lead to improved analysis, interpretation, and integration of human genomics data.

  8. 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.

  9. An approach to the identification of T cell epitopes in the genomic era: application to Francisella tularensis.

    Science.gov (United States)

    Valentino, Michael; Frelinger, John

    2009-12-01

    The identification and characterization of epitopes is essential for modern immunologic studies. Here, we describe a novel methodology we have developed to identify T cell epitopes exploiting the phenomenon of cross presentation. Particulate antigens, in the form of beads, are very effective in delivering exogenous antigen to both the class I and class II pathways. We will review our efforts to screen entire genomes of pathogens for T cell epitopes taking advantage of the advances in genomics using Francisella tularensis as a model. By automating aspects of this technology we will be able to functionally screen the entire genome of F. tularensis for T cell epitopes. This technology should be applicable not only to F. tularensis, but also to many other pathogens as well.

  10. 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.

  11. The CRISPR/Cas Genome-Editing Tool: Application in Improvement of Crops

    OpenAIRE

    Khatodia, Surender; Bhatotia, Kirti; Passricha, Nishat; Khurana, S. M. P.; Tuteja, Narendra

    2016-01-01

    The Clustered Regularly Interspaced Short Palindromic Repeats associated Cas9/sgRNA system is a novel targeted genome-editing technique derived from bacterial immune system. It is an inexpensive, easy, most user friendly and rapidly adopted genome editing tool transforming to revolutionary paradigm. This technique enables precise genomic modifications in many different organisms and tissues. Cas9 protein is an RNA guided endonuclease utilized for creating targeted double-stranded breaks with ...

  12. 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.

  13. epidemix-An interactive multi-model application for teaching and visualizing infectious disease transmission.

    Science.gov (United States)

    Muellner, Ulrich; Fournié, Guillaume; Muellner, Petra; Ahlstrom, Christina; Pfeiffer, Dirk U

    2017-12-11

    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-specialists - including policy

  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. 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......, and the VEPs were recognized and classified using subject-specific algorithms. The system provided the ability of controlling a wheelchair model (LEGO R MINDSTORM R EV3 robot) in 4 different directions based on the elicited c-VEPs. Ten healthy subjects were evaluated in testing the system where an average...

  16. Applications of aerospace technology in industry: A technology transfer profile. Visual display systems

    Science.gov (United States)

    1972-01-01

    The growth of common as well as emerging visual display technologies are surveyed. The major inference is that contemporary society is rapidly growing evermore reliant on visual display for a variety of purposes. Because of its unique mission requirements, the National Aeronautics and Space Administration has contributed in an important and specific way to the growth of visual display technology. These contributions are characterized by the use of computer-driven visual displays to provide an enormous amount of information concisely, rapidly and accurately.

  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. ESTIMATION OF GENOMIC VARIATION IN CERVIDS USING CROSS-SPECIES APPLICATION OF SNP ARRAYS

    Directory of Open Access Journals (Sweden)

    Nina Moravčíková

    2015-09-01

    Full Text Available The aim of this study was to assess the utility of commercially developed genotyping array for cross-species genotyping in order to estimate the genetic variation across two species from family Cervidae. The genotyping of individuals was carried out using Illumina BovineSNP50 BeadChip. The cross-species application of bovine array was tested overall in 3 farmed and 5 free range Red deer (Cervus elaphus and 2 free range Fallow deer (Dama dama. After applying data quality control 97.2% of SNPs localized on the chip were removed and only 1,530 autosomal markers showed polymorphism across all analysed individuals. Across all polymorphic SNPs the minor allele frequency reached the average value 0.23±0.16. The analysis based on Bayesian clustering approach clearly showed a partition of deer in two separate clusters in relation to their phylogenetical relationship. Moreover, the PCA analysis indicated that the genetic differences between farmed and free range Red deer caused the division of analysed individuals into the two subpopulations. But the results of cross-species genotyping should be present with caution, because the bovine chip developed primarily for taurine cattle breeds is not fully representative to the evolutionary changes in genome of cervids. Nevertheless, our results suggested that the utility of bovine array alongside microsatellite markers and mtDNA can be very perspective for genetic diversity estimation in deer populations.

  19. The application of MutMap in forward genetic studies based on whole-genome sequencing.

    Science.gov (United States)

    Yuan, Jin Hong; Li, Jun Hua; Yuan, Jiao Jiao; Jia, Ke Li; Li, Shu Fen; Deng, Chuan Liang; Gao, Wu Jun

    2017-12-20

    Classical forward genetic analysis relies on construction of complicated progeny populations and development of many molecular markers for linkage analysis in genetic mapping, which is both time- and cost-consuming. The recently developed MutMap is a new forward genetic approach based on high-throughput next-generation sequencing technologies. It is more efficient and affordable than traditional methods. Moreover, new extended methods based on MutMap have been developed: MutMap+, which is based on self-crossing; MutMap-Gap, which is used to recognize the causative variations occurring in genome gap regions; QTL-seq, a method similar to MutMap for mapping quantitative trait loci. These methods are free from constructing complicated mapping population, genetic hybridization and linkage information. They have greatly accelerated the identification of genetic elements associated with interested phenotypic variation. Here, we review the basic principles of MutMap, and discuss their future applications in next generation sequencing-based forward genetic mapping and crop improvement.

  20. 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.

  1. Effects of genome duplication on phenotypes and industrial applications of Saccharomyces cerevisiae strains.

    Science.gov (United States)

    Zhang, Ke; Fang, Ya-Hong; Gao, Ke-Hui; Sui, Yang; Zheng, Dao-Qiong; Wu, Xue-Chang

    2017-07-01

    Polyploidy is common in Saccharomyces cerevisiae strains, but the physiological and phenotypic effects of ploidy changes have not been fully clarified. Here, isogenic diploid, triploid, and tetraploid S. cerevisiae strains were constructed from a haploid strain, CEN.PK2-1C. Stress tolerance and ethanol fermentation performance of the four euploid strains were compared. Each euploid strain had strengths and weaknesses in tolerance to certain stressors, and no single strain was tolerant of all stressors. The diploid had higher ethanol production than the other strains in normal fermentation medium, while the triploid strain showed the fastest fermentation rate in the presence of inhibitors found in lignocellulosic hydrolysate. Physiological determination revealed diverse physiological attributes, such as trehalose, ergosterol, glutathione, and anti-oxidative enzymes among the strains. Our analyses suggest that both ploidy parity and number of chromosome sets contribute to changes in physiological status. Using qRT-PCR, different expression patterns of genes involved in the regulation of cell morphology and the biosynthesis of key physiological attributes among strains were determined. Our data provide novel insights into the multiple effects of genome duplication on yeast cells and are a useful reference for breeding excellent strains used in specific industrial applications.

  2. Multi-omic data integration and analysis using systems genomics approaches: methods and applications in animal production, health and welfare.

    Science.gov (United States)

    Suravajhala, Prashanth; Kogelman, Lisette J A; Kadarmideen, Haja N

    2016-04-29

    In the past years, there has been a remarkable development of high-throughput omics (HTO) technologies such as genomics, epigenomics, transcriptomics, proteomics and metabolomics across all facets of biology. This has spearheaded the progress of the systems biology era, including applications on animal production and health traits. However, notwithstanding these new HTO technologies, there remains an emerging challenge in data analysis. On the one hand, different HTO technologies judged on their own merit are appropriate for the identification of disease-causing genes, biomarkers for prevention and drug targets for the treatment of diseases and for individualized genomic predictions of performance or disease risks. On the other hand, integration of multi-omic data and joint modelling and analyses are very powerful and accurate to understand the systems biology of healthy and sustainable production of animals. We present an overview of current and emerging HTO technologies each with a focus on their applications in animal and veterinary sciences before introducing an integrative systems genomics framework for analysing and integrating multi-omic data towards improved animal production, health and welfare. We conclude that there are big challenges in multi-omic data integration, modelling and systems-level analyses, particularly with the fast emerging HTO technologies. We highlight existing and emerging systems genomics approaches and discuss how they contribute to our understanding of the biology of complex traits or diseases and holistic improvement of production performance, disease resistance and welfare.

  3. 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.

  4. 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.

  5. 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.

  6. A correction factor for, and its application to, visual censuses of ...

    African Journals Online (AJOL)

    Visual estimation techniques were used between October 1976 and. May 1977 on .... In support of this assumption, it was noted ... Results. Visual censuses. Gibson (1969) divides the littoral fish fauna into four groups - true and partial residents, seasonal and tidal visitors. Of the 18 fish species observed in Pool 1 between.

  7. 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

  8. SSW library: an SIMD Smith-Waterman C/C++ library for use in genomic applications.

    Directory of Open Access Journals (Sweden)

    Mengyao Zhao

    Full Text Available The Smith-Waterman algorithm, which produces the optimal pairwise alignment between two sequences, is frequently used as a key component of fast heuristic read mapping and variation detection tools for next-generation sequencing data. Though various fast Smith-Waterman implementations are developed, they are either designed as monolithic protein database searching tools, which do not return detailed alignment, or are embedded into other tools. These issues make reusing these efficient Smith-Waterman implementations impractical.To facilitate easy integration of the fast Single-Instruction-Multiple-Data Smith-Waterman algorithm into third-party software, we wrote a C/C++ library, which extends Farrar's Striped Smith-Waterman (SSW to return alignment information in addition to the optimal Smith-Waterman score. In this library we developed a new method to generate the full optimal alignment results and a suboptimal score in linear space at little cost of efficiency. This improvement makes the fast Single-Instruction-Multiple-Data Smith-Waterman become really useful in genomic applications. SSW is available both as a C/C++ software library, as well as a stand-alone alignment tool at: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library.The SSW library has been used in the primary read mapping tool MOSAIK, the split-read mapping program SCISSORS, the MEI detector TANGRAM, and the read-overlap graph generation program RZMBLR. The speeds of the mentioned software are improved significantly by replacing their ordinary Smith-Waterman or banded Smith-Waterman module with the SSW Library.

  9. 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.

  10. 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

  11. 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

  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...

  13. 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

    , 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...... of foreign/conserved DNA, and plasmid-host similarity comparisons. Additionally, the reliability of the methods was tested by comparing both real and random genomic DNA. RESULTS: Our findings show that the optimal method is context dependent. ROFs were best suited for distant homology searches, whilst......BACKGROUND: The increasing number of sequenced prokaryotic genomes contains a wealth of genomic data that needs to be effectively analysed. A set of statistical tools exists for such analysis, but their strengths and weaknesses have not been fully explored. The statistical methods we are concerned...

  14. 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)

  15. Climate Signal Maps: Assessment and visualization of the robustness of climate change information - an application within IMPACT2C.

    Science.gov (United States)

    Pfeifer, Susanne; Balkovic, Juraj; Kotova, Lola; Preuschmann, Swantje; Teichmann, Claas; Jacob, Daniela

    2015-04-01

    The method of the Climate Signal Maps has been developed to assess and visualize the robustness of projected climate changes from an ensemble of climate change simulations in an user- and application oriented way. It builds on complex methods as e.g. presented by Tebaldi et al. (2011), and used in the latest IPCC Report, but gives reduced information understandable at a glance. The method will be presented, and an application in the context of the EU FP7 project IMPACT2C will be shown, where similar methods are applied not only for the climate model data, but also for the results of the climate change impact models.

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

    Science.gov (United States)

    2016-07-14

    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...through some third-party service provider. Thus, in this work we look at private genomic computation in the light of server- mediated setting and utilize...adversaries who corrupt them) do not col- lude, at any given point of time there might be multiple adver- saries, but they are independent of each other

  17. 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.

  18. 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)

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

    OpenAIRE

    SURENDER eKHATODIA; KIRTI eBHATOTIA; NISHAT ePASSRICHA; S M PAUL KHURANA; NARENDRA eTUTEJA; NARENDRA eTUTEJA

    2016-01-01

    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 ge...

  20. 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.

  1. 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.

  2. Towards a CRISPR view of early human development: applications, limitations and ethical concerns of genome editing in human embryos.

    Science.gov (United States)

    Plaza Reyes, Alvaro; Lanner, Fredrik

    2017-01-01

    Developmental biologists have become increasingly aware that the wealth of knowledge generated through genetic studies of pre-implantation mouse development might not easily be translated to the human embryo. Comparative studies have been fueled by recent technological advances in single-cell analysis, allowing in-depth analysis of the human embryo. This field could shortly gain more momentum as novel genome editing technologies might, for the first time, also allow functional genetic studies in the human embryo. In this Spotlight article, we summarize the CRISPR-Cas9 genome editing system and discuss its potential applications and limitations in human pre-implantation embryos, and the ethical considerations thereof. © 2017. Published by The Company of Biologists Ltd.

  3. 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

  4. Visual learning in drosophila: application on a roving robot and comparisons

    Science.gov (United States)

    Arena, P.; De Fiore, S.; Patané, L.; Termini, P. S.; Strauss, R.

    2011-05-01

    Visual learning is an important aspect of fly life. Flies are able to extract visual cues from objects, like colors, vertical and horizontal distributedness, and others, that can be used for learning to associate a meaning to specific features (i.e. a reward or a punishment). Interesting biological experiments show trained stationary flying flies avoiding flying towards specific visual objects, appearing on the surrounding environment. Wild-type flies effectively learn to avoid those objects but this is not the case for the learning mutant rutabaga defective in the cyclic AMP dependent pathway for plasticity. A bio-inspired architecture has been proposed to model the fly behavior and experiments on roving robots were performed. Statistical comparisons have been considered and mutant-like effect on the model has been also investigated.

  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. 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.

  7. 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

  8. Development and application of a novel genome-wide SNP array reveals domestication history in soybean.

    Science.gov (United States)

    Wang, Jiao; Chu, Shanshan; Zhang, Huairen; Zhu, Ying; Cheng, Hao; Yu, Deyue

    2016-02-09

    Domestication of soybeans occurred under the intense human-directed selections aimed at developing high-yielding lines. Tracing the domestication history and identifying the genes underlying soybean domestication require further exploration. Here, we developed a high-throughput NJAU 355 K SoySNP array and used this array to study the genetic variation patterns in 367 soybean accessions, including 105 wild soybeans and 262 cultivated soybeans. The population genetic analysis suggests that cultivated soybeans have tended to originate from northern and central China, from where they spread to other regions, accompanied with a gradual increase in seed weight. Genome-wide scanning for evidence of artificial selection revealed signs of selective sweeps involving genes controlling domestication-related agronomic traits including seed weight. To further identify genomic regions related to seed weight, a genome-wide association study (GWAS) was conducted across multiple environments in wild and cultivated soybeans. As a result, a strong linkage disequilibrium region on chromosome 20 was found to be significantly correlated with seed weight in cultivated soybeans. Collectively, these findings should provide an important basis for genomic-enabled breeding and advance the study of functional genomics in soybean.

  9. Three invariant Hi-C interaction patterns: applications to genome assembly.

    Science.gov (United States)

    Oddes, Sivan; Zelig, Aviv; Kaplan, Noam

    2018-04-20

    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.

  10. Development and application of a novel genome-wide SNP array reveals domestication history in soybean

    Science.gov (United States)

    Wang, Jiao; Chu, Shanshan; Zhang, Huairen; Zhu, Ying; Cheng, Hao; Yu, Deyue

    2016-01-01

    Domestication of soybeans occurred under the intense human-directed selections aimed at developing high-yielding lines. Tracing the domestication history and identifying the genes underlying soybean domestication require further exploration. Here, we developed a high-throughput NJAU 355 K SoySNP array and used this array to study the genetic variation patterns in 367 soybean accessions, including 105 wild soybeans and 262 cultivated soybeans. The population genetic analysis suggests that cultivated soybeans have tended to originate from northern and central China, from where they spread to other regions, accompanied with a gradual increase in seed weight. Genome-wide scanning for evidence of artificial selection revealed signs of selective sweeps involving genes controlling domestication-related agronomic traits including seed weight. To further identify genomic regions related to seed weight, a genome-wide association study (GWAS) was conducted across multiple environments in wild and cultivated soybeans. As a result, a strong linkage disequilibrium region on chromosome 20 was found to be significantly correlated with seed weight in cultivated soybeans. Collectively, these findings should provide an important basis for genomic-enabled breeding and advance the study of functional genomics in soybean. PMID:26856884

  11. Genomic impact of cigarette smoke, with application to three smoking-related diseases.

    Science.gov (United States)

    Talikka, M; Sierro, N; Ivanov, N V; Chaudhary, N; Peck, M J; Hoeng, J; Coggins, C R E; Peitsch, M C

    2012-11-01

    There is considerable evidence that inhaled toxicants such as cigarette smoke can cause both irreversible changes to the genetic material (DNA mutations) and putatively reversible changes to the epigenetic landscape (changes in the DNA methylation and chromatin modification state). The diseases that are believed to involve genetic and epigenetic perturbations include lung cancer, chronic obstructive pulmonary disease (COPD), and cardiovascular disease (CVD), all of which are strongly linked epidemiologically to cigarette smoking. In this review, we highlight the significance of genomics and epigenomics in these major smoking-related diseases. We also summarize the in vitro and in vivo findings on the specific perturbations that smoke and its constituent compounds can inflict upon the genome, particularly on the pulmonary system. Finally, we review state-of-the-art genomics and new techniques such as high-throughput sequencing and genome-wide chromatin assays, rapidly evolving techniques which have allowed epigenetic changes to be characterized at the genome level. These techniques have the potential to significantly improve our understanding of the specific mechanisms by which exposure to environmental chemicals causes disease. Such mechanistic knowledge provides a variety of opportunities for enhanced product safety assessment and the discovery of novel therapeutic interventions.

  12. Modern Atomic Force Microscopy and Its Application to the Study of Genome Architecture

    Science.gov (United States)

    Takeyasu, Kunio; Maruyama, Hugo; Suzuki, Yuki; Hizume, Kohji; Yoshimura, Shige H.

    Recent development of atomic force microscopy (AFM) has been accomplished by various technical and instrumental innovation including high-resolution imaging technology in solution, fast-scanning AFM, and general methods for cantilever modification and force measurement. These modern AFM technologies have made it possible to conduct biological studies under physiological conditions. Application of the recognition imaging mode that can simultaneously obtain a topographic image together with a recognition signal is now successful by using protein- (antibody-) coupled cantilever, and revealed the specific protein bindings on the chromatin. AFM can also be combined with biochemical and cytochemical methods. Recent AFM researches involving series of reconstitution experiments have shown that the efficiency of the chromatin reconstitution by salt-dialysis method is drastically increased simply by using longer ( > 100 kb) and supercoiled DNA. This suggests that the physical properties of DNA are critical for the higher-order chromatin folding. Since double-stranded DNA, like other polymer chains, carries certain elasticity and flexibility, the length of DNA could affect the stability of nucleosome and chromatin fiber. This notion is well supported by the fact that in eukaryotic chromosome, the averaged length of a single chromatin loop is ˜ 100 kb. On the contrary, the large-scale structure of chromatin fiber is affected by a local protein binding. Indeed, histone H1 is essential for the reconstitution of 30 nm fibers. Type II topoisomerase (Topo II) has been known as a major component of chromosomal scaffold and an essential protein for mitotic chromosome condensation. AFM has shown that Topo II binds to bear DNA and clamps two DNA strands even in the absence of ATP, and promotes chromatin compaction depending on the existence of histone H1. Namely, H1-induced 30-nm chromatin fibers were converted into large complex by the effect of Topo II. On the basis of these results

  13. 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

  14. Application and development of genome editing technologies to the Solanaceae plants.

    Science.gov (United States)

    Yamamoto, Tsuyoshi; Kashojiya, Sachiko; Kamimura, Saori; Kameyama, Takato; Ariizumi, Tohru; Ezura, Hiroshi; Miura, Kenji

    2018-03-02

    Genome editing technology using artificial nucleases, including zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regulatory interspaced short palindromic repeats (CRISPR)-Cas9, can mutagenize the target sites of genes of interest. This technology has been successfully applied in several crops, including the Solanaceae plants, such as tomato, potato, tobacco, and petunia. Among the three nucleases, CRISPR-Cas9 is the best for breeding, crop improvement, and the functional analysis of genes of interest, because of its simplicity and high efficiency. Although the technology is useful for reverse genetics, its use in plants is limited due to a lack of regeneration protocols and sequence information. In this review, the present status of genome editing technology in Solanaceae plants is described, and techniques that may improve genome editing technologies are discussed. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

  15. [Application of CRISPR-Cas9 genome editing for constructing animal models of human diseases].

    Science.gov (United States)

    Ou, Zhanhui; Sun, Xiaofang

    2016-08-01

    The CRISPR-Cas9 system is a new targeted nuclease for genome editing, which can directly introduce modifications at the targeted genomic locus. The system utilizes a short single guide RNA (sgRNA) to direct the endonuclease Cas9 in the genome. Upon targeting, Cas9 can generate DNA double-strand breaks (DSBs). As such DSBs are repaired by non-homologous end joining (NHEJ) or homology directed repair (HDR), therefore facilitates introduction of random or specific mutations, repair of endogenous mutations, or insertion of DNA elements. The system has been successfully used to generate gene targeted cell lines including those of human, animals and plants. This article reviews recent advances made in this rapidly evolving technique for the generation of animal models for human diseases.

  16. 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.

  17. Purification of BsuE methyltransferase and its application in genome mapping.

    OpenAIRE

    Shukla, H; Kobayashi, Y; Arenstorf, H; Yasukochi, Y; Weissman, S M

    1991-01-01

    We have used a combination of BsuE methyltransferase (M-BsuE) and NotI restriction enzyme to cut genomic DNA at a subset of NotI sites. The usefulness of this system is shown in a re-examination of the restriction map of the human MHC. Combinations of methylases and restriction enzymes can be used to generate cuts at different frequencies in genomic DNA, such that they generate ends complementary to NotI ends, and can be used in conjunction with NotI linking clones in chromosome jumping exper...

  18. 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.

  19. 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…

  20. An Analysis and Proposal of 3D Printing Applications for the Visually Impaired.

    Science.gov (United States)

    Minatani, Kazunori

    2017-01-01

    The full 3D printing process is divided into discrete 3 steps. With user-centric approach, the study confirmed that people with visual impairments could use CAD to carry out 3D printing tasks by managing the entire process as long as they had a certain amount of 3D data.

  1. 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

  2. Application of imputation methods to genomic selection in Chinese Holstein cattle

    Directory of Open Access Journals (Sweden)

    Weng Ziqing

    2012-02-01

    Full Text Available Abstract Missing genotypes are a common feature of high density SNP datasets obtained using SNP chip technology and this is likely to decrease the accuracy of genomic selection. This problem can be circumvented by imputing the missing genotypes with estimated genotypes. When implementing imputation, the criteria used for SNP data quality control and whether to perform imputation before or after data quality control need to consider. In this paper, we compared six strategies of imputation and quality control using different imputation methods, different quality control criteria and by changing the order of imputation and quality control, against a real dataset of milk production traits in Chinese Holstein cattle. The results demonstrated that, no matter what imputation method and quality control criteria were used, strategies with imputation before quality control performed better than strategies with imputation after quality control in terms of accuracy of genomic selection. The different imputation methods and quality control criteria did not significantly influence the accuracy of genomic selection. We concluded that performing imputation before quality control could increase the accuracy of genomic selection, especially when the rate of missing genotypes is high and the reference population is small.

  3. Analysis of n-gram based promoter recognition methods and application to whole genome promoter prediction.

    Science.gov (United States)

    Rani, T Sobha; Bapi, Raju S

    2009-01-01

    Promoter prediction is an important and complex problem. Pattern recognition algorithms typically require features that could capture this complexity. A special bias towards certain combinations of base pairs in the promoter sequences may be possible. In order to determine these biases n-grams are usually extracted and analyzed. An n-gram is a selection of n contiguous characters from a given character stream, DNA sequence segments in this case. Here a systematic study is made to discover the efficacy of n-grams for n = 2, 3, 4, 5 in promoter prediction. A study of n-grams as features for a neural network classifier for E. coli and Drosophila promoters is made. In case of E. coli n=3 and in case of Drosophila n=4 seem to give optimal prediction values. Using the 3-gram features, promoter prediction in the genome sequence of E. coli is done. The results are encouraging in positive identification of promoters in the genome compared to software packages such as BPROM, NNPP, and SAK. Whole genome promoter prediction in Drosophila genome was also performed but with 4-gram features.

  4. 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 ...

  5. 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...

  6. 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.

  7. 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)

  8. [Application progress of CRISPR/Cas9 genome editing technology in the treatment of HIV-1 infection].

    Science.gov (United States)

    Han, Ying-lun; Li, Qing-wei

    2016-01-01

    The goal of gene therapy is to introduce foreign genes into human target cells in a certain way to correct or compensate diseases caused by defective or abnormal genes. Therefore, gene therapy has great practical significance in studying the treatment of persistent or latent HIV-1 infection. At present, the existing methods of gene therapy have some major defects such as limited target site recognition and high frequency of off-targets. The latest research showed that the clustered regularly interspaced short palindromic repeats (CRISPR) /CRISPR-associated nuclease 9 (Cas9) system from bacteria and archaea has been successfully reformed to a targeted genome editing tool. Thus, how to achieve the goal of treating HIV-1 infection by modifying targeted HIV-1 virus genome effectively using the CRISPR/Cas9 system has become a current research focus. Here we review the latest achievements worldwide and briefly introduce applications of the CRISPR/Cas9 genome editing technology in the treatment of HIV-1 infection, including CCR5 gene editing, removal of HIV-1 virus and activation of HIV-1 virus, in order to provide reference for the prevention and treatment of HIV-1 infection.

  9. 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.

  10. A computational pipeline to discover highly phylogenetically informative genes in sequenced genomes: application to Saccharomyces cerevisiae natural strains.

    Science.gov (United States)

    Ramazzotti, Matteo; Berná, Luisa; Stefanini, Irene; Cavalieri, Duccio

    2012-05-01

    The quest for genes representing genetic relationships of strains or individuals within populations and their evolutionary history is acquiring a novel dimension of complexity with the advancement of next-generation sequencing (NGS) technologies. In fact, sequencing an entire genome uncovers genetic variation in coding and non-coding regions and offers the possibility of studying Saccharomyces cerevisiae populations at the strain level. Nevertheless, the disadvantageous cost-benefit ratio (the amount of details disclosed by NGS against the time-expensive and expertise-demanding data assembly process) still precludes the application of these techniques to the routinely assignment of yeast strains, making the selection of the most reliable molecular markers greatly desirable. In this work we propose an original computational approach to discover genes that can be used as a descriptor of the population structure. We found 13 genes whose variability can be used to recapitulate the phylogeny obtained from genome-wide sequences. The same approach that we prove to be successful in yeasts can be generalized to any other population of individuals given the availability of high-quality genomic sequences and of a clear population structure to be targeted.

  11. 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.

  12. 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.

  13. 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...

  14. 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

  15. Genomics Analogy Model for Educators (GAME): VELCRO® Analogy Model to Enable the Learning of DNA Arrays for Visually Impaired and Blind Students

    Science.gov (United States)

    Bello, Julia; Butler, Charles; Radavich, Rosanne; York, Alan; Oseto, Christian; Orvis, Kathryn; Pittendrigh, Barry R.

    2007-01-01

    Although members of the general public have often heard of the terms "genetic engineering" and, more recently, genomics, they typically have little to no knowledge about these topics, and in some cases are confused about basic concepts in these areas. There is currently a need for teaching models to explain concepts behind genomics.…

  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. 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.

  18. Best practice guidelines for the use of next-generation sequencing applications in genome diagnostics: a national collaborative study of Dutch genome diagnostic laboratories.

    Science.gov (United States)

    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

    2013-10-01

    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 Society for Clinical Genetic Laboratory Diagnostics (VKGL) set up a working group in 2012. The results of their discussions are presented here. We provide best practice guidelines and criteria for implementing and validating NGS applications in a clinical setting. We introduce the concept of "diagnostic yield" as the main performance characteristic for evaluating diagnostic tests. We recommend that the laboratory procedures, including the tested genes, should be recorded in a publicly available document describing the complete "diagnostic routing." We also propose that laboratories should use a list of "core disease genes" for specific genetic diseases. This core list contains the essential genes for each disease, and they should all be included in a diagnostic test to establish a reliable and accurate molecular diagnosis. The guidelines will ensure a clear and standardized quality of care provided by genetic diagnostic laboratories. The best practice guidelines and criteria that are presented here were adopted by the VKGL in January 2013. © 2013 WILEY PERIODICALS, INC.

  19. 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

  20. 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.

  1. A tool for integrating genetic and mass spectrometry-based peptide data: Proteogenomics Viewer: PV: A genome browser-like tool, which includes MS data visualization and peptide identification parameters.

    Science.gov (United States)

    Kroll, José Eduardo; da Silva, Vandeclécio Lira; de Souza, Sandro José; de Souza, Gustavo Antonio

    2017-07-01

    In this manuscript we describe Proteogenomics Viewer, a web-based tool that collects MS peptide identification, indexes to genomic sequence and structure, assigns exon usage, reports the identified protein isoforms with genomic alignments and, most importantly, allows the inspection of MS2 information for proper peptide identification. It also provides all performed indexing to facilitate global analysis of the data. The relevance of such tool is that there has been an increase in the number of proteogenomic efforts to improve the annotation of both genomics and proteomics data, culminating with the release of the two human proteome drafts. It is now clear that mass spectrometry-based peptide identification of uncharacterized sequences, such as those resulting from unpredicted exon joints or non-coding regions, is still prone to a higher than expected false discovery rate. Therefore, proper visualization of the raw data and the corresponding genome alignments are fundamental for further data validation and interpretation. Also see the video abstract here: http://youtu.be/5NzyRvuk4Ac. © 2017 WILEY Periodicals, Inc.

  2. Potential applications of atomic force microscopy of DNA to the human genome project

    Science.gov (United States)

    Hansma, Helen G.; Hansma, Paul K.

    1993-06-01

    A simple calculation shows that the information contained in the base sequence of the human genome could be recorded onto less than two compact discs. To read amounts of information comparable in size to the human genome, scanning probes are used routinely in both biology (i.e., living systems) and technology. The atomic force microscope (AFM) is a scanning probe that is now capable of imaging DNA routinely and reproducibly. The minimum size of structures seen reproducibly along DNA strands with the AFM is presently 2 to 3 nm, which is an order of magnitude less resolution than would be required to sequence DNA. At present, the AFM shows great potential for high-resolution mapping of DNA but is not capable of sequencing DNA without further improvements.

  3. Clinical Application of a Modular Genomics Technique in Systemic Lupus Erythematosus: Progress towards Precision Medicine

    Directory of Open Access Journals (Sweden)

    Eric Zollars

    2016-01-01

    Full Text Available Monitoring disease activity in a complex, heterogeneous disease such as lupus is difficult. Both over- and undertreatment lead to damage. Current standard of care serologies are unreliable. Better measures of disease activity are necessary as we move into the era of precision medicine. We show here the use of a data-driven, modular approach to genomic biomarker development within lupus—specifically lupus nephritis.

  4. 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.

  5. 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

  6. Advances and Applications of Ion Torrent Personal Genome Machine in Cutaneous Squamous Cell Carcinoma Reveal Novel Gene Mutations

    Directory of Open Access Journals (Sweden)

    Yu-Ping Hsiao

    2016-06-01

    Full Text Available The Ion Torrent Personal Genome Machine (Ion PGM is a semiconductor-based sequencing technology that is high quality, scalable, and economic. Its applications include genomic sequencing, drug resistance testing, microbial characterization, and targeted sequencing in cancer studies. However, little is known about the application of Ion PGM in cutaneous squamous cell carcinoma (cSCC. We therefore investigated the utility and validity of Ion PGM in cSCC and also gained a better understanding of the underlying molecular biology of cSCC. We detected novel gene mutations (KDR, FGFR2, and EGFR in two cSCC patients. Moreover, we validated these mutations by pyrosequencing and Sanger sequencing. Our results indicated that the mutation screen using Ion PGM is consistent with traditional sequencing methods. Notably, these identified mutations were present at significantly higher rates in high-risk cSCC. Our results demonstrate a method to detect targetable genes in high-risk cSCC, and suggest that Ion PGM may enable therapeutic decision-making and future potential targets for personalized therapies in cSCC.

  7. Application of the CRISPR/Cas9 gene editing technique to research on functional genomes of parasites.

    Science.gov (United States)

    Cui, Yubao; Yu, Lili

    2016-12-01

    The clustered regularly-interspaced short palindromic repeats (CRISPR) structural family functions as an acquired immune system in prokaryotes. Gene editing techniques have co-opted CRISPR and the associated Cas nucleases to allow for the precise genetic modification of human cells, zebrafish, mice, and other eukaryotes. Indeed, this approach has been used to induce a variety of modifications including directed insertion/deletion (InDel) of bases, gene knock-in, introduction of mutations in both alleles of a target gene, and deletion of small DNA fragments. Thus, CRISPR technology offers a precise molecular tool for directed genome modification with a range of potential applications; further, its high mutation efficiency, simple process, and low cost provide additional advantages over prior editing techniques. This paper will provide an overview of the basic structure and function of the CRISPR gene editing system as well as current and potential applications to research on parasites. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. A Web Application For Visualizing Empirical Models of the Space-Atmosphere Interface Region: AtModWeb

    Science.gov (United States)

    Knipp, D.; Kilcommons, L. M.; Damas, M. C.

    2015-12-01

    We have created a simple and user-friendly web application to visualize output from empirical atmospheric models that describe the lower atmosphere and the Space-Atmosphere Interface Region (SAIR). The Atmospheric Model Web Explorer (AtModWeb) is a lightweight, multi-user, Python-driven application which uses standard web technology (jQuery, HTML5, CSS3) to give an in-browser interface that can produce plots of modeled quantities such as temperature and individual species and total densities of neutral and ionized upper-atmosphere. Output may be displayed as: 1) a contour plot over a map projection, 2) a pseudo-color plot (heatmap) which allows visualization of a variable as a function of two spatial coordinates, or 3) a simple line plot of one spatial coordinate versus any number of desired model output variables. The application is designed around an abstraction of an empirical atmospheric model, essentially treating the model code as a black box, which makes it simple to add additional models without modifying the main body of the application. Currently implemented are the Naval Research Laboratory NRLMSISE00 model for neutral atmosphere and the International Reference Ionosphere (IRI). These models are relevant to the Low Earth Orbit environment and the SAIR. The interface is simple and usable, allowing users (students and experts) to specify time and location, and choose between historical (i.e. the values for the given date) or manual specification of whichever solar or geomagnetic activity drivers are required by the model. We present a number of use-case examples from research and education: 1) How does atmospheric density between the surface and 1000 km vary with time of day, season and solar cycle?; 2) How do ionospheric layers change with the solar cycle?; 3 How does the composition of the SAIR vary between day and night at a fixed altitude?

  13. Identification, evaluation, and application of the genomic-SSR loci in ramie

    Directory of Open Access Journals (Sweden)

    Ming-Bao Luan

    2016-09-01

    Full Text Available To provide a theoretical and practical foundation for ramie genetic analysis, simple sequence repeats (SSRs were identified in the ramie genome and employed in this study. From the 115 369 sequences of a specific-locus amplified fragment library, a type of reduced representation library obtained by high-throughput sequencing, we identified 4774 sequences containing 5064 SSR motifs. SSRs of ramie included repeat motifs with lengths of 1 to 6 nucleotides, and the abundance of each motif type varied greatly. We found that mononucleotide, dinucleotide, and trinucleotide repeat motifs were the most prevalent (95.91%. A total of 98 distinct motif types were detected in the genomic-SSRs of ramie. Of them, The A/T mononucleotide motif was the most abundant, accounting for 41.45% of motifs, followed by AT/TA, accounting for 20.30%. The number of alleles per locus in 31 polymorphic microsatellite loci ranged from 2 to 7, and observed and expected heterozygosities ranged from 0.04 to 1.00 and 0.04 to 0.83, respectively. Furthermore, molecular identity cards (IDs of the germplasms were constructed employing the ID Analysis 3.0 software. In the current study, the 26 germplasms of ramie can be distinguished by a combination of five SSR primers including Ibg5-5, Ibg3-210, Ibg1-11, Ibg6-468, and Ibg6-481. The allele polymorphisms produced by all SSR primers were used to analyze genetic relationships among the germplasms. The similarity coefficients ranged from 0.41 to 0.88. We found that these 26 germplasms were clustered into five categories using UPGMA, with poor correlation between germplasm and geographical distribution. Our study is the first large-scale SSR identification from ramie genomic sequences. We have further studied the SSR distribution pattern in the ramie genome, and proposed that it is possible to develop SSR loci from genomic data for population genetics studies, linkage mapping, quantitative trait locus mapping, cultivar fingerprinting

  14. 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.

  15. 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.

  16. 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...

  17. 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

  18. Kernel-Based Sensor Fusion With Application to Audio-Visual Voice Activity Detection

    Science.gov (United States)

    Dov, David; Talmon, Ronen; Cohen, Israel

    2016-12-01

    In this paper, we address the problem of multiple view data fusion in the presence of noise and interferences. Recent studies have approached this problem using kernel methods, by relying particularly on a product of kernels constructed separately for each view. From a graph theory point of view, we analyze this fusion approach in a discrete setting. More specifically, based on a statistical model for the connectivity between data points, we propose an algorithm for the selection of the kernel bandwidth, a parameter, which, as we show, has important implications on the robustness of this fusion approach to interferences. Then, we consider the fusion of audio-visual speech signals measured by a single microphone and by a video camera pointed to the face of the speaker. Specifically, we address the task of voice activity detection, i.e., the detection of speech and non-speech segments, in the presence of structured interferences such as keyboard taps and office noise. We propose an algorithm for voice activity detection based on the audio-visual signal. Simulation results show that the proposed algorithm outperforms competing fusion and voice activity detection approaches. In addition, we demonstrate that a proper selection of the kernel bandwidth indeed leads to improved performance.

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. Sparsely correlated hidden Markov models with application to genome-wide location studies.

    Science.gov (United States)

    Choi, Hyungwon; Fermin, Damian; Nesvizhskii, Alexey I; Ghosh, Debashis; Qin, Zhaohui S

    2013-03-01

    Multiply correlated datasets have become increasingly common in genome-wide location analysis of regulatory proteins and epigenetic modifications. Their correlation can be directly incorporated into a statistical model to capture underlying biological interactions, but such modeling quickly becomes computationally intractable. We present sparsely correlated hidden Markov models (scHMM), a novel method for performing simultaneous hidden Markov model (HMM) inference for multiple genomic datasets. In scHMM, a single HMM is assumed for each series, but the transition probability in each series depends on not only its own hidden states but also the hidden states of other related series. For each series, scHMM uses penalized regression to select a subset of the other data series and estimate their effects on the odds of each transition in the given series. Following this, hidden states are inferred using a standard forward-backward algorithm, with the transition probabilities adjusted by the model at each position, which helps retain the order of computation close to fitting independent HMMs (iHMM). Hence, scHMM is a collection of inter-dependent non-homogeneous HMMs, capable of giving a close approximation to a fully multivariate HMM fit. A simulation study shows that scHMM achieves comparable sensitivity to the multivariate HMM fit at a much lower computational cost. The method was demonstrated in the joint analysis of 39 histone modifications, CTCF and RNA polymerase II in human CD4+ T cells. scHMM reported fewer high-confidence regions than iHMM in this dataset, but scHMM could recover previously characterized histone modifications in relevant genomic regions better than iHMM. In addition, the resulting combinatorial patterns from scHMM could be better mapped to the 51 states reported by the multivariate HMM method of Ernst and Kellis. The scHMM package can be freely downloaded from http://sourceforge.net/p/schmm/ and is recommended for use in a linux environment.

  5. Functional genomic screening approaches in mechanistic toxicology and potential future applications of CRISPR-Cas9.

    Science.gov (United States)

    Shen, Hua; McHale, Cliona M; Smith, Martyn T; Zhang, Luoping

    2015-01-01

    Characterizing variability in the extent and nature of responses to environmental exposures is a critical aspect of human health risk assessment. Chemical toxicants act by many different mechanisms, however, and the genes involved in adverse outcome pathways (AOPs) and AOP networks are not yet characterized. Functional genomic approaches can reveal both toxicity pathways and susceptibility genes, through knockdown or knockout of all non-essential genes in a cell of interest, and identification of genes associated with a toxicity phenotype following toxicant exposure. Screening approaches in yeast and human near-haploid leukemic KBM7 cells have identified roles for genes and pathways involved in response to many toxicants but are limited by partial homology among yeast and human genes and limited relevance to normal diploid cells. RNA interference (RNAi) suppresses mRNA expression level but is limited by off-target effects (OTEs) and incomplete knockdown. The recently developed gene editing approach called clustered regularly interspaced short palindrome repeats-associated nuclease (CRISPR)-Cas9, can precisely knock-out most regions of the genome at the DNA level with fewer OTEs than RNAi, in multiple human cell types, thus overcoming the limitations of the other approaches. It has been used to identify genes involved in the response to chemical and microbial toxicants in several human cell types and could readily be extended to the systematic screening of large numbers of environmental chemicals. CRISPR-Cas9 can also repress and activate gene expression, including that of non-coding RNA, with near-saturation, thus offering the potential to more fully characterize AOPs and AOP networks. Finally, CRISPR-Cas9 can generate complex animal models in which to conduct preclinical toxicity testing at the level of individual genotypes or haplotypes. Therefore, CRISPR-Cas9 is a powerful and flexible functional genomic screening approach that can be harnessed to provide

  6. 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

  7. SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications.

    Science.gov (United States)

    Iquebal, Mir Asif; Jaiswal, Sarika; Angadi, U B; Sablok, Gaurav; Arora, Vasu; Kumar, Sunil; Rai, Anil; Kumar, Dinesh

    2015-01-01

    DNA marker plays important role as valuable tools to increase crop productivity by finding plausible answers to genetic variations and linking the Quantitative Trait Loci (QTL) of beneficial trait. Prior approaches in development of Short Tandem Repeats (STR) markers were time consuming and inefficient. Recent methods invoking the development of STR markers using whole genomic or transcriptomics data has gained wide importance with immense potential in developing breeding and cultivator improvement approaches. Availability of whole genome sequences and in silico approaches has revolutionized bulk marker discovery. We report world's first sugarbeet whole genome marker discovery having 145 K markers along with 5 K functional domain markers unified in common platform using MySQL, Apache and PHP in SBMDb. Embedded markers and corresponding location information can be selected for desired chromosome, location/interval and primers can be generated using Primer3 core, integrated at backend. Our analyses revealed abundance of 'mono' repeat (76.82%) over 'di' repeats (13.68%). Highest density (671.05 markers/Mb) was found in chromosome 1 and lowest density (341.27 markers/Mb) in chromosome 6. Current investigation of sugarbeet genome marker density has direct implications in increasing mapping marker density. This will enable present linkage map having marker distance of ∼2 cM, i.e. from 200 to 2.6 Kb, thus facilitating QTL/gene mapping. We also report e-PCR-based detection of 2027 polymorphic markers in panel of five genotypes. These markers can be used for DUS test of variety identification and MAS/GAS in variety improvement program. The present database presents wide source of potential markers for developing and implementing new approaches for molecular breeding required to accelerate industrious use of this crop, especially for sugar, health care products, medicines and color dye. Identified markers will also help in improvement of bioenergy trait of

  8. 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.

  9. 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

  10. A Multimedia Data Visualization Based on Ad Hoc Communication Networks and Its Application to Disaster Management

    Directory of Open Access Journals (Sweden)

    Youhei Kawamura

    2015-10-01

    Full Text Available After massive earthquakes and other large-scale disasters, existing communication infrastructure may become unavailable and, therefore, it can be quite difficult for relief organizations to fully grasp the impact of the disaster on the affected region. Consequently, this will be the cause of delays to offer the strategic assistance, and to provide water and food, etc. In order to solve the problem of re-establishing communication infrastructure to allow for information gathering, we developed an ad hoc mobile communications network for disaster-struck areas using ZigBee. As the communication speed of ZigBee is low, we propose a problem-specific image compression method for the multimedia data visualization. By using the proposed method combined with GPS information, it is possible to quickly grasp the damage situation in the region. Through our communication experiments in Tsukuba City, Japan we confirm the effectiveness of our system as a disaster information gathering and management system.

  11. 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).

  12. Visualization and comparison of DEM-derived parameters. Application to volcanic areas

    Science.gov (United States)

    Favalli, Massimiliano; Fornaciai, Alessandro

    2017-08-01

    Digital Elevation Models (DEMs) are fruitfully used in volcanology as the topographic base for mapping and quantifying volcanic landforms. The increasing availability of free topographic data on the web, decreasing production costs for high-accuracy data and advances in computer technology, has triggered rapid growth of the number of DEM users in the volcanological community. DEMs are often visualized only as hill-shaded maps, and while this is among the major advantages in using them, the possibility of deriving a very large number of parameters from a single grid of elevation data makes DEMs a powerful tool for morphometric analysis. However, many of these parameters have almost the same informative content, and before starting to elaborate topographic data it is recommended to know a-priori what parameters best visualize the investigated landform, and therefore what is necessary and what is redundant. In this work, we review a number of analytical procedures used to parameterize and represent DEMs. A LIDAR-derived DEM matrix acquired over the Valle del Bove valley, on Mt. Etna, is used as test-case elevation data for deriving the parameters. We first review well known parameters such as hill-shading, slope and aspect, curvature, and roughness, before extending the review to some less common parameters such as Sky View Factor (SVF), openness, and Red Relief Image Maps (RRIM). For each parameter a description is given emphasizing how it can be used for identifying and delimiting specific volcanic elements. The analyzed surface parameters are then cross-compared in order to infer which of them is most uncorrelated, and the results are represented in the form of a correlation matrix. Finally, the reviewed DEM-derived parameters and the correlation matrix are used for analyzing the volcanic landforms of two case studies: Michoacán-Guanajuato volcanic field and a phonolitic lava flow at the Island of Tenerife.

  13. 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.

  14. Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects.

    Science.gov (United States)

    Kole, Chittaranjan; Muthamilarasan, Mehanathan; Henry, Robert; Edwards, David; Sharma, Rishu; Abberton, Michael; Batley, Jacqueline; Bentley, Alison; Blakeney, Michael; Bryant, John; Cai, Hongwei; Cakir, Mehmet; Cseke, Leland J; Cockram, James; de Oliveira, Antonio Costa; De Pace, Ciro; Dempewolf, Hannes; Ellison, Shelby; Gepts, Paul; Greenland, Andy; Hall, Anthony; Hori, Kiyosumi; Hughes, Stephen; Humphreys, Mike W; Iorizzo, Massimo; Ismail, Abdelbagi M; Marshall, Athole; Mayes, Sean; Nguyen, Henry T; Ogbonnaya, Francis C; Ortiz, Rodomiro; Paterson, Andrew H; Simon, Philipp W; Tohme, Joe; Tuberosa, Roberto; Valliyodan, Babu; Varshney, Rajeev K; Wullschleger, Stan D; Yano, Masahiro; Prasad, Manoj

    2015-01-01

    Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase 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, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in 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 for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.

  15. 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.

  16. Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects

    Science.gov (United States)

    Kole, Chittaranjan; Muthamilarasan, Mehanathan; Henry, Robert; Edwards, David; Sharma, Rishu; Abberton, Michael; Batley, Jacqueline; Bentley, Alison; Blakeney, Michael; Bryant, John; Cai, Hongwei; Cakir, Mehmet; Cseke, Leland J.; Cockram, James; de Oliveira, Antonio Costa; De Pace, Ciro; Dempewolf, Hannes; Ellison, Shelby; Gepts, Paul; Greenland, Andy; Hall, Anthony; Hori, Kiyosumi; Hughes, Stephen; Humphreys, Mike W.; Iorizzo, Massimo; Ismail, Abdelbagi M.; Marshall, Athole; Mayes, Sean; Nguyen, Henry T.; Ogbonnaya, Francis C.; Ortiz, Rodomiro; Paterson, Andrew H.; Simon, Philipp W.; Tohme, Joe; Tuberosa, Roberto; Valliyodan, Babu; Varshney, Rajeev K.; Wullschleger, Stan D.; Yano, Masahiro; Prasad, Manoj

    2015-01-01

    Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase 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, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in 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 for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security. PMID:26322050

  17. ZCURVE_CoV: a new system to recognize protein coding genes in coronavirus genomes, and its applications in analyzing SARS-CoV genomes.

    Science.gov (United States)

    Chen, Ling-Ling; Ou, Hong-Yu; Zhang, Ren; Zhang, Chun-Ting

    2003-07-25

    A new system to recognize protein coding genes in the coronavirus genomes, specially suitable for the SARS-CoV genomes, has been proposed in this paper. Compared with some existing systems, the new program package has the merits of simplicity, high accuracy, reliability, and quickness. The system ZCURVE_CoV has been run for each of the 11 newly sequenced SARS-CoV genomes. Consequently, six genomes not annotated previously have been annotated, and some problems of previous annotations in the remaining five genomes have been pointed out and discussed. In addition to the polyprotein chain ORFs 1a and 1b and the four genes coding for the major structural proteins, spike (S), small envelop (E), membrane (M), and nuleocaspid (N), respectively, ZCURVE_CoV also predicts 5-6 putative proteins in length between 39 and 274 amino acids with unknown functions. Some single nucleotide mutations within these putative coding sequences have been detected and their biological implications are discussed. A web service is provided, by which a user can obtain the annotated result immediately by pasting the SARS-CoV genome sequences into the input window on the web site (http://tubic.tju.edu.cn/sars/). The software ZCURVE_CoV can also be downloaded freely from the web address mentioned above and run in computers under the platforms of Windows or Linux.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. [Visualization and analysis of drug information on adverse reactions using data mining method, and its clinical application].

    Science.gov (United States)

    Kawakami, Junko

    2014-01-01

    Sources of drug information such as package inserts (PIs) and interview forms (IFs) and existing drug information databases provide primarily document-based and numerical information. For this reason, it is not easy to obtain a complete picture of the information concerning many drugs with similar effects or to understand differences among drugs. The visualization of drug information may help provide a large amount of information in a short period, relieve the burden on medical workers, facilitate a comprehensive understanding and comparison of drugs, and contribute to improvements in patients' QOL. At our department, we are developing an approach to convert information on side effects obtained from PIs of many drugs with similar effects into visual maps reflecting the data structure through competitive learning using the self-organizing map (SOM) technique of Kohonen, which is a powerful method for pattern recognition, to facilitate the grasping of all available information and differences among drugs, to anticipate the appearance of side effects; we are also evaluating the possibility of its clinical application. In this paper, this approach is described by taking the examples of antibiotics, antihypertensive drugs, and diabetes drugs.

  3. REPRODUCIBILITY AND COMPARISON OF VISUAL ACUITY OBTAINED WITH SIGHTBOOK MOBILE APPLICATION TO NEAR CARD AND SNELLEN CHART.

    Science.gov (United States)

    Phung, Lam; Gregori, Ninel Z; Ortiz, Angelica; Shi, Wei; Schiffman, Joyce C

    2016-05-01

    To investigate test-retest reproducibility of visual acuities obtained with a popular mobile application (app) and to explore the agreement with the standard clinic charts. Records of patients who had visual acuity measured during the same routine clinic visit with Snellen chart, Rosenbaum near vision card, and SightBook mobile app were reviewed. Acuities were converted to approximate ETDRS letters for statistical purposes. One hundred and twenty-six patients were identified. SightBook, Snellen, and near card acuities had excellent test-retest reproducibility. SightBook acuities were significantly different from the near card acuities (mean absolute difference of 5.4 and 6.1 letters in the right and left eyes) and the Snellen acuities (mean absolute difference of 7.7 and 7.9 letters in the right and left eyes). The agreement was also poor between the near card and the Snellen acuities (mean absolute difference of 6.4 and 7.6 letters in the right and left eyes). The discrepancy between SightBook mobile app and the clinic charts acuities may be large; however, the results are highly reproducible. Obtaining baseline SightBook acuity allows future vision comparisons. SightBook mobile app offers a new portable vision assessment tool for the office and remote patient monitoring.

  4. VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data

    Directory of Open Access Journals (Sweden)

    Peterson Elena S

    2012-04-01

    Full Text Available Abstract Background The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq, global microarrays, and tandem mass spectrometry (MS/MS-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. Results VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric and transcriptomics (probe or RNA-Seq data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002 to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. Conclusions VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis

  5. VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data

    Science.gov (United States)

    2012-01-01

    Background The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. Results VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. Conclusions VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic

  6. A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis

    Directory of Open Access Journals (Sweden)

    Denoeud France

    2001-03-01

    Full Text Available Abstract Background Some pathogenic bacteria are genetically very homogeneous, making strain discrimination difficult. In the last few years, tandem repeats have been increasingly recognized as markers of choice for genotyping a number of pathogens. The rapid evolution of these structures appears to contribute to the phenotypic flexibility of pathogens. The availability of whole-genome sequences has opened the way to the systematic evaluation of tandem repeats diversity and application to epidemiological studies. Results This report presents a database (http://minisatellites.u-psud.fr of tandem repeats from publicly available bacterial genomes which facilitates the identification and selection of tandem repeats. We illustrate the use of this database by the characterization of minisatellites from two important human pathogens, Yersinia pestis and Bacillus anthracis. In order to avoid simple sequence contingency loci which may be of limited value as epidemiological markers, and to provide genotyping tools amenable to ordinary agarose gel electrophoresis, only tandem repeats with repeat units at least 9 bp long were evaluated. Yersinia pestis contains 64 such minisatellites in which the unit is repeated at least 7 times. An additional collection of 12 loci with at least 6 units, and a high internal conservation were also evaluated. Forty-nine are polymorphic among five Yersinia strains (twenty-five among three Y. pestis strains. Bacillus anthracis contains 30 comparable structures in which the unit is repeated at least 10 times. Half of these tandem repeats show polymorphism among the strains tested. Conclusions Analysis of the currently available bacterial genome sequences classifies Bacillus anthracis and Yersinia pestis as having an average (approximately 30 per Mb density of tandem repeat arrays longer than 100 bp when compared to the other bacterial genomes analysed to date. In both cases, testing a fraction of these sequences for

  7. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew David; Kupczok, Anne

    2017-01-01

    evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics.......Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...

  8. 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.

  9. 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.

  10. Application of genomic and molecular methods to fundamental questions in canine and feline reproductive health.

    Science.gov (United States)

    Meyers-Wallen, V N

    2012-12-01

    Molecular tools are becoming increasingly available to investigate the genetic basis of reproductive disorders in dogs and cats. These were first successful in identifying the molecular basis of diseases inherited as simple Mendelian traits, and these are now being applied to those that are inherited as complex traits. In order to promote similar studies of reproductive disorders, we need to understand how we can play a proactive role in accumulating sufficient case material. We also need to understand these mutation discovery tools and identify collaborators who have experience with their use. The candidate gene and genomic approaches to mutation discovery in dogs are presented, including new sequencing methods and those used to confirm that a mutation has a role in disease pathology. As the final goal is to use our study results to prevent inherited disorders, we need to consider how we can promote efficiency in obtaining DNA test results and providing genetic counselling. © 2012 Blackwell Verlag GmbH.

  11. Functional genomics of apocarotenoids in saffron: insights from chemistry, molecular biology and therapeutic applications.

    Science.gov (United States)

    Dhar, Manoj K; Sharma, Munish; Bhat, Archana; Chrungoo, Nikhil K; Kaul, Sanjana

    2017-11-01

    Saffron is considered to be the costliest spice of the world. It has been regarded as highly valued medicinal plant in Ayurveda to treat various ailments. Over the past few years, considerable interest has developed in saffron because of its anticancer, antimutagenic, antioxidant and immunomodulatory properties. Saffron's colour, bitter taste and aroma are its three main and peculiar characteristics, which are conferred by three chemicals namely: crocin, picrocrocin and safranal, respectively. The present review focuses on recent research/progress made in saffron in the area of functional genomics and highlights the potential of several genes and transcription factors involved in carotenoid/apocarotenoid pathway and responsible for flavour and aroma of saffron. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  12. 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.

  13. 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.

  14. Application of CRISPR-Cas9 Based Genome-Wide Screening Approaches to Study Cellular Signalling Mechanisms

    Directory of Open Access Journals (Sweden)

    Sumana Sharma

    2018-03-01

    Full Text Available The cellular signalling process is a highly complex mechanism, involving multiple players, which together orchestrate the cell’s response to environmental changes and perturbations. Given the multitude of genes that participate in the process of cellular signalling, its study in a genome-wide manner has proven challenging. Recent advances in gene editing technologies, including clustered regularly-interspaced short palindromic repeats/Cas9 (CRISPR/Cas9 approaches, have opened new opportunities to investigate global regulatory signalling programs of cells in an unbiased manner. In this review, we focus on how the application of pooled genetic screening approaches using the CRISPR/Cas9 system has contributed to a systematic understanding of cellular signalling processes in normal and disease contexts.

  15. 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.

  16. 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)

  17. Visual Recognition Software for Binary Classification and Its Application to Spruce Pollen Identification.

    Directory of Open Access Journals (Sweden)

    David K Tcheng

    Full Text Available Discriminating between black and white spruce (Picea mariana and Picea glauca is a difficult palynological classification problem that, if solved, would provide valuable data for paleoclimate reconstructions. We developed an open-source visual recognition software (ARLO, Automated Recognition with Layered Optimization capable of differentiating between these two species at an accuracy on par with human experts. The system applies pattern recognition and machine learning to the analysis of pollen images and discovers general-purpose image features, defined by simple features of lines and grids of pixels taken at different dimensions, size, spacing, and resolution. It adapts to a given problem by searching for the most effective combination of both feature representation and learning strategy. This results in a powerful and flexible framework for image classification. We worked with images acquired using an automated slide scanner. We first applied a hash-based "pollen spotting" model to segment pollen grains from the slide background. We next tested ARLO's ability to reconstruct black to white spruce pollen ratios using artificially constructed slides of known ratios. We then developed a more scalable hash-based method of image analysis that was able to distinguish between the pollen of black and white spruce with an estimated accuracy of 83.61%, comparable to human expert performance. Our results demonstrate the capability of machine learning systems to automate challenging taxonomic classifications in pollen analysis, and our success with simple image representations suggests that our approach is generalizable to many other object recognition problems.

  18. 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.

  19. 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.

  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.