WorldWideScience

Sample records for building genomics visualization

  1. 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

  2. Visualization for genomics: the Microbial Genome Viewer.

    Science.gov (United States)

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

    2004-07-22

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

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

    Science.gov (United States)

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

    2015-07-15

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

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

    Science.gov (United States)

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

    2018-05-15

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

  5. Visualizing conserved gene location across microbe genomes

    Science.gov (United States)

    Shaw, Chris D.

    2009-01-01

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

  6. Boxes of Model Building and Visualization.

    Science.gov (United States)

    Turk, Dušan

    2017-01-01

    Macromolecular crystallography and electron microscopy (single-particle and in situ tomography) are merging into a single approach used by the two coalescing scientific communities. The merger is a consequence of technical developments that enabled determination of atomic structures of macromolecules by electron microscopy. Technological progress in experimental methods of macromolecular structure determination, computer hardware, and software changed and continues to change the nature of model building and visualization of molecular structures. However, the increase in automation and availability of structure validation are reducing interactive manual model building to fiddling with details. On the other hand, interactive modeling tools increasingly rely on search and complex energy calculation procedures, which make manually driven changes in geometry increasingly powerful and at the same time less demanding. Thus, the need for accurate manual positioning of a model is decreasing. The user's push only needs to be sufficient to bring the model within the increasing convergence radius of the computing tools. It seems that we can now better than ever determine an average single structure. The tools work better, requirements for engagement of human brain are lowered, and the frontier of intellectual and scientific challenges has moved on. The quest for resolution of new challenges requires out-of-the-box thinking. A few issues such as model bias and correctness of structure, ongoing developments in parameters defining geometric restraints, limitations of the ideal average single structure, and limitations of Bragg spot data are discussed here, together with the challenges that lie ahead.

  7. 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.

  8. Customizable Visualizations with Formula-Linked Building Blocks

    DEFF Research Database (Denmark)

    Kuhail, Mohammad Amin; Lauesen, Søren

    different appearance or behavior than what the widgets support. Another approach is to combine primitive graphical elements using traditional programming or visualization toolkits. Traditional programming allows high customizability, but it is time consuming and hard to develop advanced visualizations......One approach to visualization construction is to use complex blocks (widgets) that are tailored for specific visualizations, and customize the visualizations by setting the properties of the widgets. This approach allows fast and easy visualization construction but falls short if the user wants....... Visualization toolkits allow easier visualization creation in some cases, but customization and interaction are tedious. As an alternative, we developed uVis visualization tool that uses spreadsheet-like formulas to connect building blocks. uVis formulas can refer to building blocks and database tables. We...

  9. Visualization environment and its utilization in the ITBL building

    International Nuclear Information System (INIS)

    Yasuhara, Yuko

    2004-12-01

    In recent years, visualization techniques have become more and more important in various fields. Especially in scientific fields, a large amount of numerical output data crucially needs to be changed into visualized form, because computations have grown to larger and larger scales as well as have become more complicated, so that computed results must be intuitively comprehensible by using various visualization techniques like 3D or stereo image construction. In the visualization room in the ITBL building, a 3-screen Virtual Reality system, a Portable Virtual Reality system, a Mixed Reality system, and Visualization tools like alchemy etc. are installed for the above-mentioned use. These devices enable us to easily change numerical data into visualized images of a virtual reality world with the use of eye-glasses or a head-mount-display device. This article describes the visualization environment in the ITBL building, it's use, and the tasks to be solved. (author)

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

    DEFF Research Database (Denmark)

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

    2008-01-01

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

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

    Science.gov (United States)

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

    2017-12-01

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

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

    Science.gov (United States)

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

    2012-07-01

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

  14. Building Interactive Visualizations for Geochronological Data

    Science.gov (United States)

    Zeringue, J.; Bowring, J. F.; McLean, N. M.; Pastor, F.

    2014-12-01

    Since the early 1990s, Ken Ludwig's Isoplot software has been the tool of choice for visualization and analysis of isotopic data used for geochronology. The software is an add-in to Microsoft Excel that allows users to generate visual representations of data. However, recent changes to Excel have made Isoplot more difficult to use and maintain, and the software is no longer supported. In the last several years, the Cyber Infrastructure Research and Development Lab for the Earth Sciences (CIRDLES), at the College of Charleston, has worked collaboratively with geochronologists to develop U-Pb_Redux, a software product that provides some of Isoplot's functionality for U-Pb geochronology. However, the community needs a full and complete Isoplot replacement that is open source, platform independent, and not dependent on proprietary software. This temporary lapse in tooling also presents a tremendous opportunity for scientific computing in the earth sciences. When Isoplot was written for Excel, it gained much of the platform's flexibility and power but also was burdened with its limitations. For example, Isoplot could not be used outside of Excel, could not be cross-platform (so long as Excel wasn't), could not be embedded in other applications, and only static images could be produced. Nonetheless this software was and still is a powerful tool that has served the community for more than two decades and the trade-offs were more than acceptable. In 2014, we seek to gain flexibility not available with Excel. We propose that the next generation of charting software be reusable, platform-agnostic, and interactive. This new software should allow scientists to easily explore—not just passively view—their data. Beginning in the fall of 2013, researchers at CIRDLES began planning for and prototyping a 21st-century replacement for Isoplot, which we call Topsoil, an anagram of Isoplot. This work is being conducted in the public domain at https://github.com/CIRDLES/topsoil. We

  15. Multiple Learning Strategies Project. Building Maintenance & Engineering. Visually Impaired.

    Science.gov (United States)

    Smith, Dwight; And Others

    This instructional package is designed for visually impaired students in the vocational area of building maintenance and engineering. The twenty-eight learning modules are organized into six units: floor care, general maintenance tasks; restrooms; carpet care; power and hand tools; and cabinet construction. Each module, printed in large block…

  16. 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.

  17. 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.

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

    Science.gov (United States)

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

    2013-03-01

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

  19. 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.

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

    Directory of Open Access Journals (Sweden)

    Nix David A

    2010-09-01

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

  1. 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.

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

    Science.gov (United States)

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

    2012-05-08

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

  3. 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.

  4. Learning Building Layouts with Non-geometric Visual Information: The Effects of Visual Impairment and Age

    Science.gov (United States)

    Kalia, Amy A.; Legge, Gordon E.; Giudice, Nicholas A.

    2009-01-01

    Previous studies suggest that humans rely on geometric visual information (hallway structure) rather than non-geometric visual information (e.g., doors, signs and lighting) for acquiring cognitive maps of novel indoor layouts. This study asked whether visual impairment and age affect reliance on non-geometric visual information for layout learning. We tested three groups of participants—younger (sighted, older (50–70 years) normally sighted, and low vision (people with heterogeneous forms of visual impairment ranging in age from 18–67). Participants learned target locations in building layouts using four presentation modes: a desktop virtual environment (VE) displaying only geometric cues (Sparse VE), a VE displaying both geometric and non-geometric cues (Photorealistic VE), a Map, and a Real building. Layout knowledge was assessed by map drawing and by asking participants to walk to specified targets in the real space. Results indicate that low-vision and older normally-sighted participants relied on additional non-geometric information to accurately learn layouts. In conclusion, visual impairment and age may result in reduced perceptual and/or memory processing that makes it difficult to learn layouts without non-geometric visual information. PMID:19189732

  5. Supporting interactive visual analytics of energy behavior in buildings through affine visualizations

    DEFF Research Database (Denmark)

    Nielsen, Matthias; Brewer, Robert S.; Grønbæk, Kaj

    2016-01-01

    Domain experts dealing with big data are typically not familiar with advanced data mining tools. This especially holds true for domain experts within energy management. In this paper, we introduce a visual analytics approach that empowers such users to visually analyze energy behavior based......Viz, that interactively maps data from real world buildings. It is an overview +detail inter-active visual analytics tool supporting both rapid ad hoc explorations and structured evaluation of hypotheses about patterns and anomalies in resource consumption data mixed with occupant survey data. We have evaluated...... the approach with five domain experts within energy management, and further with 10 data analytics experts and found that it was easily attainable and that it supported visual analysis of mixed consumption and survey data. Finally, we discuss future perspectives of affine visual analytics for mixed...

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

    Science.gov (United States)

    Cleary, Alan; Farmer, Andrew

    2018-05-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-03-14

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

  8. 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/.

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Sinha Amit U

    2011-11-01

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

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

    Science.gov (United States)

    Miyanari, Yusuke

    2016-01-01

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

  12. 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.

  13. Methodology for the Efficient Progressive Distribution and Visualization of 3D Building Objects

    Directory of Open Access Journals (Sweden)

    Bo Mao

    2016-10-01

    Full Text Available Three-dimensional (3D, city models have been applied in a variety of fields. One of the main problems in 3D city model utilization, however, is the large volume of data. In this paper, a method is proposed to generalize the 3D building objects in 3D city models at different levels of detail, and to combine multiple Levels of Detail (LODs for a progressive distribution and visualization of the city models. First, an extended structure for multiple LODs of building objects, BuildingTree, is introduced that supports both single buildings and building groups; second, constructive solid geometry (CSG representations of buildings are created and generalized. Finally, the BuildingTree is stored in the NoSQL database MongoDB for dynamic visualization requests. The experimental results indicate that the proposed progressive method can efficiently visualize 3D city models, especially for large areas.

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

    Science.gov (United States)

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

    2017-05-02

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

  15. Building the sequence map of the human pan-genome

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Li, Yingrui; Zheng, Hancheng

    2010-01-01

    analysis of predicted genes indicated that the novel sequences contain potentially functional coding regions. We estimate that a complete human pan-genome would contain approximately 19-40 Mb of novel sequence not present in the extant reference genome. The extensive amount of novel sequence contributing...

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

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  17. Building visual identity of scientific and research units and the role of visualization in cooperation with business

    Directory of Open Access Journals (Sweden)

    Alfreda Kamińska

    2014-12-01

    Full Text Available The need for commercialization of scientific research leads to the necessity of changing the orientation of scientific-research units to marketing orientation, which is characterized by, among others, conducting research aimed at learning the clients’ needs and building better communication with the recipients. What is an important element of a unit’s marketing communication is its visual identity system, which the recipients use to build their opinion and their picture of the unit. The goal of this article is an attempt to define the key rules of designing visual identity of scientific and research institutions, as well as presenting the role of visualization in their cooperation with business. In the article the notions of image, identity, corporate identity and visual identity are subject to analysis. The article also presents the significance of visualization in the functioning of research and scientific units, elements of visual identity system and the rules of designing visual identity of scientific and research institutions. An analysis of chosen research-scientific units was carried out with regard to visualization.

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

    Science.gov (United States)

    Mader, Malte; Simon, Ronald; Kurtz, Stefan

    2014-03-31

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

  19. 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

  20. Visualization of Genome Diversity in German Shepherd Dogs

    OpenAIRE

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

    2016-01-01

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

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

    Science.gov (United States)

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

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

    Science.gov (United States)

    Abe, Takashi; Hamano, Yuta; Ikemura, Toshimichi

    2014-01-01

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

  3. 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. Methods of choosing the best methods of building a dynamic visualization environment

    Directory of Open Access Journals (Sweden)

    В.А. Бородін

    2009-02-01

    Full Text Available In work is offered the methods of the choice of the most optimum combination of the methods which provides the building of the visual image of the dynamic scenes on the displays of real-time ANGS, which defines the optimal percent of the use for each of m software programs, that are in complex, n methods, optimizing velocity of the image of the visual image. The calculation of the ratio is carried out using the details of this problem to the linear programming problem. In work is offered the calculation of the optimum methods for building a visual image of a dynamic scenes for a specific task.

  5. Building a genome database using an object-oriented approach.

    Science.gov (United States)

    Barbasiewicz, Anna; Liu, Lin; Lang, B Franz; Burger, Gertraud

    2002-01-01

    GOBASE is a relational database that integrates data associated with mitochondria and chloroplasts. The most important data in GOBASE, i. e., molecular sequences and taxonomic information, are obtained from the public sequence data repository at the National Center for Biotechnology Information (NCBI), and are validated by our experts. Maintaining a curated genomic database comes with a towering labor cost, due to the shear volume of available genomic sequences and the plethora of annotation errors and omissions in records retrieved from public repositories. Here we describe our approach to increase automation of the database population process, thereby reducing manual intervention. As a first step, we used Unified Modeling Language (UML) to construct a list of potential errors. Each case was evaluated independently, and an expert solution was devised, and represented as a diagram. Subsequently, the UML diagrams were used as templates for writing object-oriented automation programs in the Java programming language.

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

    Science.gov (United States)

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

    2017-01-11

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

  7. 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

  8. Building a model: developing genomic resources for common milkweed (Asclepias syriaca with low coverage genome sequencing

    Directory of Open Access Journals (Sweden)

    Weitemier Kevin

    2011-05-01

    Full Text Available Abstract Background Milkweeds (Asclepias L. have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L. could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution. Results A 0.5× genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp and 5S rDNA (120 bp sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp, with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae unigenes (median coverage of 0.29× and 66% of single copy orthologs (COSII in asterids (median coverage of 0.14×. From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites and phylogenetics (low-copy nuclear genes studies were developed. Conclusions The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species

  9. Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing.

    Science.gov (United States)

    Straub, Shannon C K; Fishbein, Mark; Livshultz, Tatyana; Foster, Zachary; Parks, Matthew; Weitemier, Kevin; Cronn, Richard C; Liston, Aaron

    2011-05-04

    Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L.) could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution. A 0.5× genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp) and 5S rDNA (120 bp) sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp), with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae) unigenes (median coverage of 0.29×) and 66% of single copy orthologs (COSII) in asterids (median coverage of 0.14×). From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites) and phylogenetics (low-copy nuclear genes) studies were developed. The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species and its relatives. This study represents a first

  10. Creative Organizational Vision Building through Collaborative, Visual-Metaphorical Thought.

    Science.gov (United States)

    Ambrose, Don

    1998-01-01

    Describes use of collaborative metaphorical discussions, mind mapping, and imaginative visual thinking by the faculty of the Rider University School of Education to produce an idealistic vision of the college's future. This vision is expressed as a fanciful metaphorical drawing surrounded by a mind map and accompanied by a story connecting symbols…

  11. School Building Design and Audio-Visual Resources.

    Science.gov (United States)

    National Committee for Audio-Visual Aids in Education, London (England).

    The design of new schools should facilitate the use of audiovisual resources by ensuring that the materials used in the construction of the buildings provide adequate sound insulation and acoustical and viewing conditions in all learning spaces. The facilities to be considered are: electrical services; electronic services; light control and…

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

    Directory of Open Access Journals (Sweden)

    Borowski Krzysztof

    2008-06-01

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

  13. 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.

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

    Directory of Open Access Journals (Sweden)

    Promponas Vasilis J

    2003-10-01

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

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

    International Nuclear Information System (INIS)

    Ritland Politz, Joan C.

    2006-01-01

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

  16. Building Visual Artists’ Resilience Capabilities: Current Educator Strategies and Methods

    Directory of Open Access Journals (Sweden)

    Eileen Maree Siddins

    2016-07-01

    Full Text Available Enrolments in higher education programs in the creative and performing arts are increasing in many countries. Yet graduates of these degrees, who enter the broad sector known as the creative industries, face particular challenges in terms of securing long-term and sustainable employment. In addition, creative and performing artists face a range of mental challenges, caused by such factors as: the solitary nature of much creative practice, critical feedback by audiences and gatekeepers, or the general pressures associated with maintaining artistic relevance or integrity. The concepts of resilience and professional wellbeing are therefore highly relevant to those who pursue a career in creative industries, and while there has been an emerging body of work in this area, to date it has focussed on the performing arts area (e.g. music, theatre. Hence, in order to expand knowledge relevant to resilience and artists, this paper sets out to explore the extent to which current educators in the Australian context specifically address these issues within higher visual arts curricula; specifically the areas of illustration, design, film and photography. This was achieved via interviews with seventeen current academics working in these areas. The findings propose that higher education providers of programs in the visual arts consider placing a stronger emphasis on the embedded development of resilience and professional wellbeing capacities.

  17. Gamification and Visualization of Sensor Data Analysis in Research Buildings

    Energy Technology Data Exchange (ETDEWEB)

    Stone, Jackson A [ORNL; Sanyal, Jibonananda [ORNL; Castello, Charles C [ORNL; New, Joshua Ryan [ORNL

    2015-01-01

    The use of video game elements in non-gaming systems, or gamification , has potential value in transforming data analysis. Our study focused on creating a web-based videogame that models two physical test buildings, each of which contains hundreds of sensors. After the application renders the models, the player can walk through the environments and interact with the virtual representations of the sensors inside. Rather than trudging through a database with textual commands and screens full of data, the user can (virtually) walk up to a sensor and view its data graphically. But these features only scratch the surface of what is possible using our new gamification approach. We anticipate being able to show that recent progress in game design techniques and capacities can contribute to the field of analysis through gamification. The net result could be more stimulating, intuitive, user-friendly interfaces, as well as potentially more informative and insightful applications.

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

    Science.gov (United States)

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

    2016-01-05

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

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

    Science.gov (United States)

    Amiryousefi, Ali; Hyvönen, Jaakko; Poczai, Peter

    2018-04-05

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

  20. 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

  1. Visual Sample Plan (VSP) Software: Designs and Data Analyses for Sampling Contaminated Buildings

    International Nuclear Information System (INIS)

    Pulsipher, Brent A.; Wilson, John E.; Gilbert, Richard O.; Nuffer, Lisa L.; Hassig, Nancy L.

    2005-01-01

    A new module of the Visual Sample Plan (VSP) software has been developed to provide sampling designs and data analyses for potentially contaminated buildings. An important application is assessing levels of contamination in buildings after a terrorist attack. This new module, funded by DHS through the Combating Terrorism Technology Support Office, Technical Support Working Group, was developed to provide a tailored, user-friendly and visually-orientated buildings module within the existing VSP software toolkit, the latest version of which can be downloaded from http://dqo.pnl.gov/vsp. In case of, or when planning against, a chemical, biological, or radionuclide release within a building, the VSP module can be used to quickly and easily develop and visualize technically defensible sampling schemes for walls, floors, ceilings, and other surfaces to statistically determine if contamination is present, its magnitude and extent throughout the building and if decontamination has been effective. This paper demonstrates the features of this new VSP buildings module, which include: the ability to import building floor plans or to easily draw, manipulate, and view rooms in several ways; being able to insert doors, windows and annotations into a room; 3-D graphic room views with surfaces labeled and floor plans that show building zones that have separate air handing units. The paper will also discuss the statistical design and data analysis options available in the buildings module. Design objectives supported include comparing an average to a threshold when the data distribution is normal or unknown, and comparing measurements to a threshold to detect hotspots or to insure most of the area is uncontaminated when the data distribution is normal or unknown

  2. 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

  3. 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.

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

    Science.gov (United States)

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

    2017-01-01

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

  5. Organising and learning experiences of the first semester MA Program ePedagogy / Visual Knowledge Building

    NARCIS (Netherlands)

    Jaap Jansen

    2006-01-01

    This paper will discuss the process of the MA program ePedagogy / Visual Knowledge Building during the first semester of the academic year 2005 – 2006. This MA program is a joint venture between the Universities of Helsinki, Hamburg and INHOLLAND. This publication will discuss and evaluate the

  6. Visual assessment of BIPV retrofit design proposals for selected historical buildings using the saliency map method

    Directory of Open Access Journals (Sweden)

    Ran Xu

    2015-06-01

    Full Text Available With the increasing awareness of energy efficiency, many old buildings have to undergo a massive facade energy retrofit. How to predict the visual impact which solar installations on the aesthetic cultural value of these buildings has been a heated debate in Switzerland (and throughout the world. The usual evaluation method to describe the visual impact of BIPV is based on semantic and qualitative descriptors, and strongly dependent on personal preferences. The evaluation scale is therefore relative, flexible and imprecise. This paper proposes a new method to accurately measure the visual impact which BIPV installations have on a historical building by using the saliency map method. By imitating working principles of the human eye, it is measured how much the BIPV design proposals differ from the original building facade in the aspect of attracting human visual attention. The result is directly presented in a quantitative manner, and can be used to compare the fitness of different BIPV design proposals. The measuring process is numeric, objective and more precise.  

  7. 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

  8. 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

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

    Science.gov (United States)

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

  10. The Power of Photographs of Buildings in the Dresden Urban Discourse. Towards a Visual Discourse Analysis

    Directory of Open Access Journals (Sweden)

    Gabriela B. Christmann

    2008-09-01

    Full Text Available "Old Dresden" which is known worldwide as a symbol for inept destruction in World War II stopped existing in its physical form in February 1945. The image of "old Dresden," however, has been maintained in the minds of its citizens. This is as results of the visualization of historical buildings. Buildings are artifacts that can be experienced visually and aesthetically. Thus, it is not surprising that in the context of public discourses they "demand" an appropriate representation in a visual and in an aesthetic respect. In the urban discourse of Dresden the visualization of buildings plays an important role. In the article the author exemplifies her methodical approach to visual discourse analysis. She acts on the assumption that three levels of analyzing images must be taken into consideration: 1. the composition of the image, with its content and design, 2. the context of production and publication, including the horizon of historic events, and 3. the mode of reception, with respect to communicative processes. URN: urn:nbn:de:0114-fqs0803115

  11. Effectiveness of daylighting design and occupant visual satisfaction in a LEED gold laboratory building

    Energy Technology Data Exchange (ETDEWEB)

    Hua, Ying; Oswald, Anne [Department of Design and Environmental Analysis, Cornell University, Ithaca, NY 14853 (United States); Yang, Xiaodi [School of Architecture, Carnegie Mellon University, Pittsburgh, PA 15213 (United States)

    2011-01-15

    Using daylight as primary light source has been widely recognized as an important strategy to reduce building energy demand and enhance indoor environment quality. However, to design and operate a building to make full use of daylight, which is a dynamic light source, to meet diverse occupant needs remains a challenge. This paper reports a post-occupancy study of the visual environment in a laboratory building on a university campus, and puts a spotlight on the building occupants as it examines the effectiveness of the daylighting design and systems integration in creating a visual environment to support occupant comfort and satisfaction while reducing artificial lighting demand. Results show generally high satisfaction with daylit work environment and positive effect of the horizontal shading strategy. Issues about the integration between daylighting and electric lighting systems and level of occupant control are identified and discussed for improving the effectiveness of daylighting and enhancing the quality of the visual environment in the building of study. A multiple-tool methodology is developed and tested, which included occupant surveys, interviews, illuminance measurements, continuous data loggers, fisheye-lens camera and glare-identifying software, and documentation of spatial settings, systems features, and user behavior. (author)

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2017-10-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-10-15

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

  15. 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.

  16. Building capacity for human genetics and genomics research in Trinidad and Tobago

    Directory of Open Access Journals (Sweden)

    Allana Roach

    Full Text Available Advances in human genetics and genomic sciences and the corresponding explosion of biomedical technologies have deepened current understanding of human health and revolutionized medicine. In developed nations, this has led to marked improvements in disease risk stratification and diagnosis. These advances have also led to targeted intervention strategies aimed at promoting disease prevention, prolonging disease onset, and mitigating symptoms, as in the well-known case of breast cancer and the BRCA1 gene. In contrast, in the developing nation of Trinidad and Tobago, this scientific revolution has not translated into the development and application of effective genomics-based interventions for improving public health. While the reasons for this are multifactorial, the underlying basis may be rooted in the lack of pertinence of internationally driven genomics research to the local public health needs in the country, as well as a lack of relevance of internationally conducted genetics research to the genetic and environmental contexts of the population. Indeed, if Trinidad and Tobago is able to harness substantial public health benefit from genetics/genomics research, then there is a dire need, in the near future, to build local capacity for the conduct and translation of such research. Specifically, it is essential to establish a national human genetics/genomics research agenda in order to build sustainable human capacity through education and knowledge transfer and to generate public policies that will provide the basis for the creation of a mutually beneficial framework (including partnerships with more developed nations that is informed by public health needs and contextual realities of the nation.

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

    Science.gov (United States)

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

    2005-04-15

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

  18. Global Appearance Applied to Visual Map Building and Path Estimation Using Multiscale Analysis

    Directory of Open Access Journals (Sweden)

    Francisco Amorós

    2014-01-01

    Full Text Available In this work we present a topological map building and localization system for mobile robots based on global appearance of visual information. We include a comparison and analysis of global-appearance techniques applied to wide-angle scenes in retrieval tasks. Next, we define multiscale analysis, which permits improving the association between images and extracting topological distances. Then, a topological map-building algorithm is proposed. At first, the algorithm has information only of some isolated positions of the navigation area in the form of nodes. Each node is composed of a collection of images that covers the complete field of view from a certain position. The algorithm solves the node retrieval and estimates their spatial arrangement. With these aims, it uses the visual information captured along some routes that cover the navigation area. As a result, the algorithm builds a graph that reflects the distribution and adjacency relations between nodes (map. After the map building, we also propose a route path estimation system. This algorithm takes advantage of the multiscale analysis. The accuracy in the pose estimation is not reduced to the nodes locations but also to intermediate positions between them. The algorithms have been tested using two different databases captured in real indoor environments under dynamic conditions.

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

    Science.gov (United States)

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

    2016-05-01

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

  20. Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences.

    Science.gov (United States)

    Zhang, Jianwei; Kudrna, Dave; Mu, Ting; Li, Weiming; Copetti, Dario; Yu, Yeisoo; Goicoechea, Jose Luis; Lei, Yang; Wing, Rod A

    2016-10-15

    Next generation sequencing technologies have revolutionized our ability to rapidly and affordably generate vast quantities of sequence data. Once generated, raw sequences are assembled into contigs or scaffolds. However, these assemblies are mostly fragmented and inaccurate at the whole genome scale, largely due to the inability to integrate additional informative datasets (e.g. physical, optical and genetic maps). To address this problem, we developed a semi-automated software tool-Genome Puzzle Master (GPM)-that enables the integration of additional genomic signposts to edit and build 'new-gen-assemblies' that result in high-quality 'annotation-ready' pseudomolecules. With GPM, loaded datasets can be connected to each other via their logical relationships which accomplishes tasks to 'group,' 'merge,' 'order and orient' sequences in a draft assembly. Manual editing can also be performed with a user-friendly graphical interface. Final pseudomolecules reflect a user's total data package and are available for long-term project management. GPM is a web-based pipeline and an important part of a Laboratory Information Management System (LIMS) which can be easily deployed on local servers for any genome research laboratory. The GPM (with LIMS) package is available at https://github.com/Jianwei-Zhang/LIMS CONTACTS: jzhang@mail.hzau.edu.cn or rwing@mail.arizona.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  1. Teaching Synthetic Biology, Bioinformatics and Engineering to Undergraduates: The Interdisciplinary Build-a-Genome Course

    Science.gov (United States)

    Dymond, Jessica S.; Scheifele, Lisa Z.; Richardson, Sarah; Lee, Pablo; Chandrasegaran, Srinivasan; Bader, Joel S.; Boeke, Jef D.

    2009-01-01

    A major challenge in undergraduate life science curricula is the continual evaluation and development of courses that reflect the constantly shifting face of contemporary biological research. Synthetic biology offers an excellent framework within which students may participate in cutting-edge interdisciplinary research and is therefore an attractive addition to the undergraduate biology curriculum. This new discipline offers the promise of a deeper understanding of gene function, gene order, and chromosome structure through the de novo synthesis of genetic information, much as synthetic approaches informed organic chemistry. While considerable progress has been achieved in the synthesis of entire viral and prokaryotic genomes, fabrication of eukaryotic genomes requires synthesis on a scale that is orders of magnitude higher. These high-throughput but labor-intensive projects serve as an ideal way to introduce undergraduates to hands-on synthetic biology research. We are pursuing synthesis of Saccharomyces cerevisiae chromosomes in an undergraduate laboratory setting, the Build-a-Genome course, thereby exposing students to the engineering of biology on a genomewide scale while focusing on a limited region of the genome. A synthetic chromosome III sequence was designed, ordered from commercial suppliers in the form of oligonucleotides, and subsequently assembled by students into ∼750-bp fragments. Once trained in assembly of such DNA “building blocks” by PCR, the students accomplish high-yield gene synthesis, becoming not only technically proficient but also constructively critical and capable of adapting their protocols as independent researchers. Regular “lab meeting” sessions help prepare them for future roles in laboratory science. PMID:19015540

  2. Precise photorealistic visualization for restoration of historic buildings based on tacheometry data

    Science.gov (United States)

    Ragia, Lemonia; Sarri, Froso; Mania, Katerina

    2018-03-01

    This paper puts forward a 3D reconstruction methodology applied to the restoration of historic buildings taking advantage of the speed, range and accuracy of a total geodetic station. The measurements representing geo-referenced points produced an interactive and photorealistic geometric mesh of a monument named `Neoria.' `Neoria' is a Venetian building located by the old harbor at Chania, Crete, Greece. The integration of tacheometry acquisition and computer graphics puts forward a novel integrated software framework for the accurate 3D reconstruction of a historical building. The main technical challenge of this work was the production of a precise 3D mesh based on a sufficient number of tacheometry measurements acquired fast and at low cost, employing a combination of surface reconstruction and processing methods. A fully interactive application based on game engine technologies was developed. The user can visualize and walk through the monument and the area around it as well as photorealistically view it at different times of day and night. Advanced interactive functionalities are offered to the user in relation to identifying restoration areas and visualizing the outcome of such works. The user could visualize the coordinates of the points measured, calculate distances and navigate through the complete 3D mesh of the monument. The geographical data are stored in a database connected with the application. Features referencing and associating the database with the monument are developed. The goal was to utilize a small number of acquired data points and present a fully interactive visualization of a geo-referenced 3D model.

  3. 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.

  4. Development of an exergy-electrical analogy for visualizing and modeling building integrated energy systems

    International Nuclear Information System (INIS)

    Saloux, E.; Teyssedou, A.; Sorin, M.

    2015-01-01

    Highlights: • The exergy-electrical analogy is developed for energy systems used in buildings. • This analogy has been developed for a complete set of system arrangement options. • Different possibilities of inter-connections are illustrated using analog switches. • Adaptability and utility of the diagram over traditional ones are emphasized. - Abstract: An exergy-electrical analogy, similar to the heat transfer electrical one, is developed and applied to the case of integrated energy systems operating in buildings. Its construction is presented for the case of space heating with electric heaters, heat pumps and solar collectors. The proposed analogy has been applied to a set of system arrangement options proposed for satisfying the building heating demand (space heating, domestic hot water); different alternatives to connect the units have been presented with switches in a visualization scheme. The analogy for such situation has been performed and the study of a solar assisted heat pump using ice storage has been investigated. This diagram directly permits energy paths and their associated exergy destruction to be visualized; hence, sources of irreversibility are identifiable. It can be helpful for the comprehension of the global process and its operation as well as for identifying exergy losses. The method used to construct the diagram makes it easily adaptable to others units or structures or to others models depending on the complexity of the process. The use of switches could be very useful for optimization purposes

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

    Science.gov (United States)

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

    2017-12-04

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

  6. GACT: a Genome build and Allele definition Conversion Tool for SNP imputation and meta-analysis in genetic association studies.

    Science.gov (United States)

    Sulovari, Arvis; Li, Dawei

    2014-07-19

    Genome-wide association studies (GWAS) have successfully identified genes associated with complex human diseases. Although much of the heritability remains unexplained, combining single nucleotide polymorphism (SNP) genotypes from multiple studies for meta-analysis will increase the statistical power to identify new disease-associated variants. Meta-analysis requires same allele definition (nomenclature) and genome build among individual studies. Similarly, imputation, commonly-used prior to meta-analysis, requires the same consistency. However, the genotypes from various GWAS are generated using different genotyping platforms, arrays or SNP-calling approaches, resulting in use of different genome builds and allele definitions. Incorrect assumptions of identical allele definition among combined GWAS lead to a large portion of discarded genotypes or incorrect association findings. There is no published tool that predicts and converts among all major allele definitions. In this study, we have developed a tool, GACT, which stands for Genome build and Allele definition Conversion Tool, that predicts and inter-converts between any of the common SNP allele definitions and between the major genome builds. In addition, we assessed several factors that may affect imputation quality, and our results indicated that inclusion of singletons in the reference had detrimental effects while ambiguous SNPs had no measurable effect. Unexpectedly, exclusion of genotypes with missing rate > 0.001 (40% of study SNPs) showed no significant decrease of imputation quality (even significantly higher when compared to the imputation with singletons in the reference), especially for rare SNPs. GACT is a new, powerful, and user-friendly tool with both command-line and interactive online versions that can accurately predict, and convert between any of the common allele definitions and between genome builds for genome-wide meta-analysis and imputation of genotypes from SNP-arrays or deep

  7. Biology and Architecture: Two Buildings Inspired by the Anatomy of the Visual System.

    Science.gov (United States)

    Maro Kiris, Irem

    2018-05-04

    Architectural production has been influenced by a variety of sources. Forms derived from nature, biology and live organisms, had often been utilised in art and architecture. Certain features of the human anatomy had been reflected in design process in various ways, as imitations, abstractions, interpretations of the reality. The correlation of ideal proportions had been investigated throughout centuries. Scholars, art historians starting with Vitruvius from the world of ancient Roman architecture, described the human figure as being the principal source of proportion among the classical orders of architecture. This study aims to investigate two contemporary buildings, namely Kiasma Museum in Helsinki and Eye Museum in Amsterdam, inspired directly from the anatomy of visual system. Morover the author discussed the relationship of biology and architecture through these two special buildings by viewing the eye and chiasma as metaphors for elements of architecture.

  8. Interlocking Toy Building Blocks as Hands-On Learning Modules for Blind and Visually Impaired Chemistry Students

    Science.gov (United States)

    Melaku, Samuel; Schreck, James O.; Griffin, Kameron; Dabke, Rajeev B.

    2016-01-01

    Interlocking toy building blocks (e.g., Lego) as chemistry learning modules for blind and visually impaired (BVI) students in high school and undergraduate introductory or general chemistry courses are presented. Building blocks were assembled on a baseplate to depict the relative changes in the periodic properties of elements. Modules depicting…

  9. Methods and means for building a system of visual images forming in gis of critical important objects protection

    Directory of Open Access Journals (Sweden)

    Mykhailo Vasiukhin

    2013-12-01

    Full Text Available Requirements for the visualization of dynamic scenes in security systems for are increasing in recent years. This requires develop a methods and tools for visualization of dynamic scenes for monitoring and managing the system of security like “human-operator”. The paper presents a model map data from which is a base for building real time map data, and methods of real time visualization of moving characters in air.

  10. CALCULATING SOLAR ENERGY POTENTIAL OF BUILDINGS AND VISUALIZATION WITHIN UNITY 3D GAME ENGINE

    Directory of Open Access Journals (Sweden)

    G. Buyuksalih

    2017-10-01

    Full Text Available Solar energy modelling is increasingly popular, important, and economic significant in solving energy crisis for big cities. It is a clean and renewable resource of energy that can be utilized to accommodate individual or group of buildings electrical power as well as for indoor heating. Implementing photovoltaic system (PV in urban areas is one of the best options to solve power crisis over expansion of urban and the growth of population. However, as the spaces for solar panel installation in cities are getting limited nowadays, the available strategic options are only at the rooftop and façade of the building. Thus, accurate information and selecting building with the highest potential solar energy amount collected is essential in energy planning, environmental conservation, and sustainable development of the city. Estimating the solar energy/radiation from rooftop and facade are indeed having a limitation - the shadows from other neighbouring buildings. The implementation of this solar estimation project for Istanbul uses CityGML LoD2-LoD3. The model and analyses were carried out using Unity 3D Game engine with development of several customized tools and functionalities. The results show the estimation of potential solar energy received for the whole area per day, week, month and year thus decision for installing the solar panel could be made. We strongly believe the Unity game engine platform could be utilized for near future 3D mapping visualization purposes.

  11. Calculating Solar Energy Potential of Buildings and Visualization Within Unity 3d Game Engine

    Science.gov (United States)

    Buyuksalih, G.; Bayburt, S.; Baskaraca, A. P.; Karim, H.; Rahman, A. Abdul

    2017-10-01

    Solar energy modelling is increasingly popular, important, and economic significant in solving energy crisis for big cities. It is a clean and renewable resource of energy that can be utilized to accommodate individual or group of buildings electrical power as well as for indoor heating. Implementing photovoltaic system (PV) in urban areas is one of the best options to solve power crisis over expansion of urban and the growth of population. However, as the spaces for solar panel installation in cities are getting limited nowadays, the available strategic options are only at the rooftop and façade of the building. Thus, accurate information and selecting building with the highest potential solar energy amount collected is essential in energy planning, environmental conservation, and sustainable development of the city. Estimating the solar energy/radiation from rooftop and facade are indeed having a limitation - the shadows from other neighbouring buildings. The implementation of this solar estimation project for Istanbul uses CityGML LoD2-LoD3. The model and analyses were carried out using Unity 3D Game engine with development of several customized tools and functionalities. The results show the estimation of potential solar energy received for the whole area per day, week, month and year thus decision for installing the solar panel could be made. We strongly believe the Unity game engine platform could be utilized for near future 3D mapping visualization purposes.

  12. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

    Energy Technology Data Exchange (ETDEWEB)

    Brettin, Thomas; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Thomason, James A.; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang

    2015-02-10

    The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

  13. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes.

    Science.gov (United States)

    Brettin, Thomas; Davis, James J; Disz, Terry; Edwards, Robert A; Gerdes, Svetlana; Olsen, Gary J; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D; Shukla, Maulik; Thomason, James A; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R; Xia, Fangfang

    2015-02-10

    The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

  14. The visual-landscape analysis during the integration of high-rise buildings within the historic urban environment

    Science.gov (United States)

    Akristiniy, Vera A.; Dikova, Elena A.

    2018-03-01

    The article is devoted to one of the types of urban planning studies - the visual-landscape analysis during the integration of high-rise buildings within the historic urban environment for the purposes of providing pre-design and design studies in terms of preserving the historical urban environment and the implementation of the reconstructional resource of the area. In the article formed and systematized the stages and methods of conducting the visual-landscape analysis taking into account the influence of high-rise buildings on objects of cultural heritage and valuable historical buildings of the city. Practical application of the visual-landscape analysis provides an opportunity to assess the influence of hypothetical location of high-rise buildings on the perception of a historically developed environment and optimal building parameters. The contents of the main stages in the conduct of the visual - landscape analysis and their key aspects, concerning the construction of predicted zones of visibility of the significant historically valuable urban development objects and hypothetically planned of the high-rise buildings are revealed. The obtained data are oriented to the successive development of the planning and typological structure of the city territory and preservation of the compositional influence of valuable fragments of the historical environment in the structure of the urban landscape. On their basis, an information database is formed to determine the permissible urban development parameters of the high-rise buildings for the preservation of the compositional integrity of the urban area.

  15. The visual-landscape analysis during the integration of high-rise buildings within the historic urban environment

    Directory of Open Access Journals (Sweden)

    Akristiniy Vera A.

    2018-01-01

    Full Text Available The article is devoted to one of the types of urban planning studies - the visual-landscape analysis during the integration of high-rise buildings within the historic urban environment for the purposes of providing pre-design and design studies in terms of preserving the historical urban environment and the implementation of the reconstructional resource of the area. In the article formed and systematized the stages and methods of conducting the visual-landscape analysis taking into account the influence of high-rise buildings on objects of cultural heritage and valuable historical buildings of the city. Practical application of the visual-landscape analysis provides an opportunity to assess the influence of hypothetical location of high-rise buildings on the perception of a historically developed environment and optimal building parameters. The contents of the main stages in the conduct of the visual - landscape analysis and their key aspects, concerning the construction of predicted zones of visibility of the significant historically valuable urban development objects and hypothetically planned of the high-rise buildings are revealed. The obtained data are oriented to the successive development of the planning and typological structure of the city territory and preservation of the compositional influence of valuable fragments of the historical environment in the structure of the urban landscape. On their basis, an information database is formed to determine the permissible urban development parameters of the high-rise buildings for the preservation of the compositional integrity of the urban area.

  16. HPIminer: A text mining system for building and visualizing human protein interaction networks and pathways.

    Science.gov (United States)

    Subramani, Suresh; Kalpana, Raja; Monickaraj, Pankaj Moses; Natarajan, Jeyakumar

    2015-04-01

    The knowledge on protein-protein interactions (PPI) and their related pathways are equally important to understand the biological functions of the living cell. Such information on human proteins is highly desirable to understand the mechanism of several diseases such as cancer, diabetes, and Alzheimer's disease. Because much of that information is buried in biomedical literature, an automated text mining system for visualizing human PPI and pathways is highly desirable. In this paper, we present HPIminer, a text mining system for visualizing human protein interactions and pathways from biomedical literature. HPIminer extracts human PPI information and PPI pairs from biomedical literature, and visualize their associated interactions, networks and pathways using two curated databases HPRD and KEGG. To our knowledge, HPIminer is the first system to build interaction networks from literature as well as curated databases. Further, the new interactions mined only from literature and not reported earlier in databases are highlighted as new. A comparative study with other similar tools shows that the resultant network is more informative and provides additional information on interacting proteins and their associated networks. Copyright © 2015 Elsevier Inc. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Genco Alex

    2011-07-01

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

  18. 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.

  19. Building University Capacity to Visualize Solutions to Complex Problems in the Arctic

    Science.gov (United States)

    Broderson, D.; Veazey, P.; Raymond, V. L.; Kowalski, K.; Prakash, A.; Signor, B.

    2016-12-01

    Rapidly changing environments are creating complex problems across the globe, which are particular magnified in the Arctic. These worldwide challenges can best be addressed through diverse and interdisciplinary research teams. It is incumbent on such teams to promote co-production of knowledge and data-driven decision-making by identifying effective methods to communicate their findings and to engage with the public. Decision Theater North (DTN) is a new semi-immersive visualization system that provides a space for teams to collaborate and develop solutions to complex problems, relying on diverse sets of skills and knowledge. It provides a venue to synthesize the talents of scientists, who gather information (data); modelers, who create models of complex systems; artists, who develop visualizations; communicators, who connect and bridge populations; and policymakers, who can use the visualizations to develop sustainable solutions to pressing problems. The mission of Decision Theater North is to provide a cutting-edge visual environment to facilitate dialogue and decision-making by stakeholders including government, industry, communities and academia. We achieve this mission by adopting a multi-faceted approach reflected in the theater's design, technology, networking capabilities, user support, community relationship building, and strategic partnerships. DTN is a joint project of Alaska's National Science Foundation Experimental Program to Stimulate Competitive Research (NSF EPSCoR) and the University of Alaska Fairbanks (UAF), who have brought the facility up to full operational status and are now expanding its development space to support larger team science efforts. Based in Fairbanks, Alaska, DTN is uniquely poised to address changes taking place in the Arctic and subarctic, and is connected with a larger network of decision theaters that include the Arizona State University Decision Theater Network and the McCain Institute in Washington, DC.

  20. 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.

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

    Science.gov (United States)

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

    2017-01-06

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

  2. The visual-landscape analysis during the integration of high-rise buildings within the historic urban environment

    OpenAIRE

    Akristiniy Vera A.; Dikova Elena A.

    2018-01-01

    The article is devoted to one of the types of urban planning studies - the visual-landscape analysis during the integration of high-rise buildings within the historic urban environment for the purposes of providing pre-design and design studies in terms of preserving the historical urban environment and the implementation of the reconstructional resource of the area. In the article formed and systematized the stages and methods of conducting the visual-landscape analysis taking into account t...

  3. Exploring the building blocks of social cognition: spontaneous agency perception and visual perspective taking in autism.

    Science.gov (United States)

    Zwickel, Jan; White, Sarah J; Coniston, Devorah; Senju, Atsushi; Frith, Uta

    2011-10-01

    Individuals with autism spectrum disorders have highly characteristic impairments in social interaction and this is true also for those with high functioning autism or Asperger syndrome (AS). These social cognitive impairments are far from global and it seems likely that some of the building blocks of social cognition are intact. In our first experiment, we investigated whether high functioning adults who also had a diagnosis of AS would be similar to control participants in terms of their eye movements when watching animated triangles in short movies that normally evoke mentalizing. They were. Our second experiment using the same movies, tested whether both groups would spontaneously adopt the visuo-spatial perspective of a triangle protagonist. They did. At the same time autistic participants differed in their verbal accounts of the story line underlying the movies, confirming their specific difficulties in on-line mentalizing. In spite of this difficulty, two basic building blocks of social cognition appear to be intact: spontaneous agency perception and spontaneous visual perspective taking.

  4. Building

    OpenAIRE

    Seavy, Ryan

    2014-01-01

    Building for concrete is temporary. The building of wood and steel stands against the concrete to give form and then gives way, leaving a trace of its existence behind. Concrete is not a building material. One does not build with concrete. One builds for concrete. MARCH

  5. D Visualization of a Timber Frame Historic Building: Partite Usage and its Impact on the Structural System

    Science.gov (United States)

    Günay, S.

    2017-08-01

    Throughout their lifetime, historic buildings might be altered for different kind of usage for different purposes. If this new function or new usage requires utilization of the building in separate units, this separation might affect the historic building's functionality and structure and as a result its overall condition. Yorguc Pasa Mansion conservation project was prepared as a part of the Middle East Technical University (METU) Master's Program in Documentation and Conservation of Historic Monuments and Sites for the historic Yorguc Pasa Mansion. The mansion is a 19th century Ottoman Period timber frame building in Amasya, a Black Sea Region city in Turkey that has traces from different civilizations such as Hittites, Greeks, Romans and Ottomans. This paper aims to discuss the affects of the partite usage on structural conditions of timber frame buildings with the case study of Amasya Yorguc Pasa Mansion through the 3D visualized structural systems.

  6. 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.

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

    Science.gov (United States)

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

    2017-01-01

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

  8. 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.

  9. 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.

  10. A stochastic de novo assembly algorithm for viral-sized genomes obtains correct genomes and builds consensus

    NARCIS (Netherlands)

    Bucur, Doina

    2017-01-01

    A genetic algorithm with stochastic macro mutation operators which merge, split, move, reverse and align DNA contigs on a scaffold is shown to accurately and consistently assemble raw DNA reads from an accurately sequenced single-read library into a contiguous genome. A candidate solution is a

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

    Science.gov (United States)

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

    2007-10-06

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

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

    Directory of Open Access Journals (Sweden)

    Joyce Xiuweu-Xu Gu

    2007-01-01

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

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

    Science.gov (United States)

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

    2013-07-02

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

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

    Science.gov (United States)

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

    2013-01-01

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

  15. Advances in Multi-Sensor Scanning and Visualization of Complex Plants: the Utmost Case of a Reactor Building

    Science.gov (United States)

    Hullo, J.-F.; Thibault, G.; Boucheny, C.

    2015-02-01

    In a context of increased maintenance operations and workers generational renewal, a nuclear owner and operator like Electricité de France (EDF) is interested in the scaling up of tools and methods of "as-built virtual reality" for larger buildings and wider audiences. However, acquisition and sharing of as-built data on a large scale (large and complex multi-floored buildings) challenge current scientific and technical capacities. In this paper, we first present a state of the art of scanning tools and methods for industrial plants with very complex architecture. Then, we introduce the inner characteristics of the multi-sensor scanning and visualization of the interior of the most complex building of a power plant: a nuclear reactor building. We introduce several developments that made possible a first complete survey of such a large building, from acquisition, processing and fusion of multiple data sources (3D laser scans, total-station survey, RGB panoramic, 2D floor plans, 3D CAD as-built models). In addition, we present the concepts of a smart application developed for the painless exploration of the whole dataset. The goal of this application is to help professionals, unfamiliar with the manipulation of such datasets, to take into account spatial constraints induced by the building complexity while preparing maintenance operations. Finally, we discuss the main feedbacks of this large experiment, the remaining issues for the generalization of such large scale surveys and the future technical and scientific challenges in the field of industrial "virtual reality".

  16. Design of intelligent power consumption optimization and visualization management platform for large buildings based on internet of things

    Directory of Open Access Journals (Sweden)

    Gong Shulan

    2017-01-01

    Full Text Available The buildings provide a significant contribution to total energy consumption and CO2 emission. It has been estimated that the development of an intelligent power consumption monitor and control system will result in about 30% savings in energy consumption. This design innovatively integrates the advanced technologies such as the internet of things, the internet, intelligent buildings and intelligent electricity which can offer open, efficient, convenient energy consumption detection platform in demand side and visual management demonstration application platform in power enterprises side. The system was created to maximize the effective and efficient the use of energy resource. It was development around sensor networks and intelligent gateway and the monitoring center software. This will realize the highly integration and comprehensive application in energy and information to meet the needs with intelligent buildings

  17. BRANDING AND IDENTITY BUILDING FOR A SMALL COMPANY : Focused on Visual Identity

    OpenAIRE

    Näveri, Mattea

    2015-01-01

    The topic of this thesis is branding and identity of a small business, with a focus on visual identity. The major part of this thesis focuses on the research done on visual identity and the basic ideation of branding. The other half specifically focuses on the visual identity, the creation of a logo for the company, defining typography and colour and ephemera, and particularly, the company’s business card. The main goal was to execute a unique, individualized branding, which showcases...

  18. Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database.

    Science.gov (United States)

    Allard, Marc W; Strain, Errol; Melka, David; Bunning, Kelly; Musser, Steven M; Brown, Eric W; Timme, Ruth

    2016-08-01

    The FDA has created a United States-based open-source whole-genome sequencing network of state, federal, international, and commercial partners. The GenomeTrakr network represents a first-of-its-kind distributed genomic food shield for characterizing and tracing foodborne outbreak pathogens back to their sources. The GenomeTrakr network is leading investigations of outbreaks of foodborne illnesses and compliance actions with more accurate and rapid recalls of contaminated foods as well as more effective monitoring of preventive controls for food manufacturing environments. An expanded network would serve to provide an international rapid surveillance system for pathogen traceback, which is critical to support an effective public health response to bacterial outbreaks. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  19. 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

  20. Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies.

    Science.gov (United States)

    Sharma, Deepak K; Solbrig, Harold R; Tao, Cui; Weng, Chunhua; Chute, Christopher G; Jiang, Guoqian

    2017-06-05

    Detailed Clinical Models (DCMs) have been regarded as the basis for retaining computable meaning when data are exchanged between heterogeneous computer systems. To better support clinical cancer data capturing and reporting, there is an emerging need to develop informatics solutions for standards-based clinical models in cancer study domains. The objective of the study is to develop and evaluate a cancer genome study metadata management system that serves as a key infrastructure in supporting clinical information modeling in cancer genome study domains. We leveraged a Semantic Web-based metadata repository enhanced with both ISO11179 metadata standard and Clinical Information Modeling Initiative (CIMI) Reference Model. We used the common data elements (CDEs) defined in The Cancer Genome Atlas (TCGA) data dictionary, and extracted the metadata of the CDEs using the NCI Cancer Data Standards Repository (caDSR) CDE dataset rendered in the Resource Description Framework (RDF). The ITEM/ITEM_GROUP pattern defined in the latest CIMI Reference Model is used to represent reusable model elements (mini-Archetypes). We produced a metadata repository with 38 clinical cancer genome study domains, comprising a rich collection of mini-Archetype pattern instances. We performed a case study of the domain "clinical pharmaceutical" in the TCGA data dictionary and demonstrated enriched data elements in the metadata repository are very useful in support of building detailed clinical models. Our informatics approach leveraging Semantic Web technologies provides an effective way to build a CIMI-compliant metadata repository that would facilitate the detailed clinical modeling to support use cases beyond TCGA in clinical cancer study domains.

  1. Appearance Principles of High Rise Buildings in the City Center: Visual Efect to Historical Heritage, Regulation Proposals

    Directory of Open Access Journals (Sweden)

    Lina Panavaitė

    2016-04-01

    Full Text Available High rise buildings is the phenomenon of XXI century, the expression of city’s economic and political power. This is the reflection of contemporary, modern and attractive city. Very often high rise buildings, who are characterized by a unique morphology, the parameters of high, density and intensity, are built near the historic center areas and cause irreversible visual impact on the historic sites, fundamentally altering the silhouette of the city. As a result, new problems and challenges appear. In this article the evolution of high rise buildings according to London, Jerusalem, Ottawa, Vilnius cities examples is analysed, the latest methodological principles which are applicable to control the development of high-rise buildings in the central parts of the city, while providing preservation and representation of cultural heritage are discussed. The latest computer technologies which are applied in urban regulations are presented. In case of Lithuania, high-rise building spatial development, general, spatial planning documents, urban design concepts, and monitoring of virtual city panoramas are reviewed. Comparative analysis in order to find out the essential methodological differences between cities regulation systems is done.

  2. Wrocław as a European Capital of Culture 2016. Brand Building on Facebook. Visual Identification

    Directory of Open Access Journals (Sweden)

    Urszula Wich-Szymczak

    2017-03-01

    Full Text Available The article contains research in two fields of image building. The first is describing general thoughts about city marketing communication, brand building and current trends in this area. Author pays attention to the aesthetics issue, that creates the possibility for different organizations to affect their audience through a whole range of sensory stimulators, thereby creating the conditions of mutual satisfaction. Then the author tries to answer the questions: what should be done to make the city brand exist in consumers' minds in the twenty-first century? How to exist in virtual reality without visual identification? Next step is to overview the book of visual identification of Wrocław ECOC. The second area of interest is cumulated around image building on official Facebook profile of Wroclaw ECOC. It is a platform for opinion exchange. Its focuses on a fourfold type of creation: creation of the individual, creation of the organization, creation of the company, and finally creation of the brand.

  3. 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...

  4. Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals.

    KAUST Repository

    Bayer, Till; Aranda, Manuel; Sunagawa, Shinichi; Yum, Lauren K; Desalvo, Michael K; Lindquist, Erika; Coffroth, Mary Alice; Voolstra, Christian R.; Medina, Mó nica

    2012-01-01

    Dinoflagellates are unicellular algae that are ubiquitously abundant in aquatic environments. Species of the genus Symbiodinium form symbiotic relationships with reef-building corals and other marine invertebrates. Despite their ecologic importance

  5. Building a complete image of genome regulation in the model organism Escherichia coli.

    Science.gov (United States)

    Ishihama, Akira

    2018-01-15

    The model organism, Escherichia coli, contains a total of more than 4,500 genes, but the total number of RNA polymerase (RNAP) core enzyme or the transcriptase is only about 2,000 molecules per genome. The regulatory targets of RNAP are, however, modulated by changing its promoter selectivity through two-steps of protein-protein interplay with 7 species of the sigma factor in the first step, and then 300 species of the transcription factor (TF) in the second step. Scientists working in the field of prokaryotic transcription in Japan have made considerable contributions to the elucidation of genetic frameworks and regulatory modes of the genome transcription in E. coli K-12. This review summarizes the findings by this group, first focusing on three sigma factors, the stationary-phase sigma RpoS, the heat-shock sigma RpoH, and the flagellar-chemotaxis sigma RpoF, as examples. It also presents an overview of the current state of the systematic research being carried out to identify the regulatory functions of all TFs from a single and the same bacterium E. coli K-12, using the genomic SELEX and PS-TF screening systems. All these studies have been undertaken with the aim of understanding the genome regulation in E. coli K-12 as a whole.

  6. Building on the Past, Shaping the Future: The Environmental Mutagenesis and Genomics Society

    Science.gov (United States)

    In late 2012 the members of the Environmental Mutagen Society voted to change its name to the Environmental Mutagenesis and Genomics Society. Here we describe the thought process that led to adoption of the new name, which both respects the rich history of a Society founded in 19...

  7. Building effective learning experiences around visualizations: NASA Eyes on the Solar System and Infiniscope

    Science.gov (United States)

    Tamer, A. J. J.; Anbar, A. D.; Elkins-Tanton, L. T.; Klug Boonstra, S.; Mead, C.; Swann, J. L.; Hunsley, D.

    2017-12-01

    Advances in scientific visualization and public access to data have transformed science outreach and communication, but have yet to realize their potential impacts in the realm of education. Computer-based learning is a clear bridge between visualization and education, but creating high-quality learning experiences that leverage existing visualizations requires close partnerships among scientists, technologists, and educators. The Infiniscope project is working to foster such partnerships in order to produce exploration-driven learning experiences around NASA SMD data and images, leveraging the principles of ETX (Education Through eXploration). The visualizations inspire curiosity, while the learning design promotes improved reasoning skills and increases understanding of space science concepts. Infiniscope includes both a web portal to host these digital learning experiences, as well as a teaching network of educators using and modifying these experiences. Our initial efforts to enable student discovery through active exploration of the concepts associated with Small Worlds, Kepler's Laws, and Exoplanets led us to develop our own visualizations at Arizona State University. Other projects focused on Astrobiology and Mars geology led us to incorporate an immersive Virtual Field Trip platform into the Infiniscope portal in support of virtual exploration of scientifically significant locations. Looking to apply ETX design practices with other visualizations, our team at Arizona State partnered with the Jet Propulsion Lab to integrate the web-based version of NASA Eyes on the Eclipse within Smart Sparrow's digital learning platform in a proof-of-concept focused on the 2017 Eclipse. This goes a step beyond the standard features of "Eyes" by wrapping guided exploration, focused on a specific learning goal into standards-aligned lesson built around the visualization, as well as its distribution through Infiniscope and it's digital teaching network. Experience from this

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

    Science.gov (United States)

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

    2017-09-01

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

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

    Science.gov (United States)

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

    2014-04-15

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

  10. Genomic similarity and kernel methods I: advancements by building on mathematical and statistical foundations.

    Science.gov (United States)

    Schaid, Daniel J

    2010-01-01

    Measures of genomic similarity are the basis of many statistical analytic methods. We review the mathematical and statistical basis of similarity methods, particularly based on kernel methods. A kernel function converts information for a pair of subjects to a quantitative value representing either similarity (larger values meaning more similar) or distance (smaller values meaning more similar), with the requirement that it must create a positive semidefinite matrix when applied to all pairs of subjects. This review emphasizes the wide range of statistical methods and software that can be used when similarity is based on kernel methods, such as nonparametric regression, linear mixed models and generalized linear mixed models, hierarchical models, score statistics, and support vector machines. The mathematical rigor for these methods is summarized, as is the mathematical framework for making kernels. This review provides a framework to move from intuitive and heuristic approaches to define genomic similarities to more rigorous methods that can take advantage of powerful statistical modeling and existing software. A companion paper reviews novel approaches to creating kernels that might be useful for genomic analyses, providing insights with examples [1]. Copyright © 2010 S. Karger AG, Basel.

  11. Conservation genomics of natural and managed populations: building a conceptual and practical framework.

    Science.gov (United States)

    Benestan, Laura Marilyn; Ferchaud, Anne-Laure; Hohenlohe, Paul A; Garner, Brittany A; Naylor, Gavin J P; Baums, Iliana Brigitta; Schwartz, Michael K; Kelley, Joanna L; Luikart, Gordon

    2016-07-01

    The boom of massive parallel sequencing (MPS) technology and its applications in conservation of natural and managed populations brings new opportunities and challenges to meet the scientific questions that can be addressed. Genomic conservation offers a wide range of approaches and analytical techniques, with their respective strengths and weaknesses that rely on several implicit assumptions. However, finding the most suitable approaches and analysis regarding our scientific question are often difficult and time-consuming. To address this gap, a recent workshop entitled 'ConGen 2015' was held at Montana University in order to bring together the knowledge accumulated in this field and to provide training in conceptual and practical aspects of data analysis applied to the field of conservation and evolutionary genomics. Here, we summarize the expertise yield by each instructor that has led us to consider the importance of keeping in mind the scientific question from sampling to management practices along with the selection of appropriate genomics tools and bioinformatics challenges. © 2016 John Wiley & Sons Ltd.

  12. 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,

  13. Visualization and quantification of weathering effects on capillary water uptake of natural building stones by using neutron imaging

    International Nuclear Information System (INIS)

    Raneri, Simona; Barone, Germana; Mazzoleni, Paolo; Rabot, Eva

    2016-01-01

    Building stones are frequently subjected to very intense degradation due to salt crystallization, often responsible for strong modifications of their pore network. These effects have a great influence on the mechanical properties and durability of the materials, and on the penetration of water. Therefore, the quantification and visualization of water absorption into the pore network of degraded stones could provide useful information to better understand the weathering process. In this study, neutron radiography has been used (1) to monitor and visualize in two dimensions the capillary water uptake in a Sicilian calcarenite widely used as building and replace stone (namely Sabucina stone) and (2) to quantify the water content distribution, as a function of time and weathering degree. Additionally, traditional experiments based on gravimetric methods have been performed, following the standard recommendations. Results demonstrated a change in the physical properties of Sabucina stones with the intensification of the degradation process, with severe effects on the capillary imbibition dynamics. The water penetration depth at the end of the experiment was substantially higher in the fresh than in the weathered stones. The water absorption kinetics was faster in the weathered samples, and the amount of water absorbed increased with the number of weathering cycles. Good agreement between classical and neutron imaging data has also been evidenced. However, neutron radiography has allowed retrieving additional spatial information on the water absorption process, and to better understand how salt weathering affects the petrophysical properties of the studied stone and how it influences then the stone response against water. (orig.)

  14. Visualization and quantification of weathering effects on capillary water uptake of natural building stones by using neutron imaging

    Energy Technology Data Exchange (ETDEWEB)

    Raneri, Simona; Barone, Germana; Mazzoleni, Paolo [University of Catania, Department of Biological, Geological and Environment Sciences, Catania (Italy); Rabot, Eva [Laboratoire Leon Brillouin (CNRS/CEA), Gif-Sur-Yvette (France)

    2016-11-15

    Building stones are frequently subjected to very intense degradation due to salt crystallization, often responsible for strong modifications of their pore network. These effects have a great influence on the mechanical properties and durability of the materials, and on the penetration of water. Therefore, the quantification and visualization of water absorption into the pore network of degraded stones could provide useful information to better understand the weathering process. In this study, neutron radiography has been used (1) to monitor and visualize in two dimensions the capillary water uptake in a Sicilian calcarenite widely used as building and replace stone (namely Sabucina stone) and (2) to quantify the water content distribution, as a function of time and weathering degree. Additionally, traditional experiments based on gravimetric methods have been performed, following the standard recommendations. Results demonstrated a change in the physical properties of Sabucina stones with the intensification of the degradation process, with severe effects on the capillary imbibition dynamics. The water penetration depth at the end of the experiment was substantially higher in the fresh than in the weathered stones. The water absorption kinetics was faster in the weathered samples, and the amount of water absorbed increased with the number of weathering cycles. Good agreement between classical and neutron imaging data has also been evidenced. However, neutron radiography has allowed retrieving additional spatial information on the water absorption process, and to better understand how salt weathering affects the petrophysical properties of the studied stone and how it influences then the stone response against water. (orig.)

  15. A visual information tool for user participation during the lifecycle of school building design: BIM

    NARCIS (Netherlands)

    Koutamanis, Alexandros; Heuer, Jos; Könings, Karen D.

    2017-01-01

    User participation is a key element in decision processes concerning the accommodation of dynamic organisations such as schools. This article addresses the discrepancy between the perspectives of the architects and engineers, as the makers of school buildings, and school management, teachers and

  16. Environmental assessment for the proposed construction and operation of a Genome Sequencing Facility in Building 64 at Lawrence Berkeley Laboratory, Berkeley, California

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-04-01

    This document is an Environmental Assessment (EA) for a proposed project to modify 14,900 square feet of an existing building (Building 64) at Lawrence Berkeley Laboratory (LBL) to operate as a Genome Sequencing Facility. This EA addresses the potential environmental impacts from the proposed modifications to Building 64 and operation of the Genome Sequencing Facility. The proposed action is to modify Building 64 to provide space and equipment allowing LBL to demonstrate that the Directed DNA Sequencing Strategy can be scaled up from the current level of 750,000 base pairs per year to a facility that produces over 6,000,000 base pairs per year, while still retaining its efficiency.

  17. Applying Open Source Game Engine for Building Visual Simulation Training System of Fire Fighting

    Science.gov (United States)

    Yuan, Diping; Jin, Xuesheng; Zhang, Jin; Han, Dong

    There's a growing need for fire departments to adopt a safe and fair method of training to ensure that the firefighting commander is in a position to manage a fire incident. Visual simulation training systems, with their ability to replicate and interact with virtual fire scenarios through the use of computer graphics or VR, become an effective and efficient method for fire ground education. This paper describes the system architecture and functions of a visual simulated training system of fire fighting on oil storage, which adopting Delat3D, a open source game and simulation engine, to provide realistic 3D views. It presents that using open source technology provides not only the commercial-level 3D effects but also a great reduction of cost.

  18. Unlocking User-Centered Design Methods for Building Cyber Security Visualizations

    Science.gov (United States)

    2015-10-03

    3, 10, 24, 25, 30]. Personas are doc- uments meant to foster communication within a design team as archetypes of users, their behaviors, and their...to evaluation, these two user archetypes became the key motivation to justify and balance all our decisions as a design team. Outcomes We present the...domain-specific task for each archetypal user and visually illustrated the user’s cyber knowl- edge and situational awareness (SA) focus. We also

  19. Biomedical visual data analysis to build an intelligent diagnostic decision support system in medical genetics.

    Science.gov (United States)

    Kuru, Kaya; Niranjan, Mahesan; Tunca, Yusuf; Osvank, Erhan; Azim, Tayyaba

    2014-10-01

    In general, medical geneticists aim to pre-diagnose underlying syndromes based on facial features before performing cytological or molecular analyses where a genotype-phenotype interrelation is possible. However, determining correct genotype-phenotype interrelationships among many syndromes is tedious and labor-intensive, especially for extremely rare syndromes. Thus, a computer-aided system for pre-diagnosis can facilitate effective and efficient decision support, particularly when few similar cases are available, or in remote rural districts where diagnostic knowledge of syndromes is not readily available. The proposed methodology, visual diagnostic decision support system (visual diagnostic DSS), employs machine learning (ML) algorithms and digital image processing techniques in a hybrid approach for automated diagnosis in medical genetics. This approach uses facial features in reference images of disorders to identify visual genotype-phenotype interrelationships. Our statistical method describes facial image data as principal component features and diagnoses syndromes using these features. The proposed system was trained using a real dataset of previously published face images of subjects with syndromes, which provided accurate diagnostic information. The method was tested using a leave-one-out cross-validation scheme with 15 different syndromes, each of comprised 5-9 cases, i.e., 92 cases in total. An accuracy rate of 83% was achieved using this automated diagnosis technique, which was statistically significant (pbenefits of using hybrid image processing and ML-based computer-aided diagnostics for identifying facial phenotypes. Copyright © 2014. Published by Elsevier B.V.

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

    OpenAIRE

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

    2013-01-01

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

  1. The indoor environment of a modern museum building, the Sainsbury Centre for Visual Arts, Norwich, UK.

    Science.gov (United States)

    Brimblecombe, P; Blades, N; Camuffo, D; Sturaro, G; Valentino, A; Gysels, K; Van Grieken, R; Busse, H J; Kim, O; Ulrych, U; Wieser, M

    1999-09-01

    A multi-disciplinary approach was used to investigate the indoor environment of a modern museum building, and its suitability for the conservation of the collection therein. Climate, gaseous and particulate pollution and the concentrations of bacteria were measured in summer and winter campaigns. While the environment overall was found to be an acceptable one, a number of drawbacks were highlighted, the most serious of these being the large temperature and humidity fluctuations that occurred in the summer.

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

    NARCIS (Netherlands)

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

    2017-01-01

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

  3. BUILDING A BILLION SPATIO-TEMPORAL OBJECT SEARCH AND VISUALIZATION PLATFORM

    Directory of Open Access Journals (Sweden)

    D. Kakkar

    2017-10-01

    Full Text Available With funding from the Sloan Foundation and Harvard Dataverse, the Harvard Center for Geographic Analysis (CGA has developed a prototype spatio-temporal visualization platform called the Billion Object Platform or BOP. The goal of the project is to lower barriers for scholars who wish to access large, streaming, spatio-temporal datasets. The BOP is now loaded with the latest billion geo-tweets, and is fed a real-time stream of about 1 million tweets per day. The geo-tweets are enriched with sentiment and census/admin boundary codes when they enter the system. The system is open source and is currently hosted on Massachusetts Open Cloud (MOC, an OpenStack environment with all components deployed in Docker orchestrated by Kontena. This paper will provide an overview of the BOP architecture, which is built on an open source stack consisting of Apache Lucene, Solr, Kafka, Zookeeper, Swagger, scikit-learn, OpenLayers, and AngularJS. The paper will further discuss the approach used for harvesting, enriching, streaming, storing, indexing, visualizing and querying a billion streaming geo-tweets.

  4. Building a Billion Spatio-Temporal Object Search and Visualization Platform

    Science.gov (United States)

    Kakkar, D.; Lewis, B.

    2017-10-01

    With funding from the Sloan Foundation and Harvard Dataverse, the Harvard Center for Geographic Analysis (CGA) has developed a prototype spatio-temporal visualization platform called the Billion Object Platform or BOP. The goal of the project is to lower barriers for scholars who wish to access large, streaming, spatio-temporal datasets. The BOP is now loaded with the latest billion geo-tweets, and is fed a real-time stream of about 1 million tweets per day. The geo-tweets are enriched with sentiment and census/admin boundary codes when they enter the system. The system is open source and is currently hosted on Massachusetts Open Cloud (MOC), an OpenStack environment with all components deployed in Docker orchestrated by Kontena. This paper will provide an overview of the BOP architecture, which is built on an open source stack consisting of Apache Lucene, Solr, Kafka, Zookeeper, Swagger, scikit-learn, OpenLayers, and AngularJS. The paper will further discuss the approach used for harvesting, enriching, streaming, storing, indexing, visualizing and querying a billion streaming geo-tweets.

  5. A robust pointer segmentation in biomedical images toward building a visual ontology for biomedical article retrieval

    Science.gov (United States)

    You, Daekeun; Simpson, Matthew; Antani, Sameer; Demner-Fushman, Dina; Thoma, George R.

    2013-01-01

    Pointers (arrows and symbols) are frequently used in biomedical images to highlight specific image regions of interest (ROIs) that are mentioned in figure captions and/or text discussion. Detection of pointers is the first step toward extracting relevant visual features from ROIs and combining them with textual descriptions for a multimodal (text and image) biomedical article retrieval system. Recently we developed a pointer recognition algorithm based on an edge-based pointer segmentation method, and subsequently reported improvements made on our initial approach involving the use of Active Shape Models (ASM) for pointer recognition and region growing-based method for pointer segmentation. These methods contributed to improving the recall of pointer recognition but not much to the precision. The method discussed in this article is our recent effort to improve the precision rate. Evaluation performed on two datasets and compared with other pointer segmentation methods show significantly improved precision and the highest F1 score.

  6. Using Electronic Health Records to Build an Ophthalmologic Data Warehouse and Visualize Patients' Data.

    Science.gov (United States)

    Kortüm, Karsten U; Müller, Michael; Kern, Christoph; Babenko, Alexander; Mayer, Wolfgang J; Kampik, Anselm; Kreutzer, Thomas C; Priglinger, Siegfried; Hirneiss, Christoph

    2017-06-01

    To develop a near-real-time data warehouse (DW) in an academic ophthalmologic center to gain scientific use of increasing digital data from electronic medical records (EMR) and diagnostic devices. Database development. Specific macular clinic user interfaces within the institutional hospital information system were created. Orders for imaging modalities were sent by an EMR-linked picture-archiving and communications system to the respective devices. All data of 325 767 patients since 2002 were gathered in a DW running on an SQL database. A data discovery tool was developed. An exemplary search for patients with age-related macular degeneration, performed cataract surgery, and at least 10 intravitreal (excluding bevacizumab) injections was conducted. Data related to those patients (3 142 204 diagnoses [including diagnoses from other fields of medicine], 720 721 procedures [eg, surgery], and 45 416 intravitreal injections) were stored, including 81 274 optical coherence tomography measurements. A web-based browsing tool was successfully developed for data visualization and filtering data by several linked criteria, for example, minimum number of intravitreal injections of a specific drug and visual acuity interval. The exemplary search identified 450 patients with 516 eyes meeting all criteria. A DW was successfully implemented in an ophthalmologic academic environment to support and facilitate research by using increasing EMR and measurement data. The identification of eligible patients for studies was simplified. In future, software for decision support can be developed based on the DW and its structured data. The improved classification of diseases and semiautomatic validation of data via machine learning are warranted. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Building Envelope Thermal Performance Assessment Using Visual Programming and BIM, based on ETTV requirement of Green Mark and GreenRE

    Directory of Open Access Journals (Sweden)

    Taki Eddine Seghier

    2017-09-01

    Full Text Available Accomplishment of green building design requirements and the achievement of the targeted credit points under a specific green rating system are known to be a task that is very challenging. Building Information Modeling (BIM design process and tools have already made considerable advancements in green building design and performance analysis. However, Green building design process is still lack of tools and workflows that can provide real-time feedback of building sustainability and rating during the design stage. In this paper, a new workflow of green building design assessment and rating is proposed based on the integration of Visual Programing Language (VPL and BIM. Thus, the aim of this study is to develop a BIM-VPL based tool for building envelope design and assessment support. The focus performance metric in this research is building Envelope Thermal Transfer Value (ETTV which is an Energy Efficiency (EE prerequisite requirement (up to 15 credits in both Green Mark and GreenRE rating systems. The development of the tool begins first by creating a generic integration framework between BIM-VPL functionalities and ETTV requirements. Then, data is extracted from the BIM 3D model and managed using Revit, Excel and Dynamo for visual scripting. A sample project consisting of a hypothetical residential building is run and its envelope ETTV performance and rating score are obtained for the validation of the tool. This tool will support project team in building envelope design and assessment by allowing them to select the most appropriate façade configuration according to its performance efficiency and the green rating. Furthermore, this tool serves as proof of concept that building sustainability rating and compliance checking can be automatically processed through customized workflows developed based on BIM and VPL technologies.

  8. 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.

  9. Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals.

    KAUST Repository

    Bayer, Till

    2012-04-18

    Dinoflagellates are unicellular algae that are ubiquitously abundant in aquatic environments. Species of the genus Symbiodinium form symbiotic relationships with reef-building corals and other marine invertebrates. Despite their ecologic importance, little is known about the genetics of dinoflagellates in general and Symbiodinium in particular. Here, we used 454 sequencing to generate transcriptome data from two Symbiodinium species from different clades (clade A and clade B). With more than 56,000 assembled sequences per species, these data represent the largest transcriptomic resource for dinoflagellates to date. Our results corroborate previous observations that dinoflagellates possess the complete nucleosome machinery. We found a complete set of core histones as well as several H3 variants and H2A.Z in one species. Furthermore, transcriptome analysis points toward a low number of transcription factors in Symbiodinium spp. that also differ in the distribution of DNA-binding domains relative to other eukaryotes. In particular the cold shock domain was predominant among transcription factors. Additionally, we found a high number of antioxidative genes in comparison to non-symbiotic but evolutionary related organisms. These findings might be of relevance in the context of the role that Symbiodinium spp. play as coral symbionts.Our data represent the most comprehensive dinoflagellate EST data set to date. This study provides a comprehensive resource to further analyze the genetic makeup, metabolic capacities, and gene repertoire of Symbiodinium and dinoflagellates. Overall, our findings indicate that Symbiodinium possesses some unique characteristics, in particular the transcriptional regulation in Symbiodinium may differ from the currently known mechanisms of eukaryotic gene regulation.

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

    Science.gov (United States)

    2012-01-01

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

  11. 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.

  12. Building local capacity for genomics research in Africa: recommendations from analysis of publications in Sub-Saharan Africa from 2004 to 2013.

    Science.gov (United States)

    Adedokun, Babatunde O; Olopade, Christopher O; Olopade, Olufunmilayo I

    2016-01-01

    The poor genomics research capacity of Sub-Saharan Africa (SSA) could prevent maximal benefits from the applications of genomics in the practice of medicine and research. The objective of this study is to examine the author affiliations of genomic epidemiology publications in order to make recommendations for building local genomics research capacity in SSA. SSA genomic epidemiology articles published between 2004 and 2013 were extracted from the Human Genome Epidemiology (HuGE) database. Data on authorship details, country of population studied, and phenotype or disease were extracted. Factors associated with the first author, who has an SSA institution affiliation (AIAFA), were determined using a Chi-square test and multiple logistic regression analysis. The most commonly studied population was South Africa, accounting for 31.1%, followed by Ghana (10.6%) and Kenya (7.5%). About one-tenth of the papers were related to non-communicable diseases (NCDs) such as cancer (6.1%) and cardiovascular diseases (CVDs) (4.3%). Fewer than half of the first authors (46.9%) were affiliated with an African institution. Among the 238 articles with an African first author, over three-quarters (79.8%) belonged to a university or medical school, 16.8% were affiliated with a research institute, and 3.4% had affiliations with other institutions. Significant disparities currently exist among SSA countries in genomics research capacity. South Africa has the highest genomics research output, which is reflected in the investments made in its genomics and biotechnology sector. These findings underscore the need to focus on developing local capacity, especially among those affiliated with SSA universities where there are more opportunities for teaching and research.

  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. Visual Literacy and Visual Culture.

    Science.gov (United States)

    Messaris, Paul

    Familiarity with specific images or sets of images plays a role in a culture's visual heritage. Two questions can be asked about this type of visual literacy: Is this a type of knowledge that is worth building into the formal educational curriculum of our schools? What are the educational implications of visual literacy? There is a three-part…

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

    Science.gov (United States)

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

    2013-11-02

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

  16. 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.

  17. Accounting for the uncertainty related to building occupants with regards to visual comfort: A literature survey on drivers and models

    DEFF Research Database (Denmark)

    Fabi, Valentina; Andersen, Rune Korsholm; Corgnati, Stefano

    2016-01-01

    The interactions between building occupants and control systems have a high influence on energy consumption and on indoor environmental quality. In the perspective of a future of "nearly-zero" energy buildings, it is crucial to analyse the energy-related interactions deeply to predict realistic e...... who take daylight level into account and switch on lights only if necessary and people who totally disregard the natural lighting. This underlines the importance of how individuality is at the base of the definition of the different types of users....

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

    NARCIS (Netherlands)

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

    2010-01-01

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

  19. Defining Quality in Visual Art Education for Young Children: Building on the Position Statement of the Early Childhood Art Educators

    Science.gov (United States)

    McClure, Marissa; Tarr, Patricia; Thompson, Christine Marmé; Eckhoff, Angela

    2017-01-01

    This article reflects the collective voices of four early childhood visual arts educators, each of whom is a member of the Early Childhood Art Educators (ECAE) Issues Group of the National Arts Educators Association. The authors frame the article around the ECAE position statement, "Art: Essential for Early Learning" (2016), which…

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

    Science.gov (United States)

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

    2018-05-07

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

  1. Building the genomic nation: ‘Homo Brasilis’ and the ‘Genoma Mexicano’ in comparative cultural perspective

    Science.gov (United States)

    Kent, Michael; García-Deister, Vivette; López-Beltrán, Carlos; Santos, Ricardo Ventura; Schwartz-Marín, Ernesto; Wade, Peter

    2015-01-01

    This article explores the relationship between genetic research, nationalism and the construction of collective social identities in Latin America. It makes a comparative analysis of two research projects – the ‘Genoma Mexicano’ and the ‘Homo Brasilis’ – both of which sought to establish national and genetic profiles. Both have reproduced and strengthened the idea of their respective nations of focus, incorporating biological elements into debates on social identities. Also, both have placed the unifying figure of the mestizo/mestiço at the heart of national identity constructions, and in so doing have displaced alternative identity categories, such as those based on race. However, having been developed in different national contexts, these projects have had distinct scientific and social trajectories: in Mexico, the genomic mestizo is mobilized mainly in relation to health, while in Brazil the key arena is that of race. We show the importance of the nation as a frame for mobilizing genetic data in public policy debates, and demonstrate how race comes in and out of focus in different Latin American national contexts of genomic research, while never completely disappearing. PMID:27479999

  2. Uncertainty and sensitivity analyses of energy and visual performances of office building with external venetian blind shading in hot-dry climate

    International Nuclear Information System (INIS)

    Singh, Ramkishore; Lazarus, I.J.; Kishore, V.V.N.

    2016-01-01

    Highlights: • Various alternatives of glazing and venetian blind were simulated for office space. • Daylighting and energy performances were assessed for each alternative. • Large uncertainties were estimated in the energy consumptions and UDI values. • Glazing design parameters were prioritised by performing sensitivity analysis. • WWR, glazing type, blind orientation and slat angle were identified top in priority. - Abstract: Fenestration has become an integral part of the buildings and has a significant impact on the energy and indoor visual performances. Inappropriate design of the fenestration component may lead to low energy efficiency and visual discomfort as a result of high solar and thermal heat gains, excessive daylight and direct sunlight. External venetian blind has been identified as one of the effective shading devices for controlling the heat gains and daylight through fenestration. This study explores uncertainty and sensitivity analyses to identify and prioritize the most influencing parameters for designing glazed components that include external shading devices for office buildings. The study was performed for hot-dry climate of Jodhpur (Latitude 26° 180′N, longitude 73° 010′E) using EnergyPlus, a whole building energy simulation tool providing a large number of inputs for eight façade orientations. A total 150 and 845 data points (for each orientation) for input variables were generated using Hyper Cubic Sampling and extended FAST methods for uncertainty and sensitivity analyses respectively. Results indicated a large uncertainty in the lighting, HVAC, source energy consumptions and useful daylight illuminance (UDI). The estimated coefficients of variation were highest (up to 106%) for UDI, followed by lighting energy (up to 45%) and HVAC energy use (around 33%). The sensitivity analysis identified window to wall ratio, glazing type, blind type (orientation of slats) and slat angle as highly influencing factors for energy and

  3. Building the visual identity of a brand as a designer Case: Bezweena’s Moroccan Argan Oil

    OpenAIRE

    Nguyen, Hien

    2017-01-01

    Why is branding important? It is because people often choose a product based on the per-ceived value of what they think the product is worth rather than its actual value. Accordingly, visual identity, in this case, has an important role in increasing perceived value of a product and in establishing and nurturing a sustainable relationship with customers. In this project, the designer taps into her ability to see and recognize the value of her client’s brand, and transforms that understand...

  4. 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

  5. A Decade of Building a STEM Educational Community of Practice from the Ground Up: Leveraging Technology, Visualization, and Evaluation

    Science.gov (United States)

    Pisut, D.; MacIntosh, E.; McDougall, C.; Peddicord, H.; Russell, E. L.; Zepecki, S., III

    2017-12-01

    A small group of scientists and museum directors sit in a room and ponder, "What do we do with this thing?" It was ten years ago, and the Science On a Sphere was a nascent educational technology. Since that time, NOAA has built a energetic community of practice, with over 150 institutional network members ranging from museums and aquariums, to scientific laboratories, and even documentary producers. A key to the long term success of this educational community has been its constant evolution - driven by needs assessments of the network partners, NOAA's foresight on how to improve user experiences by integrating new visualizations, storytelling, and improved technology, and the ability of institutions to integrate the technologies into their other STEM offerings. In this talk we'll cover specific examples of the challenges that have arisen, and how NOAA, and its close partner NASA, has evolved the program offerings and technologies to meet the needs of this educational community of practice, along with some thoughts on the future of the Science On a Sphere Collaborative Network and NOAA's STEM educational technology portfolio.

  6. Coral life history and symbiosis: Functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata

    Directory of Open Access Journals (Sweden)

    Szmant Alina M

    2008-02-01

    -scleractinian cnidarians Nematostella vectensis and Hydra magnipapillata. Conclusion Partial sequencing of 5 cDNA libraries each for A. palmata and M. faveolata has produced a rich set of candidate genes (4,980 genes from A. palmata, and 1,732 genes from M. faveolata that we can use as a starting point for examining the life history and symbiosis of these two species, as well as to further expand the dataset of cnidarian genes for comparative genomics and evolutionary studies.

  7. Coral life history and symbiosis: functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata.

    Science.gov (United States)

    Schwarz, Jodi A; Brokstein, Peter B; Voolstra, Christian; Terry, Astrid Y; Manohar, Chitra F; Miller, David J; Szmant, Alina M; Coffroth, Mary Alice; Medina, Mónica

    2008-02-25

    Hydra magnipapillata. Partial sequencing of 5 cDNA libraries each for A. palmata and M. faveolata has produced a rich set of candidate genes (4,980 genes from A. palmata, and 1,732 genes from M. faveolata) that we can use as a starting point for examining the life history and symbiosis of these two species, as well as to further expand the dataset of cnidarian genes for comparative genomics and evolutionary studies.

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

    Science.gov (United States)

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

    2017-07-01

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

  9. Visual intelligence Microsoft tools and techniques for visualizing data

    CERN Document Server

    Stacey, Mark; Jorgensen, Adam

    2013-01-01

    Go beyond design concepts and learn to build state-of-the-art visualizations The visualization experts at Microsoft's Pragmatic Works have created a full-color, step-by-step guide to building specific types of visualizations. The book thoroughly covers the Microsoft toolset for data analysis and visualization, including Excel, and explores best practices for choosing a data visualization design, selecting tools from the Microsoft stack, and building a dynamic data visualization from start to finish. You'll examine different types of visualizations, their strengths and weaknesses, a

  10. 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

  11. Phytozome Comparative Plant Genomics Portal

    Energy Technology Data Exchange (ETDEWEB)

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  12. Building Envelope Thermal Performance Assessment Using Visual Programming and BIM, based on ETTV requirement of Green Mark and GreenRE

    OpenAIRE

    Taki Eddine Seghier; Lim Yaik Wah; Mohd Hamdan Ahmad; Williams Opeyemi Samuel

    2017-01-01

    Accomplishment of green building design requirements and the achievement of the targeted credit points under a specific green rating system are known to be a task that is very challenging. Building Information Modeling (BIM) design process and tools have already made considerable advancements in green building design and performance analysis. However, Green building design process is still lack of tools and workflows that can provide real-time feedback of building sustainability and rating du...

  13. Two Contrasting Approaches to Building High School Teacher Capacity to Teach About Local Climate Change Using Powerful Geospatial Data and Visualization Technology

    Science.gov (United States)

    Zalles, D. R.

    2011-12-01

    The presentation will compare and contrast two different place-based approaches to helping high school science teachers use geospatial data visualization technology to teach about climate change in their local regions. The approaches are being used in the development, piloting, and dissemination of two projects for high school science led by the author: the NASA-funded Data-enhanced Investigations for Climate Change Education (DICCE) and the NSF funded Studying Topography, Orographic Rainfall, and Ecosystems with Geospatial Information Technology (STORE). DICCE is bringing an extensive portal of Earth observation data, the Goddard Interactive Online Visualization and Analysis Infrastructure, to high school classrooms. STORE is making available data for viewing results of a particular IPCC-sanctioned climate change model in relation to recent data about average temperatures, precipitation, and land cover for study areas in central California and western New York State. Across the two projects, partner teachers of academically and ethnically diverse students from five states are participating in professional development and pilot testing. Powerful geospatial data representation technologies are difficult to implement in high school science because of challenges that teachers and students encounter navigating data access and making sense of data characteristics and nomenclature. Hence, on DICCE, the researchers are testing the theory that by providing a scaffolded technology-supported process for instructional design, starting from fundamental questions about the content domain, teachers will make better instructional decisions. Conversely, the STORE approach is rooted in the perspective that co-design of curricular materials among researchers and teacher partners that work off of "starter" lessons covering focal skills and understandings will lead to the most effective utilizations of the technology in the classroom. The projects' goals and strategies for student

  14. Annotation Of Novel And Conserved MicroRNA Genes In The Build 10 Sus scrofa Reference Genome And Determination Of Their Expression Levels In Ten Different Tissues

    DEFF Research Database (Denmark)

    Thomsen, Bo; Nielsen, Mathilde; Hedegaard, Jakob

    The DNA template used in the pig genome sequencing project was provided by a Duroc pig named TJ Tabasco. In an effort to annotate microRNA (miRNA) genes in the reference genome we have conducted deep sequencing to determine the miRNA transcriptomes in ten different tissues isolated from Pinky......, a genetically identical clone of TJ Tabasco. The purpose was to generate miRNA sequences that are highly homologous to the reference genome sequence, which along with computational prediction will improve confidence in the genomic annotation of miRNA genes. Based on homology searches of the sequence data...... against miRBase, we identified more than 600 conserved known miRNA/miRNA*, which is a significant increase relative to the 211 porcine miRNA/miRNA* deposited in the current version of miRBase. Furthermore, the genome-wide transcript profiles provided important information on the relative abundance...

  15. Applied building physics

    CERN Document Server

    Hens, Hugo S L C

    2012-01-01

    The energy crises of the 1970s, persisting moisture problems, complaints about sick buildings, thermal, visual and olfactory discomfort, and the move towards more sustainability in building construction have pushed Building Physics to the forefront of building innovation. The societal pressure to diminish energy consumption in buildings without impairing usability acted as a trigger to activate the whole notion of performance based design and construction. As with all engineering sciences, Building Physics is oriented towards application, which is why, after a first book on fundamentals this s

  16. Whole-genome sequence, SNP chips and pedigree structure: building demographic profiles in domestic dog breeds to optimize genetic-trait mapping

    Science.gov (United States)

    Dreger, Dayna L.; Rimbault, Maud; Davis, Brian W.; Bhatnagar, Adrienne; Parker, Heidi G.

    2016-01-01

    ABSTRACT In the decade following publication of the draft genome sequence of the domestic dog, extraordinary advances with application to several fields have been credited to the canine genetic system. Taking advantage of closed breeding populations and the subsequent selection for aesthetic and behavioral characteristics, researchers have leveraged the dog as an effective natural model for the study of complex traits, such as disease susceptibility, behavior and morphology, generating unique contributions to human health and biology. When designing genetic studies using purebred dogs, it is essential to consider the unique demography of each population, including estimation of effective population size and timing of population bottlenecks. The analytical design approach for genome-wide association studies (GWAS) and analysis of whole-genome sequence (WGS) experiments are inextricable from demographic data. We have performed a comprehensive study of genomic homozygosity, using high-depth WGS data for 90 individuals, and Illumina HD SNP data from 800 individuals representing 80 breeds. These data were coupled with extensive pedigree data analyses for 11 breeds that, together, allowed us to compute breed structure, demography, and molecular measures of genome diversity. Our comparative analyses characterize the extent, formation and implication of breed-specific diversity as it relates to population structure. These data demonstrate the relationship between breed-specific genome dynamics and population architecture, and provide important considerations influencing the technological and cohort design of association and other genomic studies. PMID:27874836

  17. Visual comparison for information visualization

    KAUST Repository

    Gleicher, M.; Albers, D.; Walker, R.; Jusufi, I.; Hansen, C. D.; Roberts, J. C.

    2011-01-01

    Data analysis often involves the comparison of complex objects. With the ever increasing amounts and complexity of data, the demand for systems to help with these comparisons is also growing. Increasingly, information visualization tools support such comparisons explicitly, beyond simply allowing a viewer to examine each object individually. In this paper, we argue that the design of information visualizations of complex objects can, and should, be studied in general, that is independently of what those objects are. As a first step in developing this general understanding of comparison, we propose a general taxonomy of visual designs for comparison that groups designs into three basic categories, which can be combined. To clarify the taxonomy and validate its completeness, we provide a survey of work in information visualization related to comparison. Although we find a great diversity of systems and approaches, we see that all designs are assembled from the building blocks of juxtaposition, superposition and explicit encodings. This initial exploration shows the power of our model, and suggests future challenges in developing a general understanding of comparative visualization and facilitating the development of more comparative visualization tools. © The Author(s) 2011.

  18. Visual comparison for information visualization

    KAUST Repository

    Gleicher, M.

    2011-09-07

    Data analysis often involves the comparison of complex objects. With the ever increasing amounts and complexity of data, the demand for systems to help with these comparisons is also growing. Increasingly, information visualization tools support such comparisons explicitly, beyond simply allowing a viewer to examine each object individually. In this paper, we argue that the design of information visualizations of complex objects can, and should, be studied in general, that is independently of what those objects are. As a first step in developing this general understanding of comparison, we propose a general taxonomy of visual designs for comparison that groups designs into three basic categories, which can be combined. To clarify the taxonomy and validate its completeness, we provide a survey of work in information visualization related to comparison. Although we find a great diversity of systems and approaches, we see that all designs are assembled from the building blocks of juxtaposition, superposition and explicit encodings. This initial exploration shows the power of our model, and suggests future challenges in developing a general understanding of comparative visualization and facilitating the development of more comparative visualization tools. © The Author(s) 2011.

  19. gb4gv: a genome browser for geminivirus

    Directory of Open Access Journals (Sweden)

    Eric S. Ho

    2017-04-01

    Full Text Available Background Geminiviruses (family Geminiviridae are prevalent plant viruses that imperil agriculture globally, causing serious damage to the livelihood of farmers, particularly in developing countries. The virus evolves rapidly, attributing to its single-stranded genome propensity, resulting in worldwide circulation of diverse and viable genomes. Genomics is a prominent approach taken by researchers in elucidating the infectious mechanism of the virus. Currently, the NCBI Viral Genome website is a popular repository of viral genomes that conveniently provides researchers a centralized data source of genomic information. However, unlike the genome of living organisms, viral genomes most often maintain peculiar characteristics that fit into no single genome architecture. By imposing a unified annotation scheme on the myriad of viral genomes may downplay their hallmark features. For example, the viron of begomoviruses prevailing in America encapsulates two similar-sized circular DNA components and both are required for systemic infection of plants. However, the bipartite components are kept separately in NCBI as individual genomes with no explicit association in linking them. Thus, our goal is to build a comprehensive Geminivirus genomics database, namely gb4gv, that not only preserves genomic characteristics of the virus, but also supplements biologically relevant annotations that help to interrogate this virus, for example, the targeted host, putative iterons, siRNA targets, etc. Methods We have employed manual and automatic methods to curate 508 genomes from four major genera of Geminiviridae, and 161 associated satellites obtained from NCBI RefSeq and PubMed databases. Results These data are available for free access without registration from our website. Besides genomic content, our website provides visualization capability inherited from UCSC Genome Browser. Discussion With the genomic information readily accessible, we hope that our database

  20. 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.

  1. Integration of genomic information with biological networks using Cytoscape.

    Science.gov (United States)

    Bauer-Mehren, Anna

    2013-01-01

    Cytoscape is an open-source software for visualizing, analyzing, and modeling biological networks. This chapter explains how to use Cytoscape to analyze the functional effect of sequence variations in the context of biological networks such as protein-protein interaction networks and signaling pathways. The chapter is divided into five parts: (1) obtaining information about the functional effect of sequence variation in a Cytoscape readable format, (2) loading and displaying different types of biological networks in Cytoscape, (3) integrating the genomic information (SNPs and mutations) with the biological networks, and (4) analyzing the effect of the genomic perturbation onto the network structure using Cytoscape built-in functions. Finally, we briefly outline how the integrated data can help in building mathematical network models for analyzing the effect of the sequence variation onto the dynamics of the biological system. Each part is illustrated by step-by-step instructions on an example use case and visualized by many screenshots and figures.

  2. DNA Sequence Patterns – A Successful Example of Grid Computing in Genome Research and Building Virtual Super-Computers for the Research Commons of e-Societies

    NARCIS (Netherlands)

    T.A. Knoch (Tobias); A. Abuseiris (Anis); M. Lesnussa (Michael); F.N. Kepper (Nick); R.M. de Graaf (Rob); F.G. Grosveld (Frank)

    2011-01-01

    textabstractThe amount of information is growing exponentially with ever-new technologies emerging and is believed to be always at the limit. In contrast, huge resources are obviously available, which are underused in the IT sector, similar as e.g. in the renewable energy sector. Genome research is

  3. Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface

    Directory of Open Access Journals (Sweden)

    Bushell Michael E

    2011-05-01

    Full Text Available Abstract Background Constraint-based approaches facilitate the prediction of cellular metabolic capabilities, based, in turn on predictions of the repertoire of enzymes encoded in the genome. Recently, genome annotations have been used to reconstruct genome scale metabolic reaction networks for numerous species, including Homo sapiens, which allow simulations that provide valuable insights into topics, including predictions of gene essentiality of pathogens, interpretation of genetic polymorphism in metabolic disease syndromes and suggestions for novel approaches to microbial metabolic engineering. These constraint-based simulations are being integrated with the functional genomics portals, an activity that requires efficient implementation of the constraint-based simulations in the web-based environment. Results Here, we present Acorn, an open source (GNU GPL grid computing system for constraint-based simulations of genome scale metabolic reaction networks within an interactive web environment. The grid-based architecture allows efficient execution of computationally intensive, iterative protocols such as Flux Variability Analysis, which can be readily scaled up as the numbers of models (and users increase. The web interface uses AJAX, which facilitates efficient model browsing and other search functions, and intuitive implementation of appropriate simulation conditions. Research groups can install Acorn locally and create user accounts. Users can also import models in the familiar SBML format and link reaction formulas to major functional genomics portals of choice. Selected models and simulation results can be shared between different users and made publically available. Users can construct pathway map layouts and import them into the server using a desktop editor integrated within the system. Pathway maps are then used to visualise numerical results within the web environment. To illustrate these features we have deployed Acorn and created a

  4. Learning Visual Basic NET

    CERN Document Server

    Liberty, Jesse

    2009-01-01

    Learning Visual Basic .NET is a complete introduction to VB.NET and object-oriented programming. By using hundreds of examples, this book demonstrates how to develop various kinds of applications--including those that work with databases--and web services. Learning Visual Basic .NET will help you build a solid foundation in .NET.

  5. Constructing visual representations

    DEFF Research Database (Denmark)

    Huron, Samuel; Jansen, Yvonne; Carpendale, Sheelagh

    2014-01-01

    tangible building blocks. We learned that all participants, most of whom had little experience in visualization authoring, were readily able to create and talk about their own visualizations. Based on our observations, we discuss participants’ actions during the development of their visual representations......The accessibility of infovis authoring tools to a wide audience has been identified as a major research challenge. A key task in the authoring process is the development of visual mappings. While the infovis community has long been deeply interested in finding effective visual mappings......, comparatively little attention has been placed on how people construct visual mappings. In this paper, we present the results of a study designed to shed light on how people transform data into visual representations. We asked people to create, update and explain their own information visualizations using only...

  6. Visualized simulation of buildings, a graphic model editor with SimuVis; Visualisierte Gebaeudesimulation, ein grafischer Modelleditor mit SimuVis

    Energy Technology Data Exchange (ETDEWEB)

    Waldhoff, C.; Raedler, J. [dezentral gbr, Berlin (Germany); Gerber, A.; Metin, E. [FH Biberach, Fachbereich Architektur und Gebaeudeklimatik (Germany)

    2003-07-01

    A software package for the visualisation of results from thermal building simulation is presented. The software is based on SimuVis and allows the results to be shown inside the three-dimensional building view. The model parameters are defined and configured by clicking on sensitive building elements in the scene view and changing the settings in the dialogs. This easy-to-use graphical user interface enables even beginners to perform thermal building simulations. The simulation model is based on the simulation environment SMILE and its multizone building model. A first application of this software is the education of architects and engineers. It is used in the educational network 'Multimediales Lernnetz Bauphysik' for the simulation of cooling loads. This application was developed by dezentral in cooperation with the University for Applied Sciences Biberach. Other modules of the network like material and weather databases are integrated and used in the application. The design is based on a client/server architecture with load balancing and a high level of modularisation. Open internet standards like XML and XMLRPC are used for communication and data storage, which allow the extension and coupling of the application with other software. Some planned extensions are the integration of solar thermal heating and other HVAC components. (orig.)

  7. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine.

    Science.gov (United States)

    Stenson, Peter D; Mort, Matthew; Ball, Edward V; Shaw, Katy; Phillips, Andrew; Cooper, David N

    2014-01-01

    The Human Gene Mutation Database (HGMD®) is a comprehensive collection of germline mutations in nuclear genes that underlie, or are associated with, human inherited disease. By June 2013, the database contained over 141,000 different lesions detected in over 5,700 different genes, with new mutation entries currently accumulating at a rate exceeding 10,000 per annum. HGMD was originally established in 1996 for the scientific study of mutational mechanisms in human genes. However, it has since acquired a much broader utility as a central unified disease-oriented mutation repository utilized by human molecular geneticists, genome scientists, molecular biologists, clinicians and genetic counsellors as well as by those specializing in biopharmaceuticals, bioinformatics and personalized genomics. The public version of HGMD (http://www.hgmd.org) is freely available to registered users from academic institutions/non-profit organizations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via BIOBASE GmbH.

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

    Directory of Open Access Journals (Sweden)

    Eleftherios Pilalis

    2015-01-01

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

  9. COGNAT: a web server for comparative analysis of genomic neighborhoods.

    Science.gov (United States)

    Klimchuk, Olesya I; Konovalov, Kirill A; Perekhvatov, Vadim V; Skulachev, Konstantin V; Dibrova, Daria V; Mulkidjanian, Armen Y

    2017-11-22

    In prokaryotic genomes, functionally coupled genes can be organized in conserved gene clusters enabling their coordinated regulation. Such clusters could contain one or several operons, which are groups of co-transcribed genes. Those genes that evolved from a common ancestral gene by speciation (i.e. orthologs) are expected to have similar genomic neighborhoods in different organisms, whereas those copies of the gene that are responsible for dissimilar functions (i.e. paralogs) could be found in dissimilar genomic contexts. Comparative analysis of genomic neighborhoods facilitates the prediction of co-regulated genes and helps to discern different functions in large protein families. We intended, building on the attribution of gene sequences to the clusters of orthologous groups of proteins (COGs), to provide a method for visualization and comparative analysis of genomic neighborhoods of evolutionary related genes, as well as a respective web server. Here we introduce the COmparative Gene Neighborhoods Analysis Tool (COGNAT), a web server for comparative analysis of genomic neighborhoods. The tool is based on the COG database, as well as the Pfam protein families database. As an example, we show the utility of COGNAT in identifying a new type of membrane protein complex that is formed by paralog(s) of one of the membrane subunits of the NADH:quinone oxidoreductase of type 1 (COG1009) and a cytoplasmic protein of unknown function (COG3002). This article was reviewed by Drs. Igor Zhulin, Uri Gophna and Igor Rogozin.

  10. The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes

    KAUST Repository

    Bracken-Grissom, Heather; Collins, Allen G.; Collins, Timothy; Crandall, Keith; Distel, Daniel; Dunn, Casey; Giribet, Gonzalo; Haddock, Steven; Knowlton, Nancy; Martindale, Mark; Medina, Monica; Messing, Charles; O'Brien, Stephen J.; Paulay, Gustav; Putnam, Nicolas; Ravasi, Timothy; Rouse, Greg W.; Ryan, Joseph F.; Schulze, Anja; Worheide, Gert; Adamska, Maja; Bailly, Xavier; Breinholt, Jesse; Browne, William E.; Diaz, M. Christina; Evans, Nathaniel; Flot, Jean-Francois; Fogarty, Nicole; Johnston, Matthew; Kamel, Bishoy; Kawahara, Akito Y.; Laberge, Tammy; Lavrov, Dennis; Michonneau, Francois; Moroz, Leonid L.; Oakley, Todd; Osborne, Karen; Pomponi, Shirley A.; Rhodes, Adelaide; Rodriguez-Lanetty, Mauricio; Santos, Scott R.; Satoh, Nori; Thacker, Robert W.; Van de Peer, Yves; Voolstra, Christian R.; Welch, David Mark; Winston, Judith; Zhou, Xin

    2013-01-01

    Over 95% of all metazoan (animal) species comprise the invertebrates, but very few genomes from these organisms have been sequenced. We have, therefore, formed a Global Invertebrate Genomics Alliance (GIGA). Our intent is to build a collaborative

  11. Rice Genome Research: Current Status and Future Perspectives

    Directory of Open Access Journals (Sweden)

    Bin Han

    2008-11-01

    Full Text Available Rice ( L. is the leading genomics system among the crop plants. The sequence of the rice genome, the first cereal plant genome, was published in 2005. This review summarizes progress made in rice genome annotations, comparative genomics, and functional genomics researches. It also maps out the status of rice genomics globally and provides a vision of future research directions and resource building.

  12. High-recovery visual identification and single-cell retrieval of circulating tumor cells for genomic analysis using a dual-technology platform integrated with automated immunofluorescence staining

    International Nuclear Information System (INIS)

    Campton, Daniel E; Ramirez, Arturo B; Nordberg, Joshua J; Drovetto, Nick; Clein, Alisa C; Varshavskaya, Paulina; Friemel, Barry H; Quarre, Steve; Breman, Amy; Dorschner, Michael; Blau, Sibel; Blau, C Anthony; Sabath, Daniel E; Stilwell, Jackie L; Kaldjian, Eric P

    2015-01-01

    Circulating tumor cells (CTCs) are malignant cells that have migrated from solid cancers into the blood, where they are typically present in rare numbers. There is great interest in using CTCs to monitor response to therapies, to identify clinically actionable biomarkers, and to provide a non-invasive window on the molecular state of a tumor. Here we characterize the performance of the AccuCyte® – CyteFinder® system, a comprehensive, reproducible and highly sensitive platform for collecting, identifying and retrieving individual CTCs from microscopic slides for molecular analysis after automated immunofluorescence staining for epithelial markers. All experiments employed a density-based cell separation apparatus (AccuCyte) to separate nucleated cells from the blood and transfer them to microscopic slides. After staining, the slides were imaged using a digital scanning microscope (CyteFinder). Precisely counted model CTCs (mCTCs) from four cancer cell lines were spiked into whole blood to determine recovery rates. Individual mCTCs were removed from slides using a single-cell retrieval device (CytePicker™) for whole genome amplification and subsequent analysis by PCR and Sanger sequencing, whole exome sequencing, or array-based comparative genomic hybridization. Clinical CTCs were evaluated in blood samples from patients with different cancers in comparison with the CellSearch® system. AccuCyte – CyteFinder presented high-resolution images that allowed identification of mCTCs by morphologic and phenotypic features. Spike-in mCTC recoveries were between 90 and 91%. More than 80% of single-digit spike-in mCTCs were identified and even a single cell in 7.5 mL could be found. Analysis of single SKBR3 mCTCs identified presence of a known TP53 mutation by both PCR and whole exome sequencing, and confirmed the reported karyotype of this cell line. Patient sample CTC counts matched or exceeded CellSearch CTC counts in a small feasibility cohort. The AccuCyte

  13. Genome Variation Map: a data repository of genome variations in BIG Data Center

    OpenAIRE

    Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

    2017-01-01

    Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research a...

  14. DEVELOPMENT OF DIGITAL COMPETENCIES OF PRIMARY SCHOOL TEACHERS THROUGH BUILDING KNOWLEDGE AND SKILLS FOR WORKING WITH VISUAL PROGRAMMING ENVIRONMENT WITHIN MATH PROJECT WORK

    Directory of Open Access Journals (Sweden)

    Rumyana Y. Papancheva

    2017-07-01

    Full Text Available The paper presents a review of the contemporary school, the digital generation and the need of teachers equipped with new knowledge and skills, in particular – basic programming skills. The last change of educational system in Bulgaria after the adoption of the new pre-school and general school education act is analysed. New primary school curricula and new standards for teacher’s qualification were implemented. The new school subject “Computer modelling” is presented. Some experience of the authors from project-based work in mathematics with teachers and students is described. The aim is the formation of skills of programming by working within Scratch – visual environment for block-based coding. Some conclusions and ideas for future work are formulated.

  15. Informing the Design of Direct-to-Consumer Interactive Personal Genomics Reports.

    Science.gov (United States)

    Shaer, Orit; Nov, Oded; Okerlund, Johanna; Balestra, Martina; Stowell, Elizabeth; Ascher, Laura; Bi, Joanna; Schlenker, Claire; Ball, Madeleine

    2015-06-12

    In recent years, people who sought direct-to-consumer genetic testing services have been increasingly confronted with an unprecedented amount of personal genomic information, which influences their decisions, emotional state, and well-being. However, these users of direct-to-consumer genetic services, who vary in their education and interests, frequently have little relevant experience or tools for understanding, reasoning about, and interacting with their personal genomic data. Online interactive techniques can play a central role in making personal genomic data useful for these users. We sought to (1) identify the needs of diverse users as they make sense of their personal genomic data, (2) consequently develop effective interactive visualizations of genomic trait data to address these users' needs, and (3) evaluate the effectiveness of the developed visualizations in facilitating comprehension. The first two user studies, conducted with 63 volunteers in the Personal Genome Project and with 36 personal genomic users who participated in a design workshop, respectively, employed surveys and interviews to identify the needs and expectations of diverse users. Building on the two initial studies, the third study was conducted with 730 Amazon Mechanical Turk users and employed a controlled experimental design to examine the effectiveness of different design interventions on user comprehension. The first two studies identified searching, comparing, sharing, and organizing data as fundamental to users' understanding of personal genomic data. The third study demonstrated that interactive and visual design interventions could improve the understandability of personal genomic reports for consumers. In particular, results showed that a new interactive bubble chart visualization designed for the study resulted in the highest comprehension scores, as well as the highest perceived comprehension scores. These scores were significantly higher than scores received using the

  16. Customizable Time-Oriented Visualizations

    DEFF Research Database (Denmark)

    Kuhail, Mohammad Amin; Pantazos, Kostas; Lauesen, Søren

    2012-01-01

    Most commercial visualization tools support an easy and quick creation of conventional time-oriented visualizations such as line charts, but customization is limited. In contrast, some academic visualization tools and programming languages support the creation of some customizable time......-oriented visualizations but it is time consuming and hard. To combine efficiency, the effort required to develop a visualization, and customizability, the ability to tailor a visualization, we developed time-oriented building blocks that address the specifics of time (e.g. linear vs. cyclic or point-based vs. interval......-based) and consist of inner customizable parts (e.g. ticks). A combination of the time-oriented and other primitive graphical building blocks allowed the creation of several customizable advanced time-oriented visualizations. The appearance and behavior of the blocks are specified using spreadsheet-like formulas. We...

  17. Early Building Design

    DEFF Research Database (Denmark)

    Østergård, Torben; Jensen, Rasmus Lund; Maagaard, Steffen

    2017-01-01

    Highlights •Development of a design methodology that can handle the vast design space in early building design. •A global design space is modelled from extensive Monte Carlo simulations. •Sensitivity analysis methods applied to guide decision-makers. •Interactive visualizations help the multi-act...

  18. Ethnographic notes on visualization practices in tissue engineering research

    NARCIS (Netherlands)

    Vyas, Dhaval; Cacciabue, P.C.

    2013-01-01

    Visual information is central to several of the scientific disciplines. This paper studies how scientists working in a multidisciplinary field produce scientific evidence through building and manipulating scientific visualizations. Using ethnographic methods, we studied visualization practices of

  19. Building Languages

    Science.gov (United States)

    ... Glossary Contact Information Information For… Media Policy Makers Building Languages Recommend on Facebook Tweet Share Compartir Communicating ... any speech and only very loud sounds. Close × “Building Blocks” “Building Blocks” refers to the different skills ...

  20. Novel Polymerase Spiral Reaction (PSR) for rapid visual detection of Bovine Herpesvirus 1 genomic DNA from aborted bovine fetus and semen.

    Science.gov (United States)

    Malla, Javed Ahmed; Chakravarti, Soumendu; Gupta, Vikas; Chander, Vishal; Sharma, Gaurav Kumar; Qureshi, Salauddin; Mishra, Adhiraj; Gupta, Vivek Kumar; Nandi, Sukdeb

    2018-02-20

    Bovine herpesvirus-1 (BHV-1) is a major viral pathogen affecting bovines leading to various clinical manifestations and causes significant economic impediment in modern livestock production system. Rapid, accurate and sensitive detection of BHV-1 infection at frozen semen stations or at dairy herds remains a priority for control of BHV-1 spread to susceptible population. Polymerase Spiral Reaction (PSR), a novel addition in the gamut of isothermal techniques, has been successfully implemented in initial optimization for detection of BHV-1 genomic DNA and further validated in clinical samples. The developed PSR assay has been validated for detection of BHV-1 from bovine semen (n=99), a major source of transmission of BHV-1 from breeding bulls to susceptible dams in artificial insemination programs. The technique has also been used for screening of BHV-1 DNA from suspected aborted fetal tissues (n=25). The developed PSR technique is 100 fold more sensitive than conventional PCR and comparable to real-time PCR. The PSR technique has been successful in detecting 13 samples positive for BHV-1 DNA in bovine semen, 4 samples more than conventional PCR. The aborted fetal tissues were negative for presence of BHV-1 DNA. The presence of BHV-1 in bovine semen samples raises a pertinent concern for extensively screening of semen from breeding bulls before been used for artificial insemination process. PSR has all the attributes for becoming a method of choice for rapid, accurate and sensitive detection of BHV-1 DNA at frozen semen stations or at dairy herds in resource constrained settings. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Exploring the possibilities and limitations of a nanomaterials genome.

    Science.gov (United States)

    Qian, Chenxi; Siler, Todd; Ozin, Geoffrey A

    2015-01-07

    What are we going to do with the cornucopia of nanomaterials appearing in the open and patent literature, every day? Imagine the benefits of an intelligent and convenient means of categorizing, organizing, sifting, sorting, connecting, and utilizing this information in scientifically and technologically innovative ways by building a Nanomaterials Genome founded upon an all-purpose Periodic Table of Nanomaterials. In this Concept article, inspired by work on the Human Genome project, which began in 1989 together with motivation from the recent emergence of the Materials Genome project initiated in 2011 and the Nanoinformatics Roadmap 2020 instigated in 2010, we envision the development of a Nanomaterials Genome (NMG) database with the most advanced data-mining tools that leverage inference engines to help connect and interpret patterns of nanomaterials information. It will be equipped with state-of-the-art visualization techniques that rapidly organize and picture, categorize and interrelate the inherited behavior of complex nanomatter from the information programmed in its constituent nanomaterials building blocks. A Nanomaterials Genome Initiative (NMGI) of the type imagined herein has the potential to serve the global nanoscience community with an opportunity to speed up the development continuum of nanomaterials through the innovation process steps of discovery, structure determination and property optimization, functionality elucidation, system design and integration, certification and manufacturing to deployment in technologies that apply these versatile nanomaterials in environmentally responsible ways. The possibilities and limitations of this concept are critically evaluated in this article. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Genomics Portals: integrative web-platform for mining genomics data.

    Science.gov (United States)

    Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

    2010-01-13

    A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

  3. Genomics Portals: integrative web-platform for mining genomics data

    Directory of Open Access Journals (Sweden)

    Ghosh Krishnendu

    2010-01-01

    Full Text Available Abstract Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc, and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

  4. Comparative Genome Viewer

    International Nuclear Information System (INIS)

    Molineris, I.; Sales, G.

    2009-01-01

    The amount of information about genomes, both in the form of complete sequences and annotations, has been exponentially increasing in the last few years. As a result there is the need for tools providing a graphical representation of such information that should be comprehensive and intuitive. Visual representation is especially important in the comparative genomics field since it should provide a combined view of data belonging to different genomes. We believe that existing tools are limited in this respect as they focus on a single genome at a time (conservation histograms) or compress alignment representation to a single dimension. We have therefore developed a web-based tool called Comparative Genome Viewer (Cgv): it integrates a bidimensional representation of alignments between two regions, both at small and big scales, with the richness of annotations present in other genome browsers. We give access to our system through a web-based interface that provides the user with an interactive representation that can be updated in real time using the mouse to move from region to region and to zoom in on interesting details.

  5. Extreme genomes

    OpenAIRE

    DeLong, Edward F

    2000-01-01

    The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.

  6. Grass genomes

    OpenAIRE

    Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

    1998-01-01

    For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

  7. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  8. ABrowse--a customizable next-generation genome browser framework.

    Science.gov (United States)

    Kong, Lei; Wang, Jun; Zhao, Shuqi; Gu, Xiaocheng; Luo, Jingchu; Gao, Ge

    2012-01-05

    With the rapid growth of genome sequencing projects, genome browser is becoming indispensable, not only as a visualization system but also as an interactive platform to support open data access and collaborative work. Thus a customizable genome browser framework with rich functions and flexible configuration is needed to facilitate various genome research projects. Based on next-generation web technologies, we have developed a general-purpose genome browser framework ABrowse which provides interactive browsing experience, open data access and collaborative work support. By supporting Google-map-like smooth navigation, ABrowse offers end users highly interactive browsing experience. To facilitate further data analysis, multiple data access approaches are supported for external platforms to retrieve data from ABrowse. To promote collaborative work, an online user-space is provided for end users to create, store and share comments, annotations and landmarks. For data providers, ABrowse is highly customizable and configurable. The framework provides a set of utilities to import annotation data conveniently. To build ABrowse on existing annotation databases, data providers could specify SQL statements according to database schema. And customized pages for detailed information display of annotation entries could be easily plugged in. For developers, new drawing strategies could be integrated into ABrowse for new types of annotation data. In addition, standard web service is provided for data retrieval remotely, providing underlying machine-oriented programming interface for open data access. ABrowse framework is valuable for end users, data providers and developers by providing rich user functions and flexible customization approaches. The source code is published under GNU Lesser General Public License v3.0 and is accessible at http://www.abrowse.org/. To demonstrate all the features of ABrowse, a live demo for Arabidopsis thaliana genome has been built at http://arabidopsis.cbi.edu.cn/.

  9. ABrowse - a customizable next-generation genome browser framework

    Science.gov (United States)

    2012-01-01

    Background With the rapid growth of genome sequencing projects, genome browser is becoming indispensable, not only as a visualization system but also as an interactive platform to support open data access and collaborative work. Thus a customizable genome browser framework with rich functions and flexible configuration is needed to facilitate various genome research projects. Results Based on next-generation web technologies, we have developed a general-purpose genome browser framework ABrowse which provides interactive browsing experience, open data access and collaborative work support. By supporting Google-map-like smooth navigation, ABrowse offers end users highly interactive browsing experience. To facilitate further data analysis, multiple data access approaches are supported for external platforms to retrieve data from ABrowse. To promote collaborative work, an online user-space is provided for end users to create, store and share comments, annotations and landmarks. For data providers, ABrowse is highly customizable and configurable. The framework provides a set of utilities to import annotation data conveniently. To build ABrowse on existing annotation databases, data providers could specify SQL statements according to database schema. And customized pages for detailed information display of annotation entries could be easily plugged in. For developers, new drawing strategies could be integrated into ABrowse for new types of annotation data. In addition, standard web service is provided for data retrieval remotely, providing underlying machine-oriented programming interface for open data access. Conclusions ABrowse framework is valuable for end users, data providers and developers by providing rich user functions and flexible customization approaches. The source code is published under GNU Lesser General Public License v3.0 and is accessible at http://www.abrowse.org/. To demonstrate all the features of ABrowse, a live demo for Arabidopsis thaliana genome

  10. ABrowse - a customizable next-generation genome browser framework

    Directory of Open Access Journals (Sweden)

    Kong Lei

    2012-01-01

    Full Text Available Abstract Background With the rapid growth of genome sequencing projects, genome browser is becoming indispensable, not only as a visualization system but also as an interactive platform to support open data access and collaborative work. Thus a customizable genome browser framework with rich functions and flexible configuration is needed to facilitate various genome research projects. Results Based on next-generation web technologies, we have developed a general-purpose genome browser framework ABrowse which provides interactive browsing experience, open data access and collaborative work support. By supporting Google-map-like smooth navigation, ABrowse offers end users highly interactive browsing experience. To facilitate further data analysis, multiple data access approaches are supported for external platforms to retrieve data from ABrowse. To promote collaborative work, an online user-space is provided for end users to create, store and share comments, annotations and landmarks. For data providers, ABrowse is highly customizable and configurable. The framework provides a set of utilities to import annotation data conveniently. To build ABrowse on existing annotation databases, data providers could specify SQL statements according to database schema. And customized pages for detailed information display of annotation entries could be easily plugged in. For developers, new drawing strategies could be integrated into ABrowse for new types of annotation data. In addition, standard web service is provided for data retrieval remotely, providing underlying machine-oriented programming interface for open data access. Conclusions ABrowse framework is valuable for end users, data providers and developers by providing rich user functions and flexible customization approaches. The source code is published under GNU Lesser General Public License v3.0 and is accessible at http://www.abrowse.org/. To demonstrate all the features of ABrowse, a live demo for

  11. Building America

    Energy Technology Data Exchange (ETDEWEB)

    Brad Oberg

    2010-12-31

    IBACOS researched the constructability and viability issues of using high performance windows as one component of a larger approach to building houses that achieve the Building America 70% energy savings target.

  12. Building calculations

    DEFF Research Database (Denmark)

    Jensen, Bjarne Christian; Hansen, Svend Ole

    Textbook on design of large panel building including rules on robustness and a method for producing the Statical documentattion......Textbook on design of large panel building including rules on robustness and a method for producing the Statical documentattion...

  13. Software for computing and annotating genomic ranges.

    Directory of Open Access Journals (Sweden)

    Michael Lawrence

    Full Text Available We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

  14. Software for computing and annotating genomic ranges.

    Science.gov (United States)

    Lawrence, Michael; Huber, Wolfgang; Pagès, Hervé; Aboyoun, Patrick; Carlson, Marc; Gentleman, Robert; Morgan, Martin T; Carey, Vincent J

    2013-01-01

    We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

  15. MIPS PlantsDB: a database framework for comparative plant genome research.

    Science.gov (United States)

    Nussbaumer, Thomas; Martis, Mihaela M; Roessner, Stephan K; Pfeifer, Matthias; Bader, Kai C; Sharma, Sapna; Gundlach, Heidrun; Spannagl, Manuel

    2013-01-01

    The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/genomes.jsp) was initially described in NAR in 2007 [Spannagl,M., Noubibou,O., Haase,D., Yang,L., Gundlach,H., Hindemitt, T., Klee,K., Haberer,G., Schoof,H. and Mayer,K.F. (2007) MIPSPlantsDB-plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834-D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB.

  16. Solar building

    OpenAIRE

    Zhang, Luxin

    2014-01-01

    In my thesis I describe the utilization of solar energy and solar energy with building integration. In introduction it is also mentioned how the solar building works, trying to make more people understand and accept the solar building. The thesis introduces different types of solar heat collectors. I compared the difference two operation modes of solar water heating system and created examples of solar water system selection. I also introduced other solar building applications. It is conv...

  17. Building envelope

    CSIR Research Space (South Africa)

    Gibberd, Jeremy T

    2009-01-01

    Full Text Available for use in the building. This is done through photovoltaic and solar water heating panels and wind turbines. Ideally these are integrated in the design of the building envelope to improve the aesthetic quality of the building and minimise material... are naturally ventilated. Renewable energy The building envelope includes renewable energy generation such as photovoltaics, wind turbines and solar water heaters and 10% of the building’s energy requirements are generated from these sources. Views All...

  18. Genomic selection: genome-wide prediction in plant improvement.

    Science.gov (United States)

    Desta, Zeratsion Abera; Ortiz, Rodomiro

    2014-09-01

    Association analysis is used to measure relations between markers and quantitative trait loci (QTL). Their estimation ignores genes with small effects that trigger underpinning quantitative traits. By contrast, genome-wide selection estimates marker effects across the whole genome on the target population based on a prediction model developed in the training population (TP). Whole-genome prediction models estimate all marker effects in all loci and capture small QTL effects. Here, we review several genomic selection (GS) models with respect to both the prediction accuracy and genetic gain from selection. Phenotypic selection or marker-assisted breeding protocols can be replaced by selection, based on whole-genome predictions in which phenotyping updates the model to build up the prediction accuracy. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. Math for visualization, visualizing math

    NARCIS (Netherlands)

    Wijk, van J.J.; Hart, G.; Sarhangi, R.

    2013-01-01

    I present an overview of our work in visualization, and reflect on the role of mathematics therein. First, mathematics can be used as a tool to produce visualizations, which is illustrated with examples from information visualization, flow visualization, and cartography. Second, mathematics itself

  20. Visual art and visual perception

    NARCIS (Netherlands)

    Koenderink, Jan J.

    2015-01-01

    Visual art and visual perception ‘Visual art’ has become a minor cul-de-sac orthogonal to THE ART of the museum directors and billionaire collectors. THE ART is conceptual, instead of visual. Among its cherished items are the tins of artist’s shit (Piero Manzoni, 1961, Merda d’Artista) “worth their

  1. Auxiliary buildings

    International Nuclear Information System (INIS)

    Lakner, I.; Lestyan, E.

    1979-01-01

    The nuclear power station represents a complicated and a particular industrial project. Consequently, the design of the auxiliary buildings serving the power station (offices, kitchen, refreshment room, workshops, depots, water treatment plant building, boiler houses, etc.) requires more attention than usual. This chapter gives a short survey of the auxiliary buildings already completed and discusses the problems of their design, location and structure. (author)

  2. Building 2000

    International Nuclear Information System (INIS)

    Den Ouden, C.; Steemers, T.C.

    1992-01-01

    This is the first volume of Building 2000, a pilot project of the Commission's R and D-programme 'Solar Energy Applications to Buildings' with the purpose of encouraging the adoption of solar architecture in large buildings. In this first rich illustrated volume the results of the design studies illustrating passive solar architecture in buildings in the European Community are presented in particular for the building categories as mentioned in the subtitle. In a second volume, a similar series of studies is presented for the building categories: office buildings, public buildings and hotels and holiday complexes. Several Design Support Workshops were organized during the Building 2000 programme during which Building 2000 design teams could directly exchange ideas with the various design advice experts represented at these workshops. In the second part of the Building 2000 final report a summary of a selection of many reports is presented (15 papers), as produced by Design Support experts. Most of the design support activities resulted in changes of the various designs, as have been reported by the design teams in the brochures presented in the first part of this book. It is to be expected that design aids and simulation tools for passive solar options, daylighting concepts, comfort criteria etc., will be utilized more frequently in the future. This will result in a better exchange of information between the actual design practitioners and the European R and D community. This technology transfer will result in buildings with a higher quality with respect to energy and environmental issues

  3. Building 2000

    Energy Technology Data Exchange (ETDEWEB)

    Den Ouden, C [EGM Engineering BV, Dordrecht (Netherlands); Steemers, T C [Commission of the European Communities, Brussels (Belgium)

    1992-01-01

    This is the first volume of Building 2000, a pilot project of the Commission's R and D-programme 'Solar Energy Applications to Buildings' with the purpose of encouraging the adoption of solar architecture in large buildings. In this first rich illustrated volume the results of the design studies illustrating passive solar architecture in buildings in the European Community are presented in particular for the building categories as mentioned in the subtitle. In a second volume, a similar series of studies is presented for the building categories: office buildings, public buildings and hotels and holiday complexes. Several Design Support Workshops were organized during the Building 2000 programme during which Building 2000 design teams could directly exchange ideas with the various design advice experts represented at these workshops. In the second part of the Building 2000 final report a summary of a selection of many reports is presented (15 papers), as produced by Design Support experts. Most of the design support activities resulted in changes of the various designs, as have been reported by the design teams in the brochures presented in the first part of this book. It is to be expected that design aids and simulation tools for passive solar options, daylighting concepts, comfort criteria etc., will be utilized more frequently in the future. This will result in a better exchange of information between the actual design practitioners and the European R and D community. This technology transfer will result in buildings with a higher quality with respect to energy and environmental issues.

  4. Molecular simulations and visualization: introduction and overview.

    Science.gov (United States)

    Hirst, Jonathan D; Glowacki, David R; Baaden, Marc

    2014-01-01

    Here we provide an introduction and overview of current progress in the field of molecular simulation and visualization, touching on the following topics: (1) virtual and augmented reality for immersive molecular simulations; (2) advanced visualization and visual analytic techniques; (3) new developments in high performance computing; and (4) applications and model building.

  5. 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

  6. RPAN: rice pan-genome browser for ∼3000 rice genomes.

    Science.gov (United States)

    Sun, Chen; Hu, Zhiqiang; Zheng, Tianqing; Lu, Kuangchen; Zhao, Yue; Wang, Wensheng; Shi, Jianxin; Wang, Chunchao; Lu, Jinyuan; Zhang, Dabing; Li, Zhikang; Wei, Chaochun

    2017-01-25

    A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes with large-sized genomes. The Asian cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. Recently, the 3000 Rice Genome Project (3K RGP) sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3×, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genome Browser (RPAN), as a tool to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding. It is available at http://cgm.sjtu.edu.cn/3kricedb/ or http://www.rmbreeding.cn/pan3k. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Style grammars for interactive visualization of architecture.

    Science.gov (United States)

    Aliaga, Daniel G; Rosen, Paul A; Bekins, Daniel R

    2007-01-01

    Interactive visualization of architecture provides a way to quickly visualize existing or novel buildings and structures. Such applications require both fast rendering and an effortless input regimen for creating and changing architecture using high-level editing operations that automatically fill in the necessary details. Procedural modeling and synthesis is a powerful paradigm that yields high data amplification and can be coupled with fast-rendering techniques to quickly generate plausible details of a scene without much or any user interaction. Previously, forward generating procedural methods have been proposed where a procedure is explicitly created to generate particular content. In this paper, we present our work in inverse procedural modeling of buildings and describe how to use an extracted repertoire of building grammars to facilitate the visualization and quick modification of architectural structures and buildings. We demonstrate an interactive application where the user draws simple building blocks and, using our system, can automatically complete the building "in the style of" other buildings using view-dependent texture mapping or nonphotorealistic rendering techniques. Our system supports an arbitrary number of building grammars created from user subdivided building models and captured photographs. Using only edit, copy, and paste metaphors, the entire building styles can be altered and transferred from one building to another in a few operations, enhancing the ability to modify an existing architectural structure or to visualize a novel building in the style of the others.

  8. Visual Electricity Demonstrator

    Science.gov (United States)

    Lincoln, James

    2017-09-01

    The Visual Electricity Demonstrator (VED) is a linear diode array that serves as a dynamic alternative to an ammeter. A string of 48 red light-emitting diodes (LEDs) blink one after another to create the illusion of a moving current. Having the current represented visually builds an intuitive and qualitative understanding about what is happening in a circuit. In this article, I describe several activities for this device and explain how using this technology in the classroom can enhance the understanding and appreciation of physics.

  9. Visualizations as Projection Devices

    DEFF Research Database (Denmark)

    Harty, Chris; Holm Jacobsen, Peter; Tryggestad, Kjell

    The aim of this paper is to inquire into the role of project visualizations in shaping healthcare spaces and practices. The study draws upon an ethnographic field study from a large on-going hospital construction project in Denmark, and focuses on the early phases of on-boarding the design team...... into the project organization. During the on-boarding visualizations multiplies in form, content and purpose, ranging from paper and digitally based projections of clinical work spaces and practices for the future hospital building in use, to paper and digitally based projections of the cost budget and time...

  10. [Ethical considerations in genomic cohort study].

    Science.gov (United States)

    Choi, Eun Kyung; Kim, Ock-Joo

    2007-03-01

    During the last decade, genomic cohort study has been developed in many countries by linking health data and genetic data in stored samples. Genomic cohort study is expected to find key genetic components that contribute to common diseases, thereby promising great advance in genome medicine. While many countries endeavor to build biobank systems, biobank-based genome research has raised important ethical concerns including genetic privacy, confidentiality, discrimination, and informed consent. Informed consent for biobank poses an important question: whether true informed consent is possible in population-based genomic cohort research where the nature of future studies is unforeseeable when consent is obtained. Due to the sensitive character of genetic information, protecting privacy and keeping confidentiality become important topics. To minimize ethical problems and achieve scientific goals to its maximum degree, each country strives to build population-based genomic cohort research project, by organizing public consultation, trying public and expert consensus in research, and providing safeguards to protect privacy and confidentiality.

  11. Visual field

    Science.gov (United States)

    ... your visual field. How the Test is Performed Confrontation visual field exam. This is a quick and ... to achieve this important distinction for online health information and services. Learn more about A.D.A. ...

  12. Building 2000

    International Nuclear Information System (INIS)

    Den Ouden, C.; Steemers, T.C.

    1992-01-01

    This is the second volume of Building 2000, a pilot project of the Commission's R and D-programme 'Solar Energy Applications to Buildings' with the purpose of encouraging the adoption of solar architecture in large buildings. In this second rich illustrated volume the results of the design studies illustrating passive solar architecture in buildings in the European Community are presented in particular for the building categories as mentioned in the subtitle. In the first volume, a similar series of studies is presented for the building categories: schools, laboratories and universities, and sports and educational centres. Several Design Support Workshops were organized during the Building 2000 programme during which Building 2000 design teams could directly exchange ideas with the various design advice experts represented at these workshops. In the second part of the Building 2000 final report a summary of a selection of many reports is presented (11 papers), as produced by Design Support experts. Most of the design support activities resulted in changes of the various designs, as have been reported by the design teams in the brochures presented in the first part of this book. It is to be expected that design aids and simulation tools for passive solar options, daylighting concepts, comfort criteria etc., will be utilized more frequently in the future. This will result in a better exchange of information between the actual design practitioners and the European R and D community. This technology transfer will result in buildings with a higher quality with respect to energy and environmental issues

  13. Building 2000

    Energy Technology Data Exchange (ETDEWEB)

    Den Ouden, C [EGM Engineering BV, Dordrecht (Netherlands); Steemers, T C [Commission of the European Communities, Brussels (Belgium)

    1992-01-01

    This is the second volume of Building 2000, a pilot project of the Commission's R and D-programme 'Solar Energy Applications to Buildings' with the purpose of encouraging the adoption of solar architecture in large buildings. In this second rich illustrated volume the results of the design studies illustrating passive solar architecture in buildings in the European Community are presented in particular for the building categories as mentioned in the subtitle. In the first volume, a similar series of studies is presented for the building categories: schools, laboratories and universities, and sports and educational centres. Several Design Support Workshops were organized during the Building 2000 programme during which Building 2000 design teams could directly exchange ideas with the various design advice experts represented at these workshops. In the second part of the Building 2000 final report a summary of a selection of many reports is presented (11 papers), as produced by Design Support experts. Most of the design support activities resulted in changes of the various designs, as have been reported by the design teams in the brochures presented in the first part of this book. It is to be expected that design aids and simulation tools for passive solar options, daylighting concepts, comfort criteria etc., will be utilized more frequently in the future. This will result in a better exchange of information between the actual design practitioners and the European R and D community. This technology transfer will result in buildings with a higher quality with respect to energy and environmental issues.

  14. Irregular Shaped Building Design Optimization with Building Information Modelling

    Directory of Open Access Journals (Sweden)

    Lee Xia Sheng

    2016-01-01

    Full Text Available This research is to recognise the function of Building Information Modelling (BIM in design optimization for irregular shaped buildings. The study focuses on a conceptual irregular shaped “twisted” building design similar to some existing sculpture-like architectures. Form and function are the two most important aspects of new buildings, which are becoming more sophisticated as parts of equally sophisticated “systems” that we are living in. Nowadays, it is common to have irregular shaped or sculpture-like buildings which are very different when compared to regular buildings. Construction industry stakeholders are facing stiff challenges in many aspects such as buildability, cost effectiveness, delivery time and facility management when dealing with irregular shaped building projects. Building Information Modelling (BIM is being utilized to enable architects, engineers and constructors to gain improved visualization for irregular shaped buildings; this has a purpose of identifying critical issues before initiating physical construction work. In this study, three variations of design options differing in rotating angle: 30 degrees, 60 degrees and 90 degrees are created to conduct quantifiable comparisons. Discussions are focused on three major aspects including structural planning, usable building space, and structural constructability. This research concludes that Building Information Modelling is instrumental in facilitating design optimization for irregular shaped building. In the process of comparing different design variations, instead of just giving “yes or no” type of response, stakeholders can now easily visualize, evaluate and decide to achieve the right balance based on their own criteria. Therefore, construction project stakeholders are empowered with superior evaluation and decision making capability.

  15. Personalized medicine: new genomics, old lessons

    OpenAIRE

    Offit, Kenneth

    2011-01-01

    Personalized medicine uses traditional, as well as emerging concepts of the genetic and environmental basis of disease to individualize prevention, diagnosis and treatment. Personalized genomics plays a vital, but not exclusive role in this evolving model of personalized medicine. The distinctions between genetic and genomic medicine are more quantitative than qualitative. Personalized genomics builds on principles established by the integration of genetics into medical practice. Principles s...

  16. Laboratory Building

    Energy Technology Data Exchange (ETDEWEB)

    Herrera, Joshua M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-03-01

    This report is an analysis of the means of egress and life safety requirements for the laboratory building. The building is located at Sandia National Laboratories (SNL) in Albuquerque, NM. The report includes a prescriptive-based analysis as well as a performance-based analysis. Following the analysis are appendices which contain maps of the laboratory building used throughout the analysis. The top of all the maps is assumed to be north.

  17. Data visualization

    CERN Document Server

    Azzam, Tarek

    2013-01-01

    Do you communicate data and information to stakeholders? In Part 1, we introduce recent developments in the quantitative and qualitative data visualization field and provide a historical perspective on data visualization, its potential role in evaluation practice, and future directions. Part 2 delivers concrete suggestions for optimally using data visualization in evaluation, as well as suggestions for best practices in data visualization design. It focuses on specific quantitative and qualitative data visualization approaches that include data dashboards, graphic recording, and geographic information systems (GIS). Readers will get a step-by-step process for designing an effective data dashboard system for programs and organizations, and various suggestions to improve their utility.

  18. Integrative Genomics Viewer (IGV) | Informatics Technology for Cancer Research (ITCR)

    Science.gov (United States)

    The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

  19. Genome Imprinting

    Indian Academy of Sciences (India)

    the cell nucleus (mitochondrial and chloroplast genomes), and. (3) traits governed ... tively good embryonic development but very poor development of membranes and ... Human homologies for the type of situation described above are naturally ..... imprint; (b) New modifications of the paternal genome in germ cells of each ...

  20. Baculovirus Genomics

    NARCIS (Netherlands)

    Oers, van M.M.; Vlak, J.M.

    2007-01-01

    Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

  1. Genomic Testing

    Science.gov (United States)

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

  2. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

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

  3. Visual Literacy and Visual Thinking.

    Science.gov (United States)

    Hortin, John A.

    It is proposed that visual literacy be defined as the ability to understand (read) and use (write) images and to think and learn in terms of images. This definition includes three basic principles: (1) visuals are a language and thus analogous to verbal language; (2) a visually literate person should be able to understand (read) images and use…

  4. Institutionalizing New Ideas Through Visualization

    DEFF Research Database (Denmark)

    Meyer, Renate; Jancsary, Dennis; Höllerer, Markus A.

    How do visualization and visual forms of communication influence the process of transforming a novel idea into established organizational practice? In this paper, we build theory with regard to the role of visuals in manifesting and giving form to an innovative idea as it proceeds through various...... stages of institutionalization. Ideas become institutionalized not merely through widespread diffusion in a cognitive-discursive form but eventually through their translation into concrete activities and transformation into specific patterns of organizational practice. We argue that visualization plays...... a pivotal and unique role in this process. Visualization bridges the ideational with the practical realm by providing representations of ideas, connecting them to existing knowledge, and illustrating the specific actions that instantiate them. Similar to verbal discourse, and often in tandem, visual...

  5. QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks.

    Directory of Open Access Journals (Sweden)

    Asa Thibodeau

    2016-06-01

    Full Text Available Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1 building and visualizing chromatin interaction networks, 2 annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3 querying network components based on gene name or chromosome location, and 4 utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions.QuIN's web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub: https://github.com/UcarLab/QuIN/.

  6. QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks.

    Science.gov (United States)

    Thibodeau, Asa; Márquez, Eladio J; Luo, Oscar; Ruan, Yijun; Menghi, Francesca; Shin, Dong-Guk; Stitzel, Michael L; Vera-Licona, Paola; Ucar, Duygu

    2016-06-01

    Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions. QuIN's web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub: https://github.com/UcarLab/QuIN/.

  7. Visual identity and rebranding

    Directory of Open Access Journals (Sweden)

    Katarzyna Wrona

    2015-06-01

    Full Text Available The goal of this article is to highlight the essence of visual identification and rebranding, as well as to discuss elements of corporate identity, which are subject to revitalization in the process of refreshing the image of a brand. In the first part the article the analysis of the term visual identification is conducted. In the analysis special attention is drawn to the role of visual identification in creating a coherent identity of an organization. In the subsequent chapters further components of corporate identity are presented in detail – starting with logotype, through business forms, advertisements, accompanying materials and Internet websites to signs on buildings. Moreover, corporate identity book as a collection of standards and guidelines for application of corporate identity rules is discussed. The deliberations are based on the study of literature. The last chapter presented the transformation of the brand of Institute of Aviation.

  8. Building a capacity building manual

    CSIR Research Space (South Africa)

    Clinton, DD

    2010-02-01

    Full Text Available Organizations 2010 Building a capacity building manual Daniel D. Clinton, Jr., P.E., F.NSPE Chair, WFEO Capacity Building Committee Dr Andrew Cleland, FIPENZ, Chief Executive, IPENZ, NZ Eng David Botha, FSAICE, Executive Director, SAICE, SA Dawit... 2010 Tertiary level University curricula Coaches and mentors Facilities EXCeeD Remuneration of Academics Experiential training Outreach to Students Students chapters Young members forum World Federation of Engineering Organizations 2010 Post...

  9. Structural building screening and evaluation

    Science.gov (United States)

    Kurniawandy, Alex; Nakazawa, Shoji; Hendry, Andy; Ridwan, Firdaus, Rahmatul

    2017-10-01

    An earthquake is a disaster that can be harmful to the community, such as financial loss and also dead injuries. Pekanbaru is a city that located in the middle of Sumatera Island. Even though the city of Pekanbaru is a city that rarely occurs earthquake, but Pekanbaru has ever felt the impact of the big earthquake that occurred in West Sumatera on September 2009. As we know, Indonesia located between Eurasia plate, Pacific plate, and Indo-Australian plate. Particularly the Sumatera Island, It has the Semangko fault or the great Sumatra fault along the island from north to south due to the shift of Eurasia and Indo-Australian Plates. An earthquake is not killing people but the building around the people that could be killing them. The failure of the building can be early prevented by doing an evaluation. In this research, the methods of evaluation have used a guideline for the Federal Emergency Management Agency (FEMA) P-154 and Applied Technology Council (ATC) 40. FEMA P-154 is a rapid visual screening of buildings for potential seismic hazards and ATC-40 is seismic evaluation and retrofit of Concrete Buildings. ATC-40 is a more complex evaluation rather than FEMA P-154. The samples to be evaluated are taken in the surroundings of Universitas Riau facility in Pekanbaru. There are four buildings as case study such as the rent student building, the building of mathematics and natural science faculty, the building teacher training and education faculty and the buildings in the faculty of Social political sciences. Vulnerability for every building facing an earthquake is different, this is depending on structural and non-structural components of the building. Among all of the samples, only the building of mathematics and the natural science faculty is in critical condition according to the FEMA P-154 evaluation. Furthermore, the results of evaluation using ATC-40 for the teacher training building are in damage control conditions, despite the other three buildings are

  10. The life cycle of a genome project: perspectives and guidelines inspired by insect genome projects.

    Science.gov (United States)

    Papanicolaou, Alexie

    2016-01-01

    Many research programs on non-model species biology have been empowered by genomics. In turn, genomics is underpinned by a reference sequence and ancillary information created by so-called "genome projects". The most reliable genome projects are the ones created as part of an active research program and designed to address specific questions but their life extends past publication. In this opinion paper I outline four key insights that have facilitated maintaining genomic communities: the key role of computational capability, the iterative process of building genomic resources, the value of community participation and the importance of manual curation. Taken together, these ideas can and do ensure the longevity of genome projects and the growing non-model species community can use them to focus a discussion with regards to its future genomic infrastructure.

  11. Reactor building

    International Nuclear Information System (INIS)

    Ebata, Sakae.

    1990-01-01

    At least one valve rack is disposed in a reactor building, on which pipeways to a main closure valve, valves and bypasses of turbines are placed and contained. The valve rack is fixed to the main body of the building or to a base mat. Since the reactor building is designed as class A earthquake-proofness and for maintaining the S 1 function, the valve rack can be fixed to the building main body or to the base mat. With such a constitution, the portions for maintaining the S 1 function are concentrated to the reactor building. As a result, the dispersion of structures of earthquake-proof portion corresponding to the reference earthquake vibration S 1 can be prevented. Accordingly, the conditions for the earthquake-proof design of the turbine building and the turbine/electric generator supporting rack are defined as only the class B earthquake-proof design conditions. In view of the above, the amount of building materials can be saved and the time for construction can be shortened. (I.S.)

  12. Traffic Visualization

    DEFF Research Database (Denmark)

    Picozzi, Matteo; Verdezoto, Nervo; Pouke, Matti

    2013-01-01

    In this paper, we present a space-time visualization to provide city's decision-makers the ability to analyse and uncover important "city events" in an understandable manner for city planning activities. An interactive Web mashup visualization is presented that integrates several visualization...... techniques to give a rapid overview of traffic data. We illustrate our approach as a case study for traffic visualization systems, using datasets from the city of Oulu that can be extended to other city planning activities. We also report the feedback of real users (traffic management employees, traffic police...

  13. Visualization Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Evaluates and improves the operational effectiveness of existing and emerging electronic warfare systems. By analyzing and visualizing simulation results...

  14. Distributed Visualization

    Data.gov (United States)

    National Aeronautics and Space Administration — Distributed Visualization allows anyone, anywhere, to see any simulation, at any time. Development focuses on algorithms, software, data formats, data systems and...

  15. Building sustainability

    CSIR Research Space (South Africa)

    Mass Media

    2007-11-01

    Full Text Available particu- lar social environment also being awarded. If a building can be used by the community after hours, it should be awarded extra points.” School sports facilities or meeting halls in corporate buildings, are some example. Multi-purpose use..., architect and senior researcher for the CSIR’s Built Environment Unit, the integra- tion of sustainability in building design cannot begin soon enough before it is too late. He says: “Unfortunately nothing is in place in South Africa. For a start...

  16. Building Acoustics

    Science.gov (United States)

    Cowan, James

    This chapter summarizes and explains key concepts of building acoustics. These issues include the behavior of sound waves in rooms, the most commonly used rating systems for sound and sound control in buildings, the most common noise sources found in buildings, practical noise control methods for these sources, and the specific topic of office acoustics. Common noise issues for multi-dwelling units can be derived from most of the sections of this chapter. Books can be and have been written on each of these topics, so the purpose of this chapter is to summarize this information and provide appropriate resources for further exploration of each topic.

  17. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  18. CyanoBase: the cyanobacteria genome database update 2010.

    Science.gov (United States)

    Nakao, Mitsuteru; Okamoto, Shinobu; Kohara, Mitsuyo; Fujishiro, Tsunakazu; Fujisawa, Takatomo; Sato, Shusei; Tabata, Satoshi; Kaneko, Takakazu; Nakamura, Yasukazu

    2010-01-01

    CyanoBase (http://genome.kazusa.or.jp/cyanobase) is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene information, gene annotations and mutant information. In this version, we updated these datasets and improved the navigation and the visual display of the data views. In addition, a web service API now enables users to retrieve the data in various formats with other tools, seamlessly.

  19. CyanoBase: the cyanobacteria genome database update 2010

    OpenAIRE

    Nakao, Mitsuteru; Okamoto, Shinobu; Kohara, Mitsuyo; Fujishiro, Tsunakazu; Fujisawa, Takatomo; Sato, Shusei; Tabata, Satoshi; Kaneko, Takakazu; Nakamura, Yasukazu

    2009-01-01

    CyanoBase (http://genome.kazusa.or.jp/cyanobase) is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene information, gene annotations and mutant information. In this version, we updated these datasets and improved the navigation and the visual display of the data views. In addition, a web service API now enables users to retrieve the data in var...

  20. Building Data

    Data.gov (United States)

    Town of Cary, North Carolina — Explore real estate information about buildings in the Town of Cary.This file is created by the Town of Cary GIS Group. It contains data from both the Wake, Chatham...

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

    Science.gov (United States)

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

    2013-01-01

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

  2. Visual Impairment

    Science.gov (United States)

    ... site Sitio para adolescentes Body Mind Sexual Health Food & Fitness Diseases & Conditions Infections Drugs & Alcohol School & Jobs Sports Expert Answers (Q&A) Staying Safe Videos for Educators Search English Español Visual Impairment KidsHealth / For Teens / Visual Impairment What's in ...

  3. Visual attention

    NARCIS (Netherlands)

    Evans, K.K.; Horowitz, T.S.; Howe, P.; Pedersini, R.; Reijnen, E.; Pinto, Y.; Wolfe, J.M.

    2011-01-01

    A typical visual scene we encounter in everyday life is complex and filled with a huge amount of perceptual information. The term, ‘visual attention’ describes a set of mechanisms that limit some processing to a subset of incoming stimuli. Attentional mechanisms shape what we see and what we can act

  4. Visual Education

    DEFF Research Database (Denmark)

    Buhl, Mie; Flensborg, Ingelise

    2010-01-01

    The intrinsic breadth of various types of images creates new possibilities and challenges for visual education. The digital media have moved the boundaries between images and other kinds of modalities (e.g. writing, speech and sound) and have augmented the possibilities for integrating the functi......The intrinsic breadth of various types of images creates new possibilities and challenges for visual education. The digital media have moved the boundaries between images and other kinds of modalities (e.g. writing, speech and sound) and have augmented the possibilities for integrating...... to emerge in the interlocutory space of a global visual repertoire and diverse local interpretations. The two perspectives represent challenges for future visual education which require visual competences, not only within the arts but also within the subjects of natural sciences, social sciences, languages...

  5. Building technolgies program. 1994 annual report

    Energy Technology Data Exchange (ETDEWEB)

    Selkowitz, S.E.

    1995-04-01

    The objective of the Building Technologies program is to assist the U.S. building industry in achieving substantial reductions in building sector energy use and associated greenhouse gas emissions while improving comfort, amenity, health, and productivity in the building sector. We have focused our past efforts on two major building systems, windows and lighting, and on the simulation tools needed by researchers and designers to integrate the full range of energy efficiency solutions into achievable, cost-effective design solutions for new and existing buildings. In addition, we are now taking more of an integrated systems and life cycle perspective to create cost-effective solutions for more energy efficient, comfortable, and productive work and living environments. More than 30% of all energy use in buildings is attributable to two sources: windows and lighting. Together they account for annual consumer energy expenditures of more than $50 billion. Each affects not only energy use by other major building systems, but also comfort and productivity-factors that influence building economics far more than does direct energy consumption alone. Windows play a unique role in the building envelope, physically separating the conditioned space from the world outside without sacrificing vital visual contact. Throughout every space in a building, lighting systems facilitate a variety of tasks associated with a wide range of visual requirements while defining the luminous qualities of the indoor environment. Window and lighting systems are thus essential components of any comprehensive building science program.

  6. The Saccharomyces Genome Database Variant Viewer.

    Science.gov (United States)

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

    2016-01-04

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

  7. Visual cognition

    Science.gov (United States)

    Cavanagh, Patrick

    2011-01-01

    Visual cognition, high-level vision, mid-level vision and top-down processing all refer to decision-based scene analyses that combine prior knowledge with retinal input to generate representations. The label “visual cognition” is little used at present, but research and experiments on mid- and high-level, inference-based vision have flourished, becoming in the 21st century a significant, if often understated part, of current vision research. How does visual cognition work? What are its moving parts? This paper reviews the origins and architecture of visual cognition and briefly describes some work in the areas of routines, attention, surfaces, objects, and events (motion, causality, and agency). Most vision scientists avoid being too explicit when presenting concepts about visual cognition, having learned that explicit models invite easy criticism. What we see in the literature is ample evidence for visual cognition, but few or only cautious attempts to detail how it might work. This is the great unfinished business of vision research: at some point we will be done with characterizing how the visual system measures the world and we will have to return to the question of how vision constructs models of objects, surfaces, scenes, and events. PMID:21329719

  8. Visual cognition.

    Science.gov (United States)

    Cavanagh, Patrick

    2011-07-01

    Visual cognition, high-level vision, mid-level vision and top-down processing all refer to decision-based scene analyses that combine prior knowledge with retinal input to generate representations. The label "visual cognition" is little used at present, but research and experiments on mid- and high-level, inference-based vision have flourished, becoming in the 21st century a significant, if often understated part, of current vision research. How does visual cognition work? What are its moving parts? This paper reviews the origins and architecture of visual cognition and briefly describes some work in the areas of routines, attention, surfaces, objects, and events (motion, causality, and agency). Most vision scientists avoid being too explicit when presenting concepts about visual cognition, having learned that explicit models invite easy criticism. What we see in the literature is ample evidence for visual cognition, but few or only cautious attempts to detail how it might work. This is the great unfinished business of vision research: at some point we will be done with characterizing how the visual system measures the world and we will have to return to the question of how vision constructs models of objects, surfaces, scenes, and events. Copyright © 2011 Elsevier Ltd. All rights reserved.

  9. 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.

  10. Enhancing learning and comprehension through strengthening visual literacy

    Directory of Open Access Journals (Sweden)

    Le Roux, Cheryl

    2009-12-01

    Full Text Available Living in an image-rich world, as we currently do, does not mean that individuals naturally possess visual literacy skills. This article explores the concept of ‘visual literacy’, and the skills needed to develop visual literacy and visual intelligence. Developing visual literacy in educational environments is important because it can contribute to individual empowerment, and it is therefore necessary to take pedagogical advantage of visual literacy’s place across the disciplines. Doing this means tapping into experiences, expertise and interest in visual communication and building a new paradigm that takes visual education seriously.

  11. Big Data Analytics for Genomic Medicine.

    Science.gov (United States)

    He, Karen Y; Ge, Dongliang; He, Max M

    2017-02-15

    Genomic medicine attempts to build individualized strategies for diagnostic or therapeutic decision-making by utilizing patients' genomic information. Big Data analytics uncovers hidden patterns, unknown correlations, and other insights through examining large-scale various data sets. While integration and manipulation of diverse genomic data and comprehensive electronic health records (EHRs) on a Big Data infrastructure exhibit challenges, they also provide a feasible opportunity to develop an efficient and effective approach to identify clinically actionable genetic variants for individualized diagnosis and therapy. In this paper, we review the challenges of manipulating large-scale next-generation sequencing (NGS) data and diverse clinical data derived from the EHRs for genomic medicine. We introduce possible solutions for different challenges in manipulating, managing, and analyzing genomic and clinical data to implement genomic medicine. Additionally, we also present a practical Big Data toolset for identifying clinically actionable genetic variants using high-throughput NGS data and EHRs.

  12. Big Data Analytics for Genomic Medicine

    Science.gov (United States)

    He, Karen Y.; Ge, Dongliang; He, Max M.

    2017-01-01

    Genomic medicine attempts to build individualized strategies for diagnostic or therapeutic decision-making by utilizing patients’ genomic information. Big Data analytics uncovers hidden patterns, unknown correlations, and other insights through examining large-scale various data sets. While integration and manipulation of diverse genomic data and comprehensive electronic health records (EHRs) on a Big Data infrastructure exhibit challenges, they also provide a feasible opportunity to develop an efficient and effective approach to identify clinically actionable genetic variants for individualized diagnosis and therapy. In this paper, we review the challenges of manipulating large-scale next-generation sequencing (NGS) data and diverse clinical data derived from the EHRs for genomic medicine. We introduce possible solutions for different challenges in manipulating, managing, and analyzing genomic and clinical data to implement genomic medicine. Additionally, we also present a practical Big Data toolset for identifying clinically actionable genetic variants using high-throughput NGS data and EHRs. PMID:28212287

  13. Multiscale modeling of three-dimensional genome

    Science.gov (United States)

    Zhang, Bin; Wolynes, Peter

    The genome, the blueprint of life, contains nearly all the information needed to build and maintain an entire organism. A comprehensive understanding of the genome is of paramount interest to human health and will advance progress in many areas, including life sciences, medicine, and biotechnology. The overarching goal of my research is to understand the structure-dynamics-function relationships of the human genome. In this talk, I will be presenting our efforts in moving towards that goal, with a particular emphasis on studying the three-dimensional organization, the structure of the genome with multi-scale approaches. Specifically, I will discuss the reconstruction of genome structures at both interphase and metaphase by making use of data from chromosome conformation capture experiments. Computationally modeling of chromatin fiber at atomistic level from first principles will also be presented as our effort for studying the genome structure from bottom up.

  14. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  15. Competence Building

    DEFF Research Database (Denmark)

    Borrás, Susana; Edquist, Charles

    The main question that guides this paper is how governments are focusing (and must focus) on competence building (education and training) when designing and implementing innovation policies. With this approach, the paper aims at filling the gap between the existing literature on competences...... on the one hand, and the real world of innovation policy-making on the other, typically not speaking to each other. With this purpose in mind, this paper discusses the role of competences and competence-building in the innovation process from a perspective of innovation systems; it examines how governments...... and public agencies in different countries and different times have actually approached the issue of building, maintaining and using competences in their innovation systems; it examines what are the critical and most important issues at stake from the point of view of innovation policy, looking particularly...

  16. Building Procurement

    DEFF Research Database (Denmark)

    Andersson, Niclas

    2007-01-01

    evolves from a simple establishment of a contractual relationship to a central and strategic part of construction. The authors relate to cultural, ethical and social and behavioural sciences as the fundamental basis for analysis and understanding of the complexity and dynamics of the procurement system......‘The procurement of construction work is complex, and a successful outcome frequently elusive’. With this opening phrase of the book, the authors take on the challenging job of explaining the complexity of building procurement. Even though building procurement systems are, and will remain, complex...... despite this excellent book, the knowledge, expertise, well-articulated argument and collection of recent research efforts that are provided by the three authors will help to make project success less elusive. The book constitutes a thorough and comprehensive investigation of building procurement, which...

  17. Visualizing phylogenetic tree landscapes.

    Science.gov (United States)

    Wilgenbusch, James C; Huang, Wen; Gallivan, Kyle A

    2017-02-02

    Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems. Discovery of efficient and accurate dimensionality reduction methods used to display at once in 2- or 3- dimensions the relationship among these competing phylogenies will help practitioners diagnose the limits of current evolutionary models and potential problems with phylogenetic reconstruction methods when analyzing large multi-source data sets. We introduce several dimensionality reduction methods to visualize in 2- and 3-dimensions the relationship among competing phylogenies obtained from gene partitions found in three mid- to large-size mitochondrial genome alignments. We test the performance of these dimensionality reduction methods by applying several goodness-of-fit measures. The intrinsic dimensionality of each data set is also estimated to determine whether projections in 2- and 3-dimensions can be expected to reveal meaningful relationships among trees from different data partitions. Several new approaches to aid in the comparison of different phylogenetic landscapes are presented. Curvilinear Components Analysis (CCA) and a stochastic gradient decent (SGD) optimization method give the best representation of the original tree-to-tree distance matrix for each of the three- mitochondrial genome alignments and greatly outperformed the method currently used to visualize tree landscapes. The CCA + SGD method converged at least as fast as previously applied methods for visualizing tree landscapes. We demonstrate for all three mtDNA alignments that 3D

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

    Science.gov (United States)

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

    2007-09-18

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

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

    Directory of Open Access Journals (Sweden)

    Gardner Timothy S

    2007-09-01

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

  20. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  1. Data visualization with d3.js

    CERN Document Server

    Teller, Swizec

    2013-01-01

    This book is a mini tutorial with plenty of code examples and strategies to give you many options when building your own visualizations.This book is ideal for anyone interested in data visualization. Some rudimentary knowledge of JavaScript is required.

  2. Supporting exploration awareness for visual analytics

    NARCIS (Netherlands)

    Shrinivasan, Y.B.; Wijk, van J.J.

    2008-01-01

    While exploring data using information visualization, analysts try to make sense of the data, build cases, and present them to others. However, if the exploration is long or done in multiple sessions, it can be hard for analysts to remember all interesting visualizations and the relationships among

  3. Visual cognition

    Energy Technology Data Exchange (ETDEWEB)

    Pinker, S.

    1985-01-01

    This book consists of essays covering issues in visual cognition presenting experimental techniques from cognitive psychology, methods of modeling cognitive processes on computers from artificial intelligence, and methods of studying brain organization from neuropsychology. Topics considered include: parts of recognition; visual routines; upward direction; mental rotation, and discrimination of left and right turns in maps; individual differences in mental imagery, computational analysis and the neurological basis of mental imagery: componental analysis.

  4. Visual search, visual streams, and visual architectures.

    Science.gov (United States)

    Green, M

    1991-10-01

    Most psychological, physiological, and computational models of early vision suggest that retinal information is divided into a parallel set of feature modules. The dominant theories of visual search assume that these modules form a "blackboard" architecture: a set of independent representations that communicate only through a central processor. A review of research shows that blackboard-based theories, such as feature-integration theory, cannot easily explain the existing data. The experimental evidence is more consistent with a "network" architecture, which stresses that: (1) feature modules are directly connected to one another, (2) features and their locations are represented together, (3) feature detection and integration are not distinct processing stages, and (4) no executive control process, such as focal attention, is needed to integrate features. Attention is not a spotlight that synthesizes objects from raw features. Instead, it is better to conceptualize attention as an aperture which masks irrelevant visual information.

  5. Existing buildings

    DEFF Research Database (Denmark)

    Gram-Hanssen, Kirsten

    2014-01-01

    their homes. These policy measures include building regulations, energy tax and different types of incentives and information dissemination. The conclusion calls for new and innovative policy measures to cope with the realities of renovations of owner-occupied houses and how energy efficiency improvement...

  6. Building Sandcastles

    DEFF Research Database (Denmark)

    Jensen, Steffen Moltrup Ernø; Korsgaard, Steffen; Shumar, Wes

    of entrepreneurship education. Our theoretical and methodological approach builds on Actor-Network Theory. The empirical settings of our study consist of two entrepreneurship courses which differ in terms of temporal extension and physical setting. Data is collected using observation and interview techniques. Our...

  7. Sustainable Buildings

    DEFF Research Database (Denmark)

    Tommerup, Henrik M.; Elle, Morten

    The scientific community agrees that: all countries must drastically and rapidly reduce their CO2 emissions and that energy efficient houses play a decisive role in this. The general attitude at the workshop on Sustainable Buildings was that we face large and serious climate change problems...

  8. INL High Performance Building Strategy

    Energy Technology Data Exchange (ETDEWEB)

    Jennifer D. Morton

    2010-02-01

    High performance buildings, also known as sustainable buildings and green buildings, are resource efficient structures that minimize the impact on the environment by using less energy and water, reduce solid waste and pollutants, and limit the depletion of natural resources while also providing a thermally and visually comfortable working environment that increases productivity for building occupants. As Idaho National Laboratory (INL) becomes the nation’s premier nuclear energy research laboratory, the physical infrastructure will be established to help accomplish this mission. This infrastructure, particularly the buildings, should incorporate high performance sustainable design features in order to be environmentally responsible and reflect an image of progressiveness and innovation to the public and prospective employees. Additionally, INL is a large consumer of energy that contributes to both carbon emissions and resource inefficiency. In the current climate of rising energy prices and political pressure for carbon reduction, this guide will help new construction project teams to design facilities that are sustainable and reduce energy costs, thereby reducing carbon emissions. With these concerns in mind, the recommendations described in the INL High Performance Building Strategy (previously called the INL Green Building Strategy) are intended to form the INL foundation for high performance building standards. This revised strategy incorporates the latest federal and DOE orders (Executive Order [EO] 13514, “Federal Leadership in Environmental, Energy, and Economic Performance” [2009], EO 13423, “Strengthening Federal Environmental, Energy, and Transportation Management” [2007], and DOE Order 430.2B, “Departmental Energy, Renewable Energy, and Transportation Management” [2008]), the latest guidelines, trends, and observations in high performance building construction, and the latest changes to the Leadership in Energy and Environmental Design

  9. Comparative Genomics

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 8. Comparative Genomics - A Powerful New Tool in Biology. Anand K Bachhawat. General Article Volume 11 Issue 8 August 2006 pp 22-40. Fulltext. Click here to view fulltext PDF. Permanent link:

  10. Visualizing water

    Science.gov (United States)

    Baart, F.; van Gils, A.; Hagenaars, G.; Donchyts, G.; Eisemann, E.; van Velzen, J. W.

    2016-12-01

    A compelling visualization is captivating, beautiful and narrative. Here we show how melding the skills of computer graphics, art, statistics, and environmental modeling can be used to generate innovative, attractive and very informative visualizations. We focus on the topic of visualizing forecasts and measurements of water (water level, waves, currents, density, and salinity). For the field of computer graphics and arts, water is an important topic because it occurs in many natural scenes. For environmental modeling and statistics, water is an important topic because the water is essential for transport, a healthy environment, fruitful agriculture, and a safe environment.The different disciplines take different approaches to visualizing water. In computer graphics, one focusses on creating water as realistic looking as possible. The focus on realistic perception (versus the focus on the physical balance pursued by environmental scientists) resulted in fascinating renderings, as seen in recent games and movies. Visualization techniques for statistical results have benefited from the advancement in design and journalism, resulting in enthralling infographics. The field of environmental modeling has absorbed advances in contemporary cartography as seen in the latest interactive data-driven maps. We systematically review the design emerging types of water visualizations. The examples that we analyze range from dynamically animated forecasts, interactive paintings, infographics, modern cartography to web-based photorealistic rendering. By characterizing the intended audience, the design choices, the scales (e.g. time, space), and the explorability we provide a set of guidelines and genres. The unique contributions of the different fields show how the innovations in the current state of the art of water visualization have benefited from inter-disciplinary collaborations.

  11. Designing Visual Character Of Raden Wijaya As Historical Figure In Visual Novel

    Directory of Open Access Journals (Sweden)

    Dendi Pratama

    2017-11-01

    Full Text Available Visual character in Visual Novel games have the power to carry messages. Creation of visual characters in historical narratives can also bring cultural meaning. This study examines the creation of Raden Wijaya visual character as a case example in Visual Novel Twist Majapahit which is set in Majapahit kingdom but with manga-style visualization. On the contrary the creation of Raden Wijaya visual character in this study is more trying to accentuate the characteristic of Indonesia. The choice of Raden Wijaya character is based on consideration because it has historically included a major influence in expanding the royal power. The study discussions are elaborated qualitatively with the Social Semiotic approach that analyzes informative functions interactive functions and imaginative functions in visual character design elements. The results of this study show that design elements can build a comprehensive association of meanings so that the creation of visual characters tailored to historical figures has the potential to bring cultural messages.

  12. Aligning the unalignable: bacteriophage whole genome alignments.

    Science.gov (United States)

    Bérard, Sèverine; Chateau, Annie; Pompidor, Nicolas; Guertin, Paul; Bergeron, Anne; Swenson, Krister M

    2016-01-13

    In recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for comparing whole genomes exist: dot plots diagrams give a mostly qualitative assessment of the similarity/dissimilarity between two or more genomes, and clustering techniques are used to classify genomes. Multiple alignments are conspicuously absent from this scene. Indeed, whole genome aligners interpret lack of similarity between sequences as an indication of rearrangements, insertions, or losses. This behavior makes them ill-prepared to align bacteriophage genomes, where even closely related strains can accomplish the same biological function with highly dissimilar sequences. In this paper, we propose a multiple alignment strategy that exploits functional collinearity shared by related strains of bacteriophages, and uses partial orders to capture mosaicism of sets of genomes. As classical alignments do, the computed alignments can be used to predict that genes have the same biological function, even in the absence of detectable similarity. The Alpha aligner implements these ideas in visual interactive displays, and is used to compute several examples of alignments of Staphylococcus aureus and Mycobacterium bacteriophages, involving up to 29 genomes. Using these datasets, we prove that Alpha alignments are at least as good as those computed by standard aligners. Comparison with the progressive Mauve aligner - which implements a partial order strategy, but whose alignments are linearized - shows a greatly improved interactive graphic display, while avoiding misalignments. Multiple alignments of whole bacteriophage genomes work, and will become an important conceptual and visual tool in comparative genomics of sets of related strains. A python implementation of Alpha, along with installation instructions for Ubuntu and OSX, is available on bitbucket (https://bitbucket.org/thekswenson/alpha).

  13. Icarus: visualizer for de novo assembly evaluation.

    Science.gov (United States)

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

    2016-11-01

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

  14. Building Bridges

    DEFF Research Database (Denmark)

    The report Building Bridges adresses the questions why, how and for whom academic audience research has public value, from the different points of view of the four working groups in the COST Action IS0906 Transforming Audiences, Transforming Societies – “New Media Genres, Media Literacy and Trust...... in the Media”, “Audience Interactivity and Participation”, “The Role of Media and ICT Use for Evolving Social Relationships” and “Audience Transformations and Social Integration”. Building Bridges is the result of an ongoing dialogue between the Action and non-academic stakeholders in the field of audience......, Brian O’Neill, Andra Siibak, Sascha Trültzsch-Wijnen, Nicoletta Vittadini, Igor Vobič and Frauke Zeller. Stakeholder feedback from: Michelle Arlotta (DeAgostini), Andreea M. Costache (Association of Consumers of Audiovisual Media in Catalonia/TAC), Francesco Diasio (AMARC Europe), Marius Dragomir (Open...

  15. Visual cognition

    Energy Technology Data Exchange (ETDEWEB)

    Pinker, S.

    1985-01-01

    This collection of research papers on visual cognition first appeared as a special issue of Cognition: International Journal of Cognitive Science. The study of visual cognition has seen enormous progress in the past decade, bringing important advances in our understanding of shape perception, visual imagery, and mental maps. Many of these discoveries are the result of converging investigations in different areas, such as cognitive and perceptual psychology, artificial intelligence, and neuropsychology. This volume is intended to highlight a sample of work at the cutting edge of this research area for the benefit of students and researchers in a variety of disciplines. The tutorial introduction that begins the volume is designed to help the nonspecialist reader bridge the gap between the contemporary research reported here and earlier textbook introductions or literature reviews.

  16. Visualizing Transformation

    DEFF Research Database (Denmark)

    Pedersen, Pia

    2012-01-01

    Transformation, defined as the step of extracting, arranging and simplifying data into visual form (M. Neurath, 1974), was developed in connection with ISOTYPE (International System Of TYpographic Picture Education) and might well be the most important legacy of Isotype to the field of graphic...... design. Recently transformation has attracted renewed interest because of the book The Transformer written by Robin Kinross and Marie Neurath. My on-going research project, summarized in this paper, identifies and depicts the essential principles of data visualization underlying the process...... of transformation with reference to Marie Neurath’s sketches on the Bilston Project. The material has been collected at the Otto and Marie Neurath Collection housed at the University of Reading, UK. By using data visualization as a research method to look directly into the process of transformation, the project...

  17. Building economics

    DEFF Research Database (Denmark)

    Pedersen, D.O.(red.)

    Publikationen er på engelsk. Den omfatter alle indlæg på det fjerde internationale symposium om byggeøkonomi, der blev arrangeret af SBI for det internationale byggeforskningsråd CIB. De fem bind omhandler: Methods of Economic Evaluation, Design Optimization, Ressource Utilization, The Building...... Market og Economics and Technological Forecasting in Construction. Et indledende bind bringer statusrapporter for de fem forskningsområder, og det sidste bind sammenfatter debatten på symposiet....

  18. Personal genomics services: whose genomes?

    Science.gov (United States)

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

  19. Integrated Genome-Based Studies of Shewanella Echophysiology

    Energy Technology Data Exchange (ETDEWEB)

    Margrethe H. Serres

    2012-06-29

    Shewanella oneidensis MR-1 is a motile, facultative {gamma}-Proteobacterium with remarkable respiratory versatility; it can utilize a range of organic and inorganic compounds as terminal electronacceptors for anaerobic metabolism. The ability to effectively reduce nitrate, S0, polyvalent metals andradionuclides has established MR-1 as an important model dissimilatory metal-reducing microorganism for genome-based investigations of biogeochemical transformation of metals and radionuclides that are of concern to the U.S. Department of Energy (DOE) sites nationwide. Metal-reducing bacteria such as Shewanella also have a highly developed capacity for extracellular transfer of respiratory electrons to solid phase Fe and Mn oxides as well as directly to anode surfaces in microbial fuel cells. More broadly, Shewanellae are recognized free-living microorganisms and members of microbial communities involved in the decomposition of organic matter and the cycling of elements in aquatic and sedimentary systems. To function and compete in environments that are subject to spatial and temporal environmental change, Shewanella must be able to sense and respond to such changes and therefore require relatively robust sensing and regulation systems. The overall goal of this project is to apply the tools of genomics, leveraging the availability of genome sequence for 18 additional strains of Shewanella, to better understand the ecophysiology and speciation of respiratory-versatile members of this important genus. To understand these systems we propose to use genome-based approaches to investigate Shewanella as a system of integrated networks; first describing key cellular subsystems - those involved in signal transduction, regulation, and metabolism - then building towards understanding the function of whole cells and, eventually, cells within populations. As a general approach, this project will employ complimentary "top-down" - bioinformatics-based genome functional predictions, high

  20. Millstone: software for multiplex microbial genome analysis and engineering.

    Science.gov (United States)

    Goodman, Daniel B; Kuznetsov, Gleb; Lajoie, Marc J; Ahern, Brian W; Napolitano, Michael G; Chen, Kevin Y; Chen, Changping; Church, George M

    2017-05-25

    Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

  1. Social Set Visualizer (SoSeVi) II

    DEFF Research Database (Denmark)

    Flesch, Benjamin; Vatrapu, Ravi

    2016-01-01

    This paper reports the second iteration of the Social Set Visualizer (SoSeVi), a set theoretical visual analytics dashboard of big social data. In order to further demonstrate its usefulness in large-scale visual analytics tasks of individual and collective behavior of actors in social networks......, the current iteration of the Social Set Visualizer (SoSeVi) in version II builds on recent advancements in visualizing set intersections. The development of the SoSeVi dashboard involved cutting-edge open source visual analytics libraries (D3.js) and creation of new visualizations such as of actor mobility...

  2. Genome engineering for microbial natural product discovery.

    Science.gov (United States)

    Choi, Si-Sun; Katsuyama, Yohei; Bai, Linquan; Deng, Zixin; Ohnishi, Yasuo; Kim, Eung-Soo

    2018-03-03

    The discovery and development of microbial natural products (MNPs) have played pivotal roles in the fields of human medicine and its related biotechnology sectors over the past several decades. The post-genomic era has witnessed the development of microbial genome mining approaches to isolate previously unsuspected MNP biosynthetic gene clusters (BGCs) hidden in the genome, followed by various BGC awakening techniques to visualize compound production. Additional microbial genome engineering techniques have allowed higher MNP production titers, which could complement a traditional culture-based MNP chasing approach. Here, we describe recent developments in the MNP research paradigm, including microbial genome mining, NP BGC activation, and NP overproducing cell factory design. Copyright © 2018 Elsevier Ltd. All rights reserved.

  3. Visual attention.

    Science.gov (United States)

    Evans, Karla K; Horowitz, Todd S; Howe, Piers; Pedersini, Roccardo; Reijnen, Ester; Pinto, Yair; Kuzmova, Yoana; Wolfe, Jeremy M

    2011-09-01

    A typical visual scene we encounter in everyday life is complex and filled with a huge amount of perceptual information. The term, 'visual attention' describes a set of mechanisms that limit some processing to a subset of incoming stimuli. Attentional mechanisms shape what we see and what we can act upon. They allow for concurrent selection of some (preferably, relevant) information and inhibition of other information. This selection permits the reduction of complexity and informational overload. Selection can be determined both by the 'bottom-up' saliency of information from the environment and by the 'top-down' state and goals of the perceiver. Attentional effects can take the form of modulating or enhancing the selected information. A central role for selective attention is to enable the 'binding' of selected information into unified and coherent representations of objects in the outside world. In the overview on visual attention presented here we review the mechanisms and consequences of selection and inhibition over space and time. We examine theoretical, behavioral and neurophysiologic work done on visual attention. We also discuss the relations between attention and other cognitive processes such as automaticity and awareness. WIREs Cogni Sci 2011 2 503-514 DOI: 10.1002/wcs.127 For further resources related to this article, please visit the WIREs website. Copyright © 2011 John Wiley & Sons, Ltd.

  4. Visualizing Series

    Science.gov (United States)

    Unal, Hasan

    2008-01-01

    The importance of visualisation and multiple representations in mathematics has been stressed, especially in a context of problem solving. Hanna and Sidoli comment that "Diagrams and other visual representations have long been welcomed as heuristic accompaniments to proof, where they not only facilitate the understanding of theorems and their…

  5. 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...

  6. Sustainable building versus ecological building

    CSIR Research Space (South Africa)

    Van Wyk, Llewellyn V

    2010-04-01

    Full Text Available and sensitivity to a site that are required to efficiently meet the energy needs of a building and occupants with renewable energy (solar, wind, geothermal, etc), designers must apply holistic design principles and take advantage of the free, naturally... monumental waste: the product which they deliver requires resources such as energy and water to operate over its entire life-cycle, a period measured in decades, and often in centuries. Throughout this process, construction activities often result...

  7. [Symptoms and lesion localization in visual agnosia].

    Science.gov (United States)

    Suzuki, Kyoko

    2004-11-01

    There are two cortical visual processing streams, the ventral and dorsal stream. The ventral visual stream plays the major role in constructing our perceptual representation of the visual world and the objects within it. Disturbance of visual processing at any stage of the ventral stream could result in impairment of visual recognition. Thus we need systematic investigations to diagnose visual agnosia and its type. Two types of category-selective visual agnosia, prosopagnosia and landmark agnosia, are different from others in that patients could recognize a face as a face and buildings as buildings, but could not identify an individual person or building. Neuronal bases of prosopagnosia and landmark agnosia are distinct. Importance of the right fusiform gyrus for face recognition was confirmed by both clinical and neuroimaging studies. Landmark agnosia is related to lesions in the right parahippocampal gyrus. Enlarged lesions including both the right fusiform and parahippocampal gyri can result in prosopagnosia and landmark agnosia at the same time. Category non-selective visual agnosia is related to bilateral occipito-temporal lesions, which is in agreement with the results of neuroimaging studies that revealed activation of the bilateral occipito-temporal during object recognition tasks.

  8. Model building

    International Nuclear Information System (INIS)

    Frampton, Paul H.

    1998-01-01

    In this talk I begin with some general discussion of model building in particle theory, emphasizing the need for motivation and testability. Three illustrative examples are then described. The first is the Left-Right model which provides an explanation for the chirality of quarks and leptons. The second is the 331-model which offers a first step to understanding the three generations of quarks and leptons. Third and last is the SU(15) model which can accommodate the light leptoquarks possibly seen at HERA

  9. Model building

    International Nuclear Information System (INIS)

    Frampton, P.H.

    1998-01-01

    In this talk I begin with some general discussion of model building in particle theory, emphasizing the need for motivation and testability. Three illustrative examples are then described. The first is the Left-Right model which provides an explanation for the chirality of quarks and leptons. The second is the 331-model which offers a first step to understanding the three generations of quarks and leptons. Third and last is the SU(15) model which can accommodate the light leptoquarks possibly seen at HERA. copyright 1998 American Institute of Physics

  10. Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0

    KAUST Repository

    Cox, Robert Sidney; Madsen, Curtis; McLaughlin, James; Nguyen, Tramy; Roehner, Nicholas; Bartley, Bryan; Bhatia, Swapnil; Bissell, Mike; Clancy, Kevin; Gorochowski, Thomas; Grunberg, Raik; Luna, Augustin; Le Novè re, Nicolas; Pocock, Matthew; Sauro, Herbert; Sexton, John T.; Stan, Guy-Bart; Tabor, Jeffrey J.; Voigt, Christopher A.; Zundel, Zach; Myers, Chris; Beal, Jacob; Wipat, Anil

    2018-01-01

    to produce a coherent language for expressing the structure and function of genetic designs. This document details version 2.0 of SBOL Visual, which builds on the prior SBOL Visual 1.0 standard by expanding diagram syntax to include functional interactions

  11. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained...... by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans...

  12. Marine genomics

    DEFF Research Database (Denmark)

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

    2017-01-01

    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...

  13. SeeDB: Efficient Data-Driven Visualization Recommendations to Support Visual Analytics.

    Science.gov (United States)

    Vartak, Manasi; Rahman, Sajjadur; Madden, Samuel; Parameswaran, Aditya; Polyzotis, Neoklis

    2015-09-01

    Data analysts often build visualizations as the first step in their analytical workflow. However, when working with high-dimensional datasets, identifying visualizations that show relevant or desired trends in data can be laborious. We propose SeeDB, a visualization recommendation engine to facilitate fast visual analysis: given a subset of data to be studied, SeeDB intelligently explores the space of visualizations, evaluates promising visualizations for trends, and recommends those it deems most "useful" or "interesting". The two major obstacles in recommending interesting visualizations are (a) scale : evaluating a large number of candidate visualizations while responding within interactive time scales, and (b) utility : identifying an appropriate metric for assessing interestingness of visualizations. For the former, SeeDB introduces pruning optimizations to quickly identify high-utility visualizations and sharing optimizations to maximize sharing of computation across visualizations. For the latter, as a first step, we adopt a deviation-based metric for visualization utility, while indicating how we may be able to generalize it to other factors influencing utility. We implement SeeDB as a middleware layer that can run on top of any DBMS. Our experiments show that our framework can identify interesting visualizations with high accuracy. Our optimizations lead to multiple orders of magnitude speedup on relational row and column stores and provide recommendations at interactive time scales. Finally, we demonstrate via a user study the effectiveness of our deviation-based utility metric and the value of recommendations in supporting visual analytics.

  14. Visual Storytelling

    OpenAIRE

    Ting-Hao; Huang; Ferraro, Francis; Mostafazadeh, Nasrin; Misra, Ishan; Agrawal, Aishwarya; Devlin, Jacob; Girshick, Ross; He, Xiaodong; Kohli, Pushmeet; Batra, Dhruv; Zitnick, C. Lawrence; Parikh, Devi; Vanderwende, Lucy; Galley, Michel

    2016-01-01

    We introduce the first dataset for sequential vision-to-language, and explore how this data may be used for the task of visual storytelling. The first release of this dataset, SIND v.1, includes 81,743 unique photos in 20,211 sequences, aligned to both descriptive (caption) and story language. We establish several strong baselines for the storytelling task, and motivate an automatic metric to benchmark progress. Modelling concrete description as well as figurative and social language, as prov...

  15. Flow visualization

    International Nuclear Information System (INIS)

    Weinstein, L.M.

    1991-01-01

    Flow visualization techniques are reviewed, with particular attention given to those applicable to liquid helium flows. Three techniques capable of obtaining qualitative and quantitative measurements of complex 3D flow fields are discussed including focusing schlieren, particle image volocimetry, and holocinematography (HCV). It is concluded that the HCV appears to be uniquely capable of obtaining full time-varying, 3D velocity field data, but is limited to the low speeds typical of liquid helium facilities. 8 refs

  16. Intelligent Buildings and pervasive computing

    DEFF Research Database (Denmark)

    Grønbæk, Kaj; Kyng, Morten; Krogh, Peter Gall

    2001-01-01

    computers are everywhere, for everyone, at all times. Where IT becomes a still more integrated part of our environments with processors, sensors, and actuators connected via high-speed networks and combined with new visualiza-tion devices ranging from projections directly in the eye to large panorama......Intelligent Buildings have been the subject of research and commercial interest for more than two decades. The different perspectives range from monitoring and controlling energy consumption over interactive rooms supporting work in offices and leisure in the home, to buildings providing...... information to by-passers in plazas and urban environments. This paper puts forward the hypothesis that the coming decade will witness a dramatic increase in both quality and quantity of intelligent buildings due to the emerging field of pervasive computing: the next generation computing environments where...

  17. GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes.

    Science.gov (United States)

    Yuan, Lina; Yu, Yang; Zhu, Yanmin; Li, Yulai; Li, Changqing; Li, Rujiao; Ma, Qin; Siu, Gilman Kit-Hang; Yu, Jun; Jiang, Taijiao; Xiao, Jingfa; Kang, Yu

    2017-01-25

    Next-generation sequencing (NGS) technologies have greatly promoted the genomic study of prokaryotes. However, highly fragmented assemblies due to short reads from NGS are still a limiting factor in gaining insights into the genome biology. Reference-assisted tools are promising in genome assembly, but tend to result in false assembly when the assigned reference has extensive rearrangements. Herein, we present GAAP, a genome assembly pipeline for scaffolding based on core-gene-defined Genome Organizational Framework (cGOF) described in our previous study. Instead of assigning references, we use the multiple-reference-derived cGOFs as indexes to assist in order and orientation of the scaffolds and build a skeleton structure, and then use read pairs to extend scaffolds, called local scaffolding, and distinguish between true and chimeric adjacencies in the scaffolds. In our performance tests using both empirical and simulated data of 15 genomes in six species with diverse genome size, complexity, and all three categories of cGOFs, GAAP outcompetes or achieves comparable results when compared to three other reference-assisted programs, AlignGraph, Ragout and MeDuSa. GAAP uses both cGOF and pair-end reads to create assemblies in genomic scale, and performs better than the currently available reference-assisted assembly tools as it recovers more assemblies and makes fewer false locations, especially for species with extensive rearranged genomes. Our method is a promising solution for reconstruction of genome sequence from short reads of NGS.

  18. Community standards for genomic resources, genetic conservation, and data integration

    Science.gov (United States)

    Jill Wegrzyn; Meg Staton; Emily Grau; Richard Cronn; C. Dana Nelson

    2017-01-01

    Genetics and genomics are increasingly important in forestry management and conservation. Next generation sequencing can increase analytical power, but still relies on building on the structure of previously acquired data. Data standards and data sharing allow the community to maximize the analytical power of high throughput genomics data. The landscape of incomplete...

  19. SNUGB: a versatile genome browser supporting comparative and functional fungal genomics

    Directory of Open Access Journals (Sweden)

    Kim Seungill

    2008-12-01

    Full Text Available Abstract Background Since the full genome sequences of Saccharomyces cerevisiae were released in 1996, genome sequences of over 90 fungal species have become publicly available. The heterogeneous formats of genome sequences archived in different sequencing centers hampered the integration of the data for efficient and comprehensive comparative analyses. The Comparative Fungal Genomics Platform (CFGP was developed to archive these data via a single standardized format that can support multifaceted and integrated analyses of the data. To facilitate efficient data visualization and utilization within and across species based on the architecture of CFGP and associated databases, a new genome browser was needed. Results The Seoul National University Genome Browser (SNUGB integrates various types of genomic information derived from 98 fungal/oomycete (137 datasets and 34 plant and animal (38 datasets species, graphically presents germane features and properties of each genome, and supports comparison between genomes. The SNUGB provides three different forms of the data presentation interface, including diagram, table, and text, and six different display options to support visualization and utilization of the stored information. Information for individual species can be quickly accessed via a new tool named the taxonomy browser. In addition, SNUGB offers four useful data annotation/analysis functions, including 'BLAST annotation.' The modular design of SNUGB makes its adoption to support other comparative genomic platforms easy and facilitates continuous expansion. Conclusion The SNUGB serves as a powerful platform supporting comparative and functional genomics within the fungal kingdom and also across other kingdoms. All data and functions are available at the web site http://genomebrowser.snu.ac.kr/.

  20. Design Buildings Optimally: A Lifecycle Assessment Approach

    KAUST Repository

    Hosny, Ossama

    2013-01-01

    This paper structures a generic framework to support optimum design for multi-buildings in desert environment. The framework is targeting an environmental friendly design with minimum lifecycle cost, using Genetic Algorithms (Gas). GAs function through a set of success measures which evaluates the design, formulates a proper objective, and reflects possible tangible/intangible constraints. The framework optimizes the design and categorizes it under a certain environmental category at minimum Life Cycle Cost (LCC). It consists of three main modules: (1) a custom Building InformationModel (BIM) for desert buildings with a compatibility checker as a central interactive database; (2) a system evaluator module to evaluate the proposed success measures for the design; and (3) a GAs optimization module to ensure optimum design. The framework functions through three levels: the building components, integrated building, and multi-building levels. At the component level the design team should be able to select components in a designed sequence to ensure compatibility among various components, while at the building level; the team can relatively locate and orient each individual building. Finally, at the multi-building (compound) level the whole design can be evaluated using success measures of natural light, site capacity, shading impact on natural lighting, thermal change, visual access and energy saving. The framework through genetic algorithms optimizes the design by determining proper types of building components and relative buildings locations and orientations which ensure categorizing the design under a specific category or meet certain preferences at minimum lifecycle cost.

  1. Application of Genomic In Situ Hybridization in Horticultural Science

    Directory of Open Access Journals (Sweden)

    Fahad Ramzan

    2017-01-01

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

  2. Genome scale engineering techniques for metabolic engineering.

    Science.gov (United States)

    Liu, Rongming; Bassalo, Marcelo C; Zeitoun, Ramsey I; Gill, Ryan T

    2015-11-01

    Metabolic engineering has expanded from a focus on designs requiring a small number of genetic modifications to increasingly complex designs driven by advances in genome-scale engineering technologies. Metabolic engineering has been generally defined by the use of iterative cycles of rational genome modifications, strain analysis and characterization, and a synthesis step that fuels additional hypothesis generation. This cycle mirrors the Design-Build-Test-Learn cycle followed throughout various engineering fields that has recently become a defining aspect of synthetic biology. This review will attempt to summarize recent genome-scale design, build, test, and learn technologies and relate their use to a range of metabolic engineering applications. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  3. GenomePeek—an online tool for prokaryotic genome and metagenome analysis

    Directory of Open Access Journals (Sweden)

    Katelyn McNair

    2015-06-01

    Full Text Available As more and more prokaryotic sequencing takes place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping error rates low, as well as offering unique data visualization options.

  4. Reactor building

    International Nuclear Information System (INIS)

    Maruyama, Toru; Murata, Ritsuko.

    1996-01-01

    In the present invention, a spent fuel storage pool of a BWR type reactor is formed at an upper portion and enlarged in the size to effectively utilize the space of the building. Namely, a reactor chamber enhouses reactor facilities including a reactor pressure vessel and a reactor container, and further, a spent fuel storage pool is formed thereabove. A second spent fuel storage pool is formed above the auxiliary reactor chamber at the periphery of the reactor chamber. The spent fuel storage pool and the second spent fuel storage pool are disposed in adjacent with each other. A wall between both of them is formed vertically movable. With such a constitution, the storage amount for spent fuels is increased thereby enabling to store the entire spent fuels generated during operation period of the plant. Further, since requirement of the storage for the spent fuels is increased stepwisely during periodical exchange operation, it can be used for other usage during the period when the enlarged portion is not used. (I.S.)

  5. Building America

    Energy Technology Data Exchange (ETDEWEB)

    Brad Oberg

    2010-12-31

    Builders generally use a 'spec and purchase' business management system (BMS) when implementing energy efficiency. A BMS is the overall operational and organizational systems and strategies that a builder uses to set up and run its company. This type of BMS treats building performance as a simple technology swap (e.g. a tank water heater to a tankless water heater) and typically compartmentalizes energy efficiency within one or two groups in the organization (e.g. purchasing and construction). While certain tools, such as details, checklists, and scopes of work, can assist builders in managing the quality of the construction of higher performance homes, they do nothing to address the underlying operational strategies and issues related to change management that builders face when they make high performance homes a core part of their mission. To achieve the systems integration necessary for attaining 40% + levels of energy efficiency, while capturing the cost tradeoffs, builders must use a 'systems approach' BMS, rather than a 'spec and purchase' BMS. The following attributes are inherent in a systems approach BMS; they are also generally seen in quality management systems (QMS), such as the National Housing Quality Certification program: Cultural and corporate alignment, Clear intent for quality and performance, Increased collaboration across internal and external teams, Better communication practices and systems, Disciplined approach to quality control, Measurement and verification of performance, Continuous feedback and improvement, and Whole house integrated design and specification.

  6. Ensembl Genomes 2016: more genomes, more complexity.

    Science.gov (United States)

    Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

    2016-01-04

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

  8. Genome Variation Map: a data repository of genome variations in BIG Data Center.

    Science.gov (United States)

    Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

    2018-01-04

    The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Genome Variation Map: a data repository of genome variations in BIG Data Center

    Science.gov (United States)

    Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang

    2018-01-01

    Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. PMID:29069473

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

    Science.gov (United States)

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

    2015-01-01

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

  11. Building energy analysis tool

    Science.gov (United States)

    Brackney, Larry; Parker, Andrew; Long, Nicholas; Metzger, Ian; Dean, Jesse; Lisell, Lars

    2016-04-12

    A building energy analysis system includes a building component library configured to store a plurality of building components, a modeling tool configured to access the building component library and create a building model of a building under analysis using building spatial data and using selected building components of the plurality of building components stored in the building component library, a building analysis engine configured to operate the building model and generate a baseline energy model of the building under analysis and further configured to apply one or more energy conservation measures to the baseline energy model in order to generate one or more corresponding optimized energy models, and a recommendation tool configured to assess the one or more optimized energy models against the baseline energy model and generate recommendations for substitute building components or modifications.

  12. The Salmonella enterica Pan-genome

    DEFF Research Database (Denmark)

    Jacobsen, Annika; Hendriksen, Rene S.; Aarestrup, Frank Møller

    2011-01-01

    Salmonella enterica is divided into four subspecies containing a large number of different serovars, several of which are important zoonotic pathogens and some show a high degree of host specificity or host preference. We compare 45 sequenced S. enterica genomes that are publicly available (22......, and the core and pan-genome of Salmonella were estimated to be around 2,800 and 10,000 gene families, respectively. The constructed pan-genomic dendrograms suggest that gene content is often, but not uniformly correlated to serotype. Any given Salmonella strain has a large stable core, whilst...... there is an abundance of accessory genes, including the Salmonella pathogenicity islands (SPIs), transposable elements, phages, and plasmid DNA. We visualize conservation in the genomes in relation to chromosomal location and DNA structural features and find that variation in gene content is localized in a selection...

  13. Gramene database: Navigating plant comparative genomics resources

    Directory of Open Access Journals (Sweden)

    Parul Gupta

    2016-11-01

    Full Text Available Gramene (http://www.gramene.org is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering. It exploits phylogenetic relationships to enrich the annotation of genomic data and provides tools to perform powerful comparative analyses across a wide spectrum of plant species. It consists of an integrated portal for querying, visualizing and analyzing data for 44 plant reference genomes, genetic variation data sets for 12 species, expression data for 16 species, curated rice pathways and orthology-based pathway projections for 66 plant species including various crops. Here we briefly describe the functions and uses of the Gramene database.

  14. Geospatial database for heritage building conservation

    Science.gov (United States)

    Basir, W. N. F. W. A.; Setan, H.; Majid, Z.; Chong, A.

    2014-02-01

    Heritage buildings are icons from the past that exist in present time. Through heritage architecture, we can learn about economic issues and social activities of the past. Nowadays, heritage buildings are under threat from natural disaster, uncertain weather, pollution and others. In order to preserve this heritage for the future generation, recording and documenting of heritage buildings are required. With the development of information system and data collection technique, it is possible to create a 3D digital model. This 3D information plays an important role in recording and documenting heritage buildings. 3D modeling and virtual reality techniques have demonstrated the ability to visualize the real world in 3D. It can provide a better platform for communication and understanding of heritage building. Combining 3D modelling with technology of Geographic Information System (GIS) will create a database that can make various analyses about spatial data in the form of a 3D model. Objectives of this research are to determine the reliability of Terrestrial Laser Scanning (TLS) technique for data acquisition of heritage building and to develop a geospatial database for heritage building conservation purposes. The result from data acquisition will become a guideline for 3D model development. This 3D model will be exported to the GIS format in order to develop a database for heritage building conservation. In this database, requirements for heritage building conservation process are included. Through this research, a proper database for storing and documenting of the heritage building conservation data will be developed.

  15. Geospatial database for heritage building conservation

    International Nuclear Information System (INIS)

    Basir, W N F W A; Setan, H; Majid, Z; Chong, A

    2014-01-01

    Heritage buildings are icons from the past that exist in present time. Through heritage architecture, we can learn about economic issues and social activities of the past. Nowadays, heritage buildings are under threat from natural disaster, uncertain weather, pollution and others. In order to preserve this heritage for the future generation, recording and documenting of heritage buildings are required. With the development of information system and data collection technique, it is possible to create a 3D digital model. This 3D information plays an important role in recording and documenting heritage buildings. 3D modeling and virtual reality techniques have demonstrated the ability to visualize the real world in 3D. It can provide a better platform for communication and understanding of heritage building. Combining 3D modelling with technology of Geographic Information System (GIS) will create a database that can make various analyses about spatial data in the form of a 3D model. Objectives of this research are to determine the reliability of Terrestrial Laser Scanning (TLS) technique for data acquisition of heritage building and to develop a geospatial database for heritage building conservation purposes. The result from data acquisition will become a guideline for 3D model development. This 3D model will be exported to the GIS format in order to develop a database for heritage building conservation. In this database, requirements for heritage building conservation process are included. Through this research, a proper database for storing and documenting of the heritage building conservation data will be developed

  16. Building trust

    International Nuclear Information System (INIS)

    Lewis, Meriel

    1995-01-01

    'Activate' is the energy magazine for secondary schools and is part of the Education Programme which is managed on behalf of the British Nuclear Industry Forum by AEA Technology. activate is the flagship communication device between the British Nuclear Industry Forum's Education Programme and secondary schools in the UK. It was developed from a previous publication, Nuclear Bulletin. There is a need for the nuclear industry to build trust with teachers and students in the UK, where for a long time, everything that the industry has said, written or printed has been disregarded by school teachers as propaganda. Over the last few years the industry has put in a great deal of effort to position itself as a provider of educationally sound and socially acceptable information. 'Activate' was an evolution of this idea and there was a hole in the market for a lively, activity and article based magazine that could be used in the classroom. The target audience is principally teachers of science, mathematics and geography, but also includes teachers of art,, English and history with students of between 11 and 18. The results were very positive in that teachers appreciated the colourful and lively nature of activate and they felt that it provided information and opinions in an un biased and non-propagandist way. Their comments about layout, number of activities style of presentation were taken into account and during the summer of 1994 activate was remodelled ready for re launch in September. The feedback so far is good with more teachers signing up every week to receive their own free copy

  17. Funding Opportunity: Genomic Data Centers

    Science.gov (United States)

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  18. Teach yourself visually Adobe Dreamweaver CS6

    CERN Document Server

    Warner, Janine

    2012-01-01

    Learn to design and maintain content-rich websites the Visual way With more than 90 percent market share, Dreamweaver is the preferred tool for professional website design and production. For those who learn best visually, this colorful, step-by-step guide is the perfect way to learn the program and start building websites with "wow". Numbered steps and full-color screen shots show you just how to navigate the program, format and style text, create web-based forms and pages, build data-driven sites, and maintain a fully functioning website. All the enhancements of the newest version are cover

  19. Initial genomics of the human nucleolus.

    Directory of Open Access Journals (Sweden)

    Attila Németh

    2010-03-01

    Full Text Available We report for the first time the genomics of a nuclear compartment of the eukaryotic cell. 454 sequencing and microarray analysis revealed the pattern of nucleolus-associated chromatin domains (NADs in the linear human genome and identified different gene families and certain satellite repeats as the major building blocks of NADs, which constitute about 4% of the genome. Bioinformatic evaluation showed that NAD-localized genes take part in specific biological processes, like the response to other organisms, odor perception, and tissue development. 3D FISH and immunofluorescence experiments illustrated the spatial distribution of NAD-specific chromatin within interphase nuclei and its alteration upon transcriptional changes. Altogether, our findings describe the nature of DNA sequences associated with the human nucleolus and provide insights into the function of the nucleolus in genome organization and establishment of nuclear architecture.

  20. Initial Genomics of the Human Nucleolus

    Science.gov (United States)

    Németh, Attila; Conesa, Ana; Santoyo-Lopez, Javier; Medina, Ignacio; Montaner, David; Péterfia, Bálint; Solovei, Irina; Cremer, Thomas; Dopazo, Joaquin; Längst, Gernot

    2010-01-01

    We report for the first time the genomics of a nuclear compartment of the eukaryotic cell. 454 sequencing and microarray analysis revealed the pattern of nucleolus-associated chromatin domains (NADs) in the linear human genome and identified different gene families and certain satellite repeats as the major building blocks of NADs, which constitute about 4% of the genome. Bioinformatic evaluation showed that NAD–localized genes take part in specific biological processes, like the response to other organisms, odor perception, and tissue development. 3D FISH and immunofluorescence experiments illustrated the spatial distribution of NAD–specific chromatin within interphase nuclei and its alteration upon transcriptional changes. Altogether, our findings describe the nature of DNA sequences associated with the human nucleolus and provide insights into the function of the nucleolus in genome organization and establishment of nuclear architecture. PMID:20361057

  1. 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

  2. Exploring Other Genomes: Bacteria.

    Science.gov (United States)

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  3. Building integrated photovoltaics

    NARCIS (Netherlands)

    Ritzen, M.J.; Vroon, Z.A.E.P.; Geurts, C.P.W.; Reinders, Angèle; Verlinden, Pierre; Sark, Wilfried; Freundlich, Alexandre

    2017-01-01

    Photovoltaic (PV) installations can be realized in different situations and on different scales, such as at a building level. PV installations at the building level can either be added to the building envelope, which is called building added PV (BAPV), or they can be integrated into the building

  4. Prediction of the visual impact of motorways using GIS

    International Nuclear Information System (INIS)

    Jiang, Like; Kang, Jian; Schroth, Olaf

    2015-01-01

    Large scale transportation projects can adversely affect the visual perception of environmental quality and require adequate visual impact assessment. In this study, we investigated the effects of the characteristics of the road project and the character of the existing landscape on the perceived visual impact of motorways, and developed a GIS-based prediction model based on the findings. An online survey using computer-visualised scenes of different motorway and landscape scenarios was carried out to obtain perception-based judgements on the visual impact. Motorway scenarios simulated included the baseline scenario without road, original motorway, motorways with timber noise barriers, transparent noise barriers and tree screen; different landscape scenarios were created by changing land cover of buildings and trees in three distance zones. The landscape content of each scene was measured in GIS. The result shows that presence of a motorway especially with the timber barrier significantly decreases the visual quality of the view. The resulted visual impact tends to be lower where it is less visually pleasant with more buildings in the view, and can be slightly reduced by the visual absorption effect of the scattered trees between the motorway and the viewpoint. Based on the survey result, eleven predictors were identified for the visual impact prediction model which was applied in GIS to generate maps of visual impact of motorways in different scenarios. The proposed prediction model can be used to achieve efficient and reliable assessment of visual impact of motorways. - Highlights: • Motorways induce significant visual impact especially with timber noise barriers. • Visual impact is negatively correlated with amount of buildings in the view. • Visual impact is positively correlated with percentage of trees in the view. • Perception-based motorway visual impact prediction model using mapped predictors • Predicted visual impacts in different scenarios are

  5. Prediction of the visual impact of motorways using GIS

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Like [School of Architecture, University of Sheffield, Sheffield S10 2TN (United Kingdom); Kang, Jian, E-mail: j.kang@sheffield.ac.uk [School of Architecture, University of Sheffield, Sheffield S10 2TN (United Kingdom); Schroth, Olaf [Department of Landscape, University of Sheffield, Sheffield S10 2TN (United Kingdom)

    2015-11-15

    Large scale transportation projects can adversely affect the visual perception of environmental quality and require adequate visual impact assessment. In this study, we investigated the effects of the characteristics of the road project and the character of the existing landscape on the perceived visual impact of motorways, and developed a GIS-based prediction model based on the findings. An online survey using computer-visualised scenes of different motorway and landscape scenarios was carried out to obtain perception-based judgements on the visual impact. Motorway scenarios simulated included the baseline scenario without road, original motorway, motorways with timber noise barriers, transparent noise barriers and tree screen; different landscape scenarios were created by changing land cover of buildings and trees in three distance zones. The landscape content of each scene was measured in GIS. The result shows that presence of a motorway especially with the timber barrier significantly decreases the visual quality of the view. The resulted visual impact tends to be lower where it is less visually pleasant with more buildings in the view, and can be slightly reduced by the visual absorption effect of the scattered trees between the motorway and the viewpoint. Based on the survey result, eleven predictors were identified for the visual impact prediction model which was applied in GIS to generate maps of visual impact of motorways in different scenarios. The proposed prediction model can be used to achieve efficient and reliable assessment of visual impact of motorways. - Highlights: • Motorways induce significant visual impact especially with timber noise barriers. • Visual impact is negatively correlated with amount of buildings in the view. • Visual impact is positively correlated with percentage of trees in the view. • Perception-based motorway visual impact prediction model using mapped predictors • Predicted visual impacts in different scenarios are

  6. SINEs as driving forces in genome evolution.

    Science.gov (United States)

    Schmitz, J

    2012-01-01

    SINEs are short interspersed elements derived from cellular RNAs that repetitively retropose via RNA intermediates and integrate more or less randomly back into the genome. SINEs propagate almost entirely vertically within their host cells and, once established in the germline, are passed on from generation to generation. As non-autonomous elements, their reverse transcription (from RNA to cDNA) and genomic integration depends on the activity of the enzymatic machinery of autonomous retrotransposons, such as long interspersed elements (LINEs). SINEs are widely distributed in eukaryotes, but are especially effectively propagated in mammalian species. For example, more than a million Alu-SINE copies populate the human genome (approximately 13% of genomic space), and few master copies of them are still active. In the organisms where they occur, SINEs are a challenge to genomic integrity, but in the long term also can serve as beneficial building blocks for evolution, contributing to phenotypic heterogeneity and modifying gene regulatory networks. They substantially expand the genomic space and introduce structural variation to the genome. SINEs have the potential to mutate genes, to alter gene expression, and to generate new parts of genes. A balanced distribution and controlled activity of such properties is crucial to maintaining the organism's dynamic and thriving evolution. Copyright © 2012 S. Karger AG, Basel.

  7. Genomics With Cloud Computing

    OpenAIRE

    Sukhamrit Kaur; Sandeep Kaur

    2015-01-01

    Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computin...

  8. Building performance simulation for sustainable buildings

    NARCIS (Netherlands)

    Hensen, J.L.M.

    2010-01-01

    This paper aims to provide a general view of the background and current state of building performance simulation, which has the potential to deliver, directly or indirectly, substantial benefits to building stakeholders and to the environment. However the building simulation community faces many

  9. 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

  10. Tribal Green Building Toolkit

    Science.gov (United States)

    This Tribal Green Building Toolkit (Toolkit) is designed to help tribal officials, community members, planners, developers, and architects develop and adopt building codes to support green building practices. Anyone can use this toolkit!

  11. BUILDING 341 Seismic Evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Halle, J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-06-15

    The Seismic Evaluation of Building 341 located at Lawrence Livermore National Laboratory in Livermore, California has been completed. The subject building consists of a main building, Increment 1, and two smaller additions; Increments 2 and 3.

  12. Industrial image processing visual quality control in manufacturing

    CERN Document Server

    Demant, Christian; Garnica, Carsten

    2013-01-01

    This practical introduction focuses on how to build integrated solutions to industrial vision problems from individual algorithms. It gives a hands-on guide for setting up automated visual inspection systems using the NeuroCheck software package.

  13. Urban Renewable Building And Neighborhood Optimization

    Energy Technology Data Exchange (ETDEWEB)

    2016-09-07

    URBANopt is a user interface for creating and running district and city scale building energy simulations. The framework is built around the OpenStudio Urban Measures which are part of the OpenStudio project. Building footprints, building height, building type, and other data can be imported from public records or other sources. Footprints and locations for new buildings and district systems can also be specified. OpenStudio Measures are used to create starting point energy models and to model energy design features and efficiency measures for each building. URBANopt allows a user to pose several scenarios such as “what if 30% of the commercial retail buildings added roof top solar” or “what if all elementary schools converted to ground source heat pumps” and then visualize the impacts at a district or city scale. URBANopt is capable of modeling existing buildings, new construction, and district energy systems. URBANopt can be used to explore options for achieving Zero Energy across a collection of buildings (e.g., Zero Energy Districts).

  14. Ginseng Genome Database: an open-access platform for genomics of Panax ginseng.

    Science.gov (United States)

    Jayakodi, Murukarthick; Choi, Beom-Soon; Lee, Sang-Choon; Kim, Nam-Hoon; Park, Jee Young; Jang, Woojong; Lakshmanan, Meiyappan; Mohan, Shobhana V G; Lee, Dong-Yup; Yang, Tae-Jin

    2018-04-12

    The ginseng (Panax ginseng C.A. Meyer) is a perennial herbaceous plant that has been used in traditional oriental medicine for thousands of years. Ginsenosides, which have significant pharmacological effects on human health, are the foremost bioactive constituents in this plant. Having realized the importance of this plant to humans, an integrated omics resource becomes indispensable to facilitate genomic research, molecular breeding and pharmacological study of this herb. The first draft genome sequences of P. ginseng cultivar "Chunpoong" were reported recently. Here, using the draft genome, transcriptome, and functional annotation datasets of P. ginseng, we have constructed the Ginseng Genome Database http://ginsengdb.snu.ac.kr /, the first open-access platform to provide comprehensive genomic resources of P. ginseng. The current version of this database provides the most up-to-date draft genome sequence (of approximately 3000 Mbp of scaffold sequences) along with the structural and functional annotations for 59,352 genes and digital expression of genes based on transcriptome data from different tissues, growth stages and treatments. In addition, tools for visualization and the genomic data from various analyses are provided. All data in the database were manually curated and integrated within a user-friendly query page. This database provides valuable resources for a range of research fields related to P. ginseng and other species belonging to the Apiales order as well as for plant research communities in general. Ginseng genome database can be accessed at http://ginsengdb.snu.ac.kr /.

  15. 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.

  16. gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances.

    Science.gov (United States)

    Domazet-Lošo, Mirjana; Domazet-Lošo, Tomislav

    2016-01-01

    Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align) a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure), a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenic Enterococcus faecium strain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos).

  17. Genome-wide DNA polymorphism analyses using VariScan

    Directory of Open Access Journals (Sweden)

    Vilella Albert J

    2006-09-01

    Full Text Available Abstract Background DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. Results We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i exhaustive population-genetic analyses including those based on the coalescent theory; ii analysis adapted to the shallow data generated by the high-throughput genome projects; iii use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v visualization of the results integrated with current genome annotations in commonly available genome browsers. Conclusion VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.

  18. Visualization in medicine and life sciences

    International Nuclear Information System (INIS)

    Linsen, L.; Hamann, B.

    2008-01-01

    Visualization technology is becoming increasingly important for medical and biomedical data processing and analysis. This technology complements traditional image processing methods as it allows scientists to visually interact with large, high-resolution three-dimensional image data, for example. Furthermore, an ever increasing number of new data acquisition methods are being used in medicine and the life sciences, in particular in genomics and proteomics. This book discusses some of the latest visualization techniques and systems for effective analysis of such diverse, large, complex, and multi-source data. Experts from all over the world were invited to participate in a workshop held in July 2006 on the island Ruegen in Germany. About 40 participants presented state-of-the-art research on the topic. Research and survey papers have been solicited and carefully refereed, resulting in this collection. The topics covered include Segmentation and Feature Detection, Surface Extraction, Volume Visualization, Graph and Network Visualization, Visual Data Exploration, Multivariate and Multidimensional Data Visualization, Large Data Visualization. (orig.)

  19. Danish building typologies and building stock analyses

    DEFF Research Database (Denmark)

    Wittchen, Kim Bjarne; Kragh, Jesper

    energy savings in residential buildings. The intension with this analysis was to investigate the possible energy reduction in Denmark if the same approach had been taken for the entire Danish building stock. The report concludes that the ZeroHome initiative clearly results in energy savings, but far from...... enough to meet the government’s plan to make Danish buildings free from use of fossil fuels by 2035. This will probably require around 50 % energy savings in the Danish building stock as a whole. However, the project has proven that dedicated engagement of locals can speed up market penetration...... for energy savings in the existing Building stock....

  20. Visual literacy in HCI

    NARCIS (Netherlands)

    Overton, K.; Sosa-Tzec, O.; Smith, N.; Blevis, E.; Odom, W.; Hauser, S.; Wakkary, R.L.

    2016-01-01

    The goal of this workshop is to develop ideas about and expand a research agenda for visual literacy in HCI. By visual literacy, we mean the competency (i) to understand visual materials, (ii) to create visuals materials, and (iii) to think visually [2]. There are three primary motivations for this

  1. Danish building typologies

    DEFF Research Database (Denmark)

    Wittchen, Kim Bjarne; Kragh, Jesper

    The objective of TABULA is to develop a harmonised building typology for European countries. Each national building typology will consist of a set of residential model buildings with characteristic energy-related properties (element areas of the thermal building envelope, U-values, supply system...... efficiencies). The model buildings will each represent a specific construction period of the country in question and a specific building size. Furthermore the number of buildings, flats and the overall floor areas will be given, which are represented by the different building types of the national typologies....

  2. Topological visual mapping in robotics.

    Science.gov (United States)

    Romero, Anna; Cazorla, Miguel

    2012-08-01

    A key problem in robotics is the construction of a map from its environment. This map could be used in different tasks, like localization, recognition, obstacle avoidance, etc. Besides, the simultaneous location and mapping (SLAM) problem has had a lot of interest in the robotics community. This paper presents a new method for visual mapping, using topological instead of metric information. For that purpose, we propose prior image segmentation into regions in order to group the extracted invariant features in a graph so that each graph defines a single region of the image. Although others methods have been proposed for visual SLAM, our method is complete, in the sense that it makes all the process: it presents a new method for image matching; it defines a way to build the topological map; and it also defines a matching criterion for loop-closing. The matching process will take into account visual features and their structure using the graph transformation matching (GTM) algorithm, which allows us to process the matching and to remove out the outliers. Then, using this image comparison method, we propose an algorithm for constructing topological maps. During the experimentation phase, we will test the robustness of the method and its ability constructing topological maps. We have also introduced new hysteresis behavior in order to solve some problems found building the graph.

  3. PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes

    Directory of Open Access Journals (Sweden)

    Wasnick Michael

    2008-03-01

    Full Text Available Abstract Background The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved. Although some tools are available for visualizing and comparing the order of genes between genomes of study, few support an efficient and organized analysis between large numbers of genomes. The Prokaryotic Sequence homology Analysis Tool (PSAT is a web tool for comparing gene neighborhoods among multiple prokaryotic genomes. Results PSAT utilizes a database that is preloaded with gene annotation, BLAST hit results, and gene-clustering scores designed to help identify regions of conserved gene order. Researchers use the PSAT web interface to find a gene of interest in a reference genome and efficiently retrieve the sequence homologs found in other bacterial genomes. The tool generates a graphic of the genomic neighborhood surrounding the selected gene and the corresponding regions for its homologs in each comparison genome. Homologs in each region are color coded to assist users with analyzing gene order among various genomes. In contrast to common comparative analysis methods that filter sequence homolog data based on alignment score cutoffs, PSAT leverages gene context information for homologs, including those with weak alignment scores, enabling a more sensitive analysis. Features for constraining or ordering results are designed to help researchers browse results from large numbers of comparison genomes in an organized manner. PSAT has been demonstrated to be useful for helping to identify gene orthologs and potential functional gene clusters, and detecting genome modifications that may result in loss of function. Conclusion PSAT allows researchers to investigate the order of genes within local genomic neighborhoods of multiple genomes. A PSAT web server for public use is available for performing analyses on a growing set of reference genomes through any

  4. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  5. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  6. Refining the Eye: Dermatology and Visual Literacy

    Science.gov (United States)

    Zimmermann, Corinne; Huang, Jennifer T.; Buzney, Elizabeth A.

    2016-01-01

    In 2014 the Museum of Fine Arts Boston and Harvard Medical School began a partnership focused on building visual literacy skills for dermatology residents in the Harvard Combined Dermatology Residency Program. "Refining the Eye: Art and Dermatology", a four session workshop, took place in the museum's galleries and utilized the Visual…

  7. Biomedical Visual Computing: Case Studies and Challenges

    KAUST Repository

    Johnson, Christopher

    2012-01-01

    Advances in computational geometric modeling, imaging, and simulation let researchers build and test models of increasing complexity, generating unprecedented amounts of data. As recent research in biomedical applications illustrates, visualization will be critical in making this vast amount of data usable; it\\'s also fundamental to understanding models of complex phenomena. © 2012 IEEE.

  8. Biomedical Visual Computing: Case Studies and Challenges

    KAUST Repository

    Johnson, Christopher

    2012-01-01

    Advances in computational geometric modeling, imaging, and simulation let researchers build and test models of increasing complexity, generating unprecedented amounts of data. As recent research in biomedical applications illustrates, visualization will be critical in making this vast amount of data usable; it's also fundamental to understanding models of complex phenomena. © 2012 IEEE.

  9. Bilateral Simultaneous Macular Infarction with Spontaneous Visual ...

    African Journals Online (AJOL)

    2018-01-30

    Jan 30, 2018 ... eyes and near acuity was; right eye: N24, left eye: N36. ... Keywords: Macular infarction, macular ischemia, sickle cell, visual loss ... and build upon the work non-commercially, as long as the author is credited and the new.

  10. Visual Memories Bypass Normalization.

    Science.gov (United States)

    Bloem, Ilona M; Watanabe, Yurika L; Kibbe, Melissa M; Ling, Sam

    2018-05-01

    How distinct are visual memory representations from visual perception? Although evidence suggests that briefly remembered stimuli are represented within early visual cortices, the degree to which these memory traces resemble true visual representations remains something of a mystery. Here, we tested whether both visual memory and perception succumb to a seemingly ubiquitous neural computation: normalization. Observers were asked to remember the contrast of visual stimuli, which were pitted against each other to promote normalization either in perception or in visual memory. Our results revealed robust normalization between visual representations in perception, yet no signature of normalization occurring between working memory stores-neither between representations in memory nor between memory representations and visual inputs. These results provide unique insight into the nature of visual memory representations, illustrating that visual memory representations follow a different set of computational rules, bypassing normalization, a canonical visual computation.

  11. Genomics With Cloud Computing

    Directory of Open Access Journals (Sweden)

    Sukhamrit Kaur

    2015-04-01

    Full Text Available Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computing to genomics are like easy access and sharing of data security of data less cost to pay for resources but still there are some demerits like large time needed to transfer data less network bandwidth.

  12. uVis: A Formula-Based Visualization Tool

    DEFF Research Database (Denmark)

    Pantazos, Kostas; Xu, Shangjin; Kuhail, Mohammad Amin

    Several tools use programming approaches for developing advanced visualizations. Others can with a few steps create simple visualizations with built-in patterns, and users with limited IT experience can use them. However, it is programming and time demanding to create and customize...... these visualizations. We introduce uVis, a tool that allows users with advanced spreadsheet-like IT knowledge and basic database understanding to create simple as well as advanced visualizations. These users construct visualizations by combining building blocks (i.e. controls, shapes). They specify spreadsheet...

  13. Learning Visualizations by Analogy: Promoting Visual Literacy through Visualization Morphing.

    Science.gov (United States)

    Ruchikachorn, Puripant; Mueller, Klaus

    2015-09-01

    We propose the concept of teaching (and learning) unfamiliar visualizations by analogy, that is, demonstrating an unfamiliar visualization method by linking it to another more familiar one, where the in-betweens are designed to bridge the gap of these two visualizations and explain the difference in a gradual manner. As opposed to a textual description, our morphing explains an unfamiliar visualization through purely visual means. We demonstrate our idea by ways of four visualization pair examples: data table and parallel coordinates, scatterplot matrix and hyperbox, linear chart and spiral chart, and hierarchical pie chart and treemap. The analogy is commutative i.e. any member of the pair can be the unfamiliar visualization. A series of studies showed that this new paradigm can be an effective teaching tool. The participants could understand the unfamiliar visualization methods in all of the four pairs either fully or at least significantly better after they observed or interacted with the transitions from the familiar counterpart. The four examples suggest how helpful visualization pairings be identified and they will hopefully inspire other visualization morphings and associated transition strategies to be identified.

  14. Symbiodinium genomes reveal adaptive evolution of functions related to symbiosis

    KAUST Repository

    Liu, Huanle; Stephens, Timothy G.; Gonzá lez-Pech, Raú l; Beltran, Victor H.; Lapeyre, Bruno; Bongaerts, Pim; Cooke, Ira; Bourne, David G.; Forê t, Sylvain; Miller, David John; van Oppen, Madeleine J. H.; Voolstra, Christian R.; Ragan, Mark A.; Chan, Cheong Xin

    2017-01-01

    Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world's coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp), previously sequenced as strain CCMP2468, to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identified extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding Symbiodinium biology and the coral-algal symbiosis.

  15. Symbiodinium genomes reveal adaptive evolution of functions related to symbiosis

    KAUST Repository

    Liu, Huanle

    2017-10-06

    Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world\\'s coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp), previously sequenced as strain CCMP2468, to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identified extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding Symbiodinium biology and the coral-algal symbiosis.

  16. Novel Scientific Visualization Interfaces for Interactive Information Visualization and Sharing

    Science.gov (United States)

    Demir, I.; Krajewski, W. F.

    2012-12-01

    As geoscientists are confronted with increasingly massive datasets from environmental observations to simulations, one of the biggest challenges is having the right tools to gain scientific insight from the data and communicate the understanding to stakeholders. Recent developments in web technologies make it easy to manage, visualize and share large data sets with general public. Novel visualization techniques and dynamic user interfaces allow users to interact with data, and modify the parameters to create custom views of the data to gain insight from simulations and environmental observations. This requires developing new data models and intelligent knowledge discovery techniques to explore and extract information from complex computational simulations or large data repositories. Scientific visualization will be an increasingly important component to build comprehensive environmental information platforms. This presentation provides an overview of the trends and challenges in the field of scientific visualization, and demonstrates information visualization and communication tools in the Iowa Flood Information System (IFIS), developed within the light of these challenges. The IFIS is a web-based platform developed by the Iowa Flood Center (IFC) to provide access to and visualization of flood inundation maps, real-time flood conditions, flood forecasts both short-term and seasonal, and other flood-related data for communities in Iowa. The key element of the system's architecture is the notion of community. Locations of the communities, those near streams and rivers, define basin boundaries. The IFIS provides community-centric watershed and river characteristics, weather (rainfall) conditions, and streamflow data and visualization tools. Interactive interfaces allow access to inundation maps for different stage and return period values, and flooding scenarios with contributions from multiple rivers. Real-time and historical data of water levels, gauge heights, and

  17. Assessment of the material properties of a fire damaged building

    OpenAIRE

    Oladipupo OLOMO; Olufikayo ADERINLEWO; Moses TANIMOLA; Silvana CROOPE

    2012-01-01

    This study identifies a process for assessing the material properties of a fire damaged building so as to determine whether the remains can be utilized in construction or be demolished. Physical and chemical analysis were carried out on concrete and steel samples taken from various elements of the building after thorough visual inspection of the entire building had been conducted. The physical (non-destructive) tests included the Schmidt hammer and ultrasonic pulse velocity tests on the concr...

  18. Flexible building stock modelling with array-programming

    DEFF Research Database (Denmark)

    Brøgger, Morten; Wittchen, Kim Bjarne

    2017-01-01

    Many building stock models employ archetype-buildings in order to capture the essential characteristics of a diverse building stock. However, these models often require multiple archetypes, which make them inflexible. This paper proposes an array-programming based model, which calculates the heat...... tend to overestimate potential energy-savings, if we do not consider these discrepancies. The proposed model makes it possible to compute and visualize potential energy-savings in a flexible and transparent way....

  19. Origins of the Human Genome Project.

    Science.gov (United States)

    Watson, J D; Cook-Deegan, R M

    1991-01-01

    The Human Genome Project has become a reality. Building on a debate that dates back to 1985, several genome projects are now in full stride around the world, and more are likely to form in the next several years. Italy began its genome program in 1987, and the United Kingdom and U.S.S.R. in 1988. The European communities mounted several genome projects on yeast, bacteria, Drosophila, and Arabidospis thaliana (a rapidly growing plant with a small genome) in 1988, and in 1990 commenced a new 2-year program on the human genome. In the United States, we have completed the first year of operation of the National Center for Human Genome Research at the National Institutes of Health (NIH), now the largest single funding source for genome research in the world. There have been dedicated budgets focused on genome-scale research at NIH, the U.S. Department of Energy, and the Howard Hughes Medical Institute for several years, and results are beginning to accumulate. There were three annual meetings on genome mapping and sequencing at Cold Spring Harbor, New York, in the spring of 1988, 1989, and 1990; the talks have shifted from a discussion about how to approach problems to presenting results from experiments already performed. We have finally begun to work rather than merely talk. The purpose of genome projects is to assemble data on the structure of DNA in human chromosomes and those of other organisms. A second goal is to develop new technologies to perform mapping and sequencing. There have been impressive technical advances in the past 5 years since the debate about the human genome project began. We are on the verge of beginning pilot projects to test several approaches to sequencing long stretches of DNA, using both automation and manual methods. Ordered sets of yeast artificial chromosome and cosmid clones have been assembled to span more than 2 million base pairs of several human chromosomes, and a region of 10 million base pairs has been assembled for

  20. A Blueprint for Genomic Nursing Science

    Science.gov (United States)

    Calzone, Kathleen A.; Jenkins, Jean; Bakos, Alexis D.; Cashion, Ann; Donaldson, Nancy; Feero, Greg; Feetham, Suzanne; Grady, Patricia A.; Hinshaw, Ada Sue; Knebel, Ann R.; Robinson, Nellie; Ropka, Mary E.; Seibert, Diane; Stevens, Kathleen R.; Tully, Lois A.; Webb, Jo Ann

    2012-01-01

    Purpose This article reports on recommendations arising from an invitational workshop series held at the National Institutes of Health for the purposes of identifying critical genomics problems important to the health of the public that can be addressed through nursing science. The overall purpose of the Genomic Nursing State of the Science Initiative is to establish a nursing research blueprint based on gaps in the evidence and expert evaluation of the current state of the science and through public comment. Organizing Constructs A Genomic Nursing State of the Science Advisory Panel was convened in 2012 to develop the nursing research blueprint. The Advisory Panel, which met via two webinars and two in-person meetings, considered existing evidence from evidence reviews, testimony from key stakeholder groups, presentations from experts in research synthesis, and public comment. Findings The genomic nursing science blueprint arising from the Genomic Nursing State of Science Advisory Panel focuses on biologic plausibility studies as well as interventions likely to improve a variety of outcomes (e.g., clinical, economic, environmental). It also includes all care settings and diverse populations. The focus is on (a) the client, defined as person, family, community, or population; (b) the context, targeting informatics support systems, capacity building, education, and environmental influences; and (c) cross-cutting themes. It was agreed that building capacity to measure the impact of nursing actions on costs, quality, and outcomes of patient care is a strategic and scientific priority if findings are to be synthesized and aggregated to inform practice and policy. Conclusions The genomic nursing science blueprint provides the framework for furthering genomic nursing science to improve health outcomes. This blueprint is an independent recommendation of the Advisory Panel with input from the public and is not a policy statement of the National Institutes of Health or the

  1. A Core Knowledge Architecture of Visual Working Memory

    Science.gov (United States)

    Wood, Justin N.

    2011-01-01

    Visual working memory (VWM) is widely thought to contain specialized buffers for retaining spatial and object information: a "spatial-object architecture." However, studies of adults, infants, and nonhuman animals show that visual cognition builds on core knowledge systems that retain more specialized representations: (1) spatiotemporal…

  2. Modern frame structure buildings

    Directory of Open Access Journals (Sweden)

    В. М. Першаков

    2013-07-01

    Full Text Available The article deals with the design, construction and implementation of reinforced concrete frame structures with span 18, 21 m for agricultural production buildings, hall-premises of public buildings and buildings of agricultural aviation. Structures are prefabricated frame buildings and have such advantages as large space inside the structure and lower cost compared with other facilities with same purpose

  3. Retrofitting Listed Buildings

    DEFF Research Database (Denmark)

    Rasmussen, Torben Valdbjørn

    2011-01-01

    The paper presents a case study where the energy demand for a listed building constructed in 1900 is reduced. Many older buildings are listed and have restrictions that include the entire building or that include only its exterior. For the building presented, only its exterior facade is listed. T...

  4. Measurement in Sustainable Building

    DEFF Research Database (Denmark)

    Hale, Lara

    2018-01-01

    Measurement is a necessary aspect of planning and constructing buildings. However, recent attempts to integrate the social dimension of sustainable building into building design and specifications demand measurement of non-technical qualities, such as well-being. The Active House Alliance, in lieu...... and continued provision of sustainable buildings to market demand....

  5. SigWin-detector: A Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences

    NARCIS (Netherlands)

    Inda, M.A.; van Batenburg, M.F.; Roos, M.; Belloum, A.S.Z.; Vasunin, D.; Wibisono, A.; van Kampen, A.H.C.; Breit, T.M.

    2008-01-01

    Background: Chromosome location is often used as a scaffold to organize genomic information in both the living cell and molecular biological research. Thus, ever-increasing amounts of data about genomic features are stored in public databases and can be readily visualized by genome browsers. To

  6. SigWin-detector: a Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences

    NARCIS (Netherlands)

    Inda, Marcia A.; van Batenburg, Marinus F.; Roos, Marco; Belloum, Adam Sz; Vasunin, Dmitry; Wibisono, Adianto; van Kampen, Antoine H. C.; Breit, Timo M.

    2008-01-01

    ABSTRACT: BACKGROUND: Chromosome location is often used as a scaffold to organize genomic information in both the living cell and molecular biological research. Thus, ever-increasing amounts of data about genomic features are stored in public databases and can be readily visualized by genome

  7. ICT Enhanced Buildings Potentials

    DEFF Research Database (Denmark)

    Christiansson, Per

    2007-01-01

    component systems that are accessed and integrated in the real world of building use in different contexts. The ICT systems may be physically or virtually embedded in the building. Already in 1982 AT&T established the 'intelligent buildings', IB, concept due to marketing reasons and the Informart building...... with focus on virtual building models support, new services and user environment definitions and development, virtual spaces and augmented reality, intelligent building components, application ontologies, and ICT systems integration to illustrate ICT enhanced buildings potentials and R&D needs.  ...

  8. Global building physics

    DEFF Research Database (Denmark)

    Rode, Carsten

    2013-01-01

    High ambitions are set for the building physics performance of buildings today. No single technology can achieve fulfilment of these ambitions alone. Integrated, multi-facetted solutions and optimization are necessary. A holistic, or ‘global’, technological perspective is needed, which includes all...... aspects of the building as defined in building engineering. We live in an international society and building solutions are developed across country borders. Building physics is a global theme. The International Association of Building Physics has global appeal. This brief article reports the keynote...

  9. Global Building Physics

    DEFF Research Database (Denmark)

    Rode, Carsten

    2012-01-01

    High ambitions are set for the building physics performance of buildings today. No single technology can achieve fulfilment of these ambitions alone. Integrated, multi-facetted solutions and optimization are necessary. A holistic, or “global”, technological perspective is needed, which includes all...... aspects of the building as defined in building engineering. We live in an international society and building solutions are developed across country borders. Building physics is a global theme. The International Association of Building Physics has global appeal. The keynote lecture and this brief paper...

  10. Comparative Genome Analysis and Genome Evolution

    NARCIS (Netherlands)

    Snel, Berend

    2002-01-01

    This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies.

  11. Variant Review with the Integrative Genomics Viewer.

    Science.gov (United States)

    Robinson, James T; Thorvaldsdóttir, Helga; Wenger, Aaron M; Zehir, Ahmet; Mesirov, Jill P

    2017-11-01

    Manual review of aligned reads for confirmation and interpretation of variant calls is an important step in many variant calling pipelines for next-generation sequencing (NGS) data. Visual inspection can greatly increase the confidence in calls, reduce the risk of false positives, and help characterize complex events. The Integrative Genomics Viewer (IGV) was one of the first tools to provide NGS data visualization, and it currently provides a rich set of tools for inspection, validation, and interpretation of NGS datasets, as well as other types of genomic data. Here, we present a short overview of IGV's variant review features for both single-nucleotide variants and structural variants, with examples from both cancer and germline datasets. IGV is freely available at https://www.igv.org Cancer Res; 77(21); e31-34. ©2017 AACR . ©2017 American Association for Cancer Research.

  12. Genomic signal processing for DNA sequence clustering.

    Science.gov (United States)

    Mendizabal-Ruiz, Gerardo; Román-Godínez, Israel; Torres-Ramos, Sulema; Salido-Ruiz, Ricardo A; Vélez-Pérez, Hugo; Morales, J Alejandro

    2018-01-01

    Genomic signal processing (GSP) methods which convert DNA data to numerical values have recently been proposed, which would offer the opportunity of employing existing digital signal processing methods for genomic data. One of the most used methods for exploring data is cluster analysis which refers to the unsupervised classification of patterns in data. In this paper, we propose a novel approach for performing cluster analysis of DNA sequences that is based on the use of GSP methods and the K-means algorithm. We also propose a visualization method that facilitates the easy inspection and analysis of the results and possible hidden behaviors. Our results support the feasibility of employing the proposed method to find and easily visualize interesting features of sets of DNA data.

  13. Self-Concepts of Children with Visual Impairments.

    Science.gov (United States)

    Alexander, Francis E.

    1996-01-01

    Ten day students and 10 residential students with visual impairments in grades 3-5 participated in 18 weekly self-esteem building exercises. No intergroup differences in self-esteem were found, and data were inconclusive on the effectiveness of the self-esteem building activities. (CR)

  14. Collaborative interactive visualization: exploratory concept

    Science.gov (United States)

    Mokhtari, Marielle; Lavigne, Valérie; Drolet, Frédéric

    2015-05-01

    Dealing with an ever increasing amount of data is a challenge that military intelligence analysts or team of analysts face day to day. Increased individual and collective comprehension goes through collaboration between people. Better is the collaboration, better will be the comprehension. Nowadays, various technologies support and enhance collaboration by allowing people to connect and collaborate in settings as varied as across mobile devices, over networked computers, display walls, tabletop surfaces, to name just a few. A powerful collaboration system includes traditional and multimodal visualization features to achieve effective human communication. Interactive visualization strengthens collaboration because this approach is conducive to incrementally building a mental assessment of the data meaning. The purpose of this paper is to present an overview of the envisioned collaboration architecture and the interactive visualization concepts underlying the Sensemaking Support System prototype developed to support analysts in the context of the Joint Intelligence Collection and Analysis Capability project at DRDC Valcartier. It presents the current version of the architecture, discusses future capabilities to help analyst(s) in the accomplishment of their tasks and finally recommends collaboration and visualization technologies allowing to go a step further both as individual and as a team.

  15. JGI Plant Genomics Gene Annotation Pipeline

    Energy Technology Data Exchange (ETDEWEB)

    Shu, Shengqiang; Rokhsar, Dan; Goodstein, David; Hayes, David; Mitros, Therese

    2014-07-14

    Plant genomes vary in size and are highly complex with a high amount of repeats, genome duplication and tandem duplication. Gene encodes a wealth of information useful in studying organism and it is critical to have high quality and stable gene annotation. Thanks to advancement of sequencing technology, many plant species genomes have been sequenced and transcriptomes are also sequenced. To use these vastly large amounts of sequence data to make gene annotation or re-annotation in a timely fashion, an automatic pipeline is needed. JGI plant genomics gene annotation pipeline, called integrated gene call (IGC), is our effort toward this aim with aid of a RNA-seq transcriptome assembly pipeline. It utilizes several gene predictors based on homolog peptides and transcript ORFs. See Methods for detail. Here we present genome annotation of JGI flagship green plants produced by this pipeline plus Arabidopsis and rice except for chlamy which is done by a third party. The genome annotations of these species and others are used in our gene family build pipeline and accessible via JGI Phytozome portal whose URL and front page snapshot are shown below.

  16. Genomic Data Commons launches

    Science.gov (United States)

    The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

  17. Rat Genome Database (RGD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  18. Design Visualization Internship Overview

    Science.gov (United States)

    Roberts, Trevor D.

    2014-01-01

    This is a report documenting the details of my work as a NASA KSC intern for the Summer Session from June 2nd to August 8th, 2014. This work was conducted within the Design Visualization Group, a Contractor staffed organization within the C1 division of the IT Directorate. The principle responsibilities of the KSC Design Visualization Group are the production of 3D simulations of NASA equipment and facilities for the purpose of planning complex operations such as hardware transportation and vehicle assembly. My role as an intern focused on aiding engineers in using 3D scanning equipment to obtain as-built measurements of NASA facilities, as well as using CATIA and DELMIA to process this data. My primary goals for this internship focused on expanding my CAD knowledge and capabilities, while also learning more about technologies I was previously unfamiliar with, such as 3D scanning. An additional goal of mine was to learn more about how NASA operates, and how the U.S. Space Program operates on a day-to-day basis. This opportunity provided me with a front-row seat to the daily maneuvers and operations of KSC and NASA as a whole. Each work day, I was able to witness, and even take part of, a small building block of the future systems that will take astronauts to other worlds. After my experiences this summer, not only can I say that my goals have been met, but also that this experience has been the highlight of my experience in higher education.

  19. Robot Tracer with Visual Camera

    Science.gov (United States)

    Jabbar Lubis, Abdul; Dwi Lestari, Yuyun; Dafitri, Haida; Azanuddin

    2017-12-01

    Robot is a versatile tool that can function replace human work function. The robot is a device that can be reprogrammed according to user needs. The use of wireless networks for remote monitoring needs can be utilized to build a robot that can be monitored movement and can be monitored using blueprints and he can track the path chosen robot. This process is sent using a wireless network. For visual robot using high resolution cameras to facilitate the operator to control the robot and see the surrounding circumstances.

  20. Genomic prediction using subsampling

    OpenAIRE

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-01-01

    Background Genome-wide assisted selection is a critical tool for the?genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each rou...

  1. Mapping the space of genomic signatures.

    Directory of Open Access Journals (Sweden)

    Lila Kari

    Full Text Available We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is computed for each pair of graphical representations of DNA sequences, and the distances are visualized as a Molecular Distance Map: Each point on the map represents a DNA sequence, and the spatial proximity between any two points reflects the degree of structural similarity between the corresponding sequences. The graphical representation of DNA sequences utilized, Chaos Game Representation (CGR, is genome- and species-specific and can thus act as a genomic signature. Consequently, Molecular Distance Maps could inform species identification, taxonomic classifications and, to a certain extent, evolutionary history. The image distance employed, Structural Dissimilarity Index (DSSIM, implicitly compares the occurrences of oligomers of length up to k (herein k = 9 in DNA sequences. We computed DSSIM distances for more than 5 million pairs of complete mitochondrial genomes, and used Multi-Dimensional Scaling (MDS to obtain Molecular Distance Maps that visually display the sequence relatedness in various subsets, at different taxonomic levels. This general-purpose method does not require DNA sequence alignment and can thus be used to compare similar or vastly different DNA sequences, genomic or computer-generated, of the same or different lengths. We illustrate potential uses of this approach by applying it to several taxonomic subsets: phylum Vertebrata, (superkingdom Protista, classes Amphibia-Insecta-Mammalia, class Amphibia, and order Primates. This analysis of an extensive dataset confirms that the oligomer composition of full mtDNA sequences can be a source of taxonomic information. This method also correctly finds the mtDNA sequences most closely related to that of the anatomically modern human (the Neanderthal

  2. Ensembl Genomes 2013: scaling up access to genome-wide data.

    Science.gov (United States)

    Kersey, Paul Julian; Allen, James E; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Hughes, Daniel Seth Toney; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Langridge, Nicholas; McDowall, Mark D; Maheswari, Uma; Maslen, Gareth; Nuhn, Michael; Ong, Chuang Kee; Paulini, Michael; Pedro, Helder; Toneva, Iliana; Tuli, Mary Ann; Walts, Brandon; Williams, Gareth; Wilson, Derek; Youens-Clark, Ken; Monaco, Marcela K; Stein, Joshua; Wei, Xuehong; Ware, Doreen; Bolser, Daniel M; Howe, Kevin Lee; Kulesha, Eugene; Lawson, Daniel; Staines, Daniel Michael

    2014-01-01

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.

  3. Ebolavirus comparative genomics

    DEFF Research Database (Denmark)

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms...

  4. Relationship between Quality of Building Maintenance System and Occupant Satisfaction for Office Buildings

    Directory of Open Access Journals (Sweden)

    Hamid A.H.A

    2014-03-01

    Full Text Available Buildings will be weary, decaying and dirty as time goes by; but with highquality maintenance management we can prolong the life-span of building, provide building services and keep the building performance at its ultimate level. The importance of carrying out a systematic and routine maintenance is to conserve building performance. However, this task is often neglected due to various factors including misunderstanding the needs of the maintenance works and lack of budget allocation. This paper highlights the current practice of maintenance management that are being implemented in 6 office buildings located in Kuala Lumpur, Johor, Kedah and Pulau Pinang. Using the responses of questionnaire answered by 150 respondents employed from these selected offices, personal interviews and visual inspection the following findings were made: the occupants were satisfied with the maintenance management of their buildings elements and the delivery characteristics of maintenance works. Visual inspection however showed that some elements are not in a good condition. In conclusion, some recommendations are made to improve the existing system including the establishment of a maintenance plan, selection of experienced contractors and the provision of a service desk.

  5. VISUAL3D - An EIT network on visualization of geomodels

    Science.gov (United States)

    Bauer, Tobias

    2017-04-01

    Universität Leoben, Slovenian National Building and Civil Engineering Institute, Tallinn University of Technology and Turku University. The infrastructure within the network comprises different types of capturing and visualization hardware, ranging from high resolution cubes, VR walls, VR goggle solutions, high resolution photogrammetry, UAVs, lidar-scanners, and many more.

  6. Sustainable Buildings in Interaction

    DEFF Research Database (Denmark)

    Elle, Morten

    2007-01-01

    The first attempts to build sustainable buildings in Denmark were typically located on the countryside. The basic idea was to create buildings that were independent of the technical infrastructure. District heating has, however, been the dominating solution to heating in buildings in Denmark......, and the focus on sustainable building have gradually turned from special houses on the countryside to normally looking houses in the urban fabric, integrated in the technical infrastructure. Some new built urban areas in Denmark will, however, not have to be supplied with district heating – these developments...... are going to consist of passive houses. The first sustainable buildings were built by their users, and the user – building interaction still play a decisive role for the performance of the present sustainable buildings. The users have to understand how the building functions. Urban design is essential...

  7. A review of genomic data warehousing systems.

    Science.gov (United States)

    Triplet, Thomas; Butler, Gregory

    2014-07-01

    To facilitate the integration and querying of genomics data, a number of generic data warehousing frameworks have been developed. They differ in their design and capabilities, as well as their intended audience. We provide a comprehensive and quantitative review of those genomic data warehousing frameworks in the context of large-scale systems biology. We reviewed in detail four genomic data warehouses (BioMart, BioXRT, InterMine and PathwayTools) freely available to the academic community. We quantified 20 aspects of the warehouses, covering the accuracy of their responses, their computational requirements and development efforts. Performance of the warehouses was evaluated under various hardware configurations to help laboratories optimize hardware expenses. Each aspect of the benchmark may be dynamically weighted by scientists using our online tool BenchDW (http://warehousebenchmark.fungalgenomics.ca/benchmark/) to build custom warehouse profiles and tailor our results to their specific needs.

  8. The Sequenced Angiosperm Genomes and Genome Databases.

    Science.gov (United States)

    Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

    2018-01-01

    Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

  9. The Solid* toolset for software visual analytics of program structure and metrics comprehension : From research prototype to product

    NARCIS (Netherlands)

    Reniers, Dennie; Voinea, Lucian; Ersoy, Ozan; Telea, Alexandru

    2014-01-01

    Software visual analytics (SVA) tools combine static program analysis and fact extraction with information visualization to support program comprehension. However, building efficient and effective SVA tools is highly challenging, as it involves extensive software development in program analysis,

  10. Advancing Water Science through Data Visualization

    Science.gov (United States)

    Li, X.; Troy, T.

    2014-12-01

    As water scientists, we are increasingly handling larger and larger datasets with many variables, making it easy to lose ourselves in the details. Advanced data visualization will play an increasingly significant role in propelling the development of water science in research, economy, policy and education. It can enable analysis within research and further data scientists' understanding of behavior and processes and can potentially affect how the public, whom we often want to inform, understands our work. Unfortunately for water scientists, data visualization is approached in an ad hoc manner when a more formal methodology or understanding could potentially significantly improve both research within the academy and outreach to the public. Firstly to broaden and deepen scientific understanding, data visualization can allow for more analyzed targets to be processed simultaneously and can represent the variables effectively, finding patterns, trends and relationships; thus it can even explores the new research direction or branch of water science. Depending on visualization, we can detect and separate the pivotal and trivial influential factors more clearly to assume and abstract the original complex target system. Providing direct visual perception of the differences between observation data and prediction results of models, data visualization allows researchers to quickly examine the quality of models in water science. Secondly data visualization can also improve public awareness and perhaps influence behavior. Offering decision makers clearer perspectives of potential profits of water, data visualization can amplify the economic value of water science and also increase relevant employment rates. Providing policymakers compelling visuals of the role of water for social and natural systems, data visualization can advance the water management and legislation of water conservation. By building the publics' own data visualization through apps and games about water

  11. Integrating Responsive Building Elements in Buildings

    DEFF Research Database (Denmark)

    Haase, Matthias; Amato, Alex; Heiselberg, Per

    2006-01-01

    energy strategies to develop guidelines and procedures for estimation of environmental performance of responsive building elements and integrated building concepts This paper introduces the ideas of this collaborative work and discusses its usefulness for Hong Kong and China. Special focus was put...

  12. Challenges in Commercial Buildings | Buildings | NREL

    Science.gov (United States)

    systems Assessing the energy and economic impacts of various technologies, giving priority to those that standardized language for commercial building energy audit data that can be used by software developers to exchange data between audit tools, and can be required by building owners and audit program managers to

  13. Bellanca building, Yellowknife : building envelope retrofit project

    Energy Technology Data Exchange (ETDEWEB)

    Rajewski, G. [A.D. Williams Engineering Inc., Edmonton, AB (Canada)

    2008-07-01

    The Bellanca building is a ten-story, commercial office building, located in Yellowknife, Northwest Territories. The owner was concerned about annual fuel consumption, relative to other buildings of similar size. Tenants reported cold drafts and some ice build-up had been reported in the past, on the exterior of the cladding. In addition, some water penetration had occurred during rainfall. This presentation provided background information on the Bellanca building and discussed a building envelope retrofit project. A.D. Williams was hired in late 2006 in order to provide an opinion on the present condition of the building envelope. This presentation described the site investigation and presented an interior and exterior review of the building. It also presented a thermographic survey in order to map thermal anomalies and establish trends. Following acceptance of the report on findings, one of five options was selected for further development. This included removal of existing cladding, exterior gypsum wallboard, fiberglass insulation and application of BASF Walltite CT foam, sheathing, rigid insulation, drainage plane and new cladding. The preliminary design was then presented. This paper also described the tender and award of the contract; construction phase; and substantial completion of the project. tabs, figs.

  14. Synthetic Biology to Engineer Bacteriophage Genomes.

    Science.gov (United States)

    Rita Costa, Ana; Milho, Catarina; Azeredo, Joana; Pires, Diana Priscila

    2018-01-01

    Recent advances in the synthetic biology field have enabled the development of new molecular biology techniques used to build specialized bacteriophages with new functionalities. Bacteriophages have been engineered towards a wide range of applications including pathogen control and detection, targeted drug delivery, or even assembly of new materials.In this chapter, two strategies that have been successfully used to genetically engineer bacteriophage genomes are addressed: a yeast-based platform and bacteriophage recombineering of electroporated DNA.

  15. Introduction: Critical Visual Theory

    Directory of Open Access Journals (Sweden)

    Peter Ludes

    2014-03-01

    Full Text Available The studies selected for publication in this special issue on Critical Visual Theory can be divided into three thematic groups: (1 image making as power making, (2 commodification and recanonization, and (3 approaches to critical visual theory. The approaches to critical visual theory adopted by the authors of this issue may be subsumed under the following headings (3.1 critical visual discourse and visual memes in general and Anonymous visual discourse in particular, (3.2 collective memory and gendered gaze, and (3.3 visual capitalism, global north and south.

  16. The global lambda visualization facility: An international ultra-high-definition wide-area visualization collaboratory

    Science.gov (United States)

    Leigh, J.; Renambot, L.; Johnson, Aaron H.; Jeong, B.; Jagodic, R.; Schwarz, N.; Svistula, D.; Singh, R.; Aguilera, J.; Wang, X.; Vishwanath, V.; Lopez, B.; Sandin, D.; Peterka, T.; Girado, J.; Kooima, R.; Ge, J.; Long, L.; Verlo, A.; DeFanti, T.A.; Brown, M.; Cox, D.; Patterson, R.; Dorn, P.; Wefel, P.; Levy, S.; Talandis, J.; Reitzer, J.; Prudhomme, T.; Coffin, T.; Davis, B.; Wielinga, P.; Stolk, B.; Bum, Koo G.; Kim, J.; Han, S.; Corrie, B.; Zimmerman, T.; Boulanger, P.; Garcia, M.

    2006-01-01

    The research outlined in this paper marks an initial global cooperative effort between visualization and collaboration researchers to build a persistent virtual visualization facility linked by ultra-high-speed optical networks. The goal is to enable the comprehensive and synergistic research and development of the necessary hardware, software and interaction techniques to realize the next generation of end-user tools for scientists to collaborate on the global Lambda Grid. This paper outlines some of the visualization research projects that were demonstrated at the iGrid 2005 workshop in San Diego, California.

  17. Re-conceiving building design quality: A review of building users in their social context.

    Science.gov (United States)

    Watson, Kelly J; Evans, James; Karvonen, Andrew; Whitley, Tim

    2016-05-01

    Considerable overlap exists between post-occupancy research evaluating building design quality and the concept of 'social value', popularised by its recent application to issues of the public realm. To outline this potential research agenda, the paper reviews design quality research on buildings in relation to users and their social context where the term 'social context' refers to building user group dynamics, a combination of organisational cultures, management strategies, and social norms and practices. The review is conducted across five key building types, namely housing, workplaces, healthcare, education, and the retail/service sector. Research commonalities and gaps are identified in order to build a more comprehensive picture of the design quality literature and its handling of users in their social context. The key findings concerning each building type are presented visually. It is concluded that the design quality field comprises a patchwork of relatively isolated studies of various building types, with significant potential for theoretical and empirical development through interdisciplinary collaboration. Users tend to be conceived as anonymous and autonomous individuals with little analysis of user identity or interaction. Further, the contextual impact of user group dynamics on the relationship between building design and building user is rarely addressed in the literature. Producing a more nuanced understanding of users in situ is proposed as an important area for future design quality research.

  18. Cortical visual impairment

    OpenAIRE

    Koželj, Urša

    2013-01-01

    In this thesis we discuss cortical visual impairment, diagnosis that is in the developed world in first place, since 20 percent of children with blindness or low vision are diagnosed with it. The objectives of the thesis are to define cortical visual impairment and the definition of characters suggestive of the cortical visual impairment as well as to search for causes that affect the growing diagnosis of cortical visual impairment. There are a lot of signs of cortical visual impairment. ...

  19. Relativity of Visual Communication

    OpenAIRE

    Arto Mutanen

    2016-01-01

    Communication is sharing and conveying information. In visual communication especially visual messages have to be formulated and interpreted. The interpretation is relative to a method of information presentation method which is human construction. This holds also in the case of visual languages. The notions of syntax and semantics for visual languages are not so well founded as they are for natural languages. Visual languages are both syntactically and semantically dense. The density is conn...

  20. Knowledge scaffolding visualizations: A guiding framework

    Directory of Open Access Journals (Sweden)

    Elitsa Alexander

    2015-06-01

    Full Text Available In this paper we provide a guiding framework for understanding and selecting visual representations in the knowledge management (KM practice. We build on an interdisciplinary analogy between two connotations of the notion of “scaffolding”: physical scaffolding from an architectural-engineering perspective and scaffolding of the “everyday knowing in practice” from a KM perspective. We classify visual structures for knowledge communication in teams into four types of scaffolds: grounded (corresponding e.g., to perspectives diagrams or dynamic facilitation diagrams, suspended (e.g., negotiation sketches, argument maps, panel (e.g., roadmaps or timelines and reinforcing (e.g., concept diagrams. The article concludes with a set of recommendations in the form of questions to ask whenever practitioners are choosing visualizations for specific KM needs. Our recommendations aim at providing a framework at a broad-brush level to aid choosing a suitable visualization template depending on the type of KM endeavour.

  1. Contemporary facades of multistorey residential buildings in Kiev: Videoecological aspect

    Directory of Open Access Journals (Sweden)

    Kozlova Nataliia

    2016-01-01

    Full Text Available The article is devoted to one of the actual problems concerning the current state of the facades on apartment buildings in residential districts in Kiev - videoecology. The main purpose of the article is to determine the degree of visual aggressiveness of multistorey residential buildings in Kiev. It also investigates the problem of finding the optimal criteria for creating an ecologically healthy and friendly inhabited environment in the capital city of Ukraine. The modern visual environment in the capital is contaminated, not only because of the increasing numbers of promotional billboards, but also because of the contemporary architecture of high-rise buildings such as office buildings, apartment buildings. Their composition is usually based on a simple description of a rhythm. There are also repetitions of the end parts of buildings in “lowercase” buildings, which are high-rise buildings that alternate with nine or identical apartment groups. It creates a sense of oppressive monotony and leads to psychological and visual fatigue, especially when these repetitions are the only pattern the eye perceives. In the article a theoretical block of ecological-aesthetic criteria is defined, which must be met by the modern architecture facades of multistorey residential houses in Kiev.

  2. A Guide to the PLAZA 3.0 Plant Comparative Genomic Database.

    Science.gov (United States)

    Vandepoele, Klaas

    2017-01-01

    PLAZA 3.0 is an online resource for comparative genomics and offers a versatile platform to study gene functions and gene families or to analyze genome organization and evolution in the green plant lineage. Starting from genome sequence information for over 35 plant species, precomputed comparative genomic data sets cover homologous gene families, multiple sequence alignments, phylogenetic trees, and genomic colinearity information within and between species. Complementary functional data sets, a Workbench, and interactive visualization tools are available through a user-friendly web interface, making PLAZA an excellent starting point to translate sequence or omics data sets into biological knowledge. PLAZA is available at http://bioinformatics.psb.ugent.be/plaza/ .

  3. Building damage assessment after the earthquake in Haiti using two postevent satellite stereo imagery and DSMs

    DEFF Research Database (Denmark)

    Tian, Jiaojiao; Nielsen, Allan Aasbjerg; Reinartz, Peter

    2015-01-01

    In this article, a novel after-disaster building damage monitoring method is presented. This method combines the multispectral imagery and digital surface models (DSMs) from stereo matching of two dates to obtain three kinds of changes: collapsed buildings, newly built buildings and temporary she...... changes after the 2010 Haiti earthquake, and the obtained results are further evaluated both visually and numerically....

  4. Requirements for existing buildings

    DEFF Research Database (Denmark)

    Thomsen, Kirsten Engelund; Wittchen, Kim Bjarne

    This report collects energy performance requirements for existing buildings in European member states by June 2012.......This report collects energy performance requirements for existing buildings in European member states by June 2012....

  5. Green Building Standards

    Science.gov (United States)

    Many organizations have developed model codes or rating systems that communities may use to develop green building programs or revise building ordinances. Some of the major options are listed on this page.

  6. Introduction: Green Building Handbook

    CSIR Research Space (South Africa)

    Van Wyk, Llewellyn V

    2010-08-01

    Full Text Available By recognising the specific environmental challenges facing South Africa, mindful of the government‘s commitment to reducing South Africa‘s Greenhouse gas emissions, and acknowledging the need to build social cohesion, the Green Building Handbook...

  7. Integrated Building Health Management

    Data.gov (United States)

    National Aeronautics and Space Administration — Abstract: Building health management is an important part in running an efficient and cost-effective building. Many problems in a building’s system can go undetected...

  8. Building the Korogwe Laboratory

    DEFF Research Database (Denmark)

    Knudsen, Jakob; von Seidlein, Lorenz; Richard, Jean Pierre

    2011-01-01

    An illustrated description of the building of a biomedical research laboratory in Korogwe, Tanzania.......An illustrated description of the building of a biomedical research laboratory in Korogwe, Tanzania....

  9. Sustainable Building Operation

    DEFF Research Database (Denmark)

    Jensen, Jesper Ole

    2009-01-01

    of sustainable building operation and a survey amongst building administrators from the private and the social housing sector. Our results show that there are many good examples on sustainable building operation in Danish housing estates, where local building managers, residents etc. have gained impressive......Energy-savings in the existing building stock have becomes a main goal in national and international policies. Often focus is on building-renovations, whereas the potential of sustainable building operation to a large extent has been neglected. Nevertheless, international research as well...... as practical experiences from Danish housing estates indicates that there are large potentials for energy savings by focusing on the operation of the buildings. We suggest that in order to achieve sustainability in the existing housing, renovation and operations should be seen as integrated parts...

  10. Robotic buildings(s)

    NARCIS (Netherlands)

    Bier, H.H.

    2014-01-01

    Technological and conceptual advances in fields such as artificial intelligence, robotics, and material science have enabled robotic building to be in the last decade prototypically implemented. In this context, robotic building implies both physically built robotic environments and robotically

  11. Environmental indicators for buildings

    DEFF Research Database (Denmark)

    Dammann, Sven

    Environmental Indicators for Buildings are studied using two different perspectives: with a technological, environmental scientific departing point and with a social scientific departing point. Different relevant groups in the building sector are identified and analysed, using the Social...

  12. Building Design & Construction - Sustainability

    Energy Technology Data Exchange (ETDEWEB)

    None

    2003-11-01

    Offers a brief history of green building; presents the results of a specially commissioned survey; and analyzes the chief trends, issues, and published research, based on interviews with dozens of experts and participants in green building.

  13. Buildings interoperability landscape - Draft

    Energy Technology Data Exchange (ETDEWEB)

    Hardin, Dave B. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Stephan, Eric G. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Wang, Weimin [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Corbin, Charles D. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Widergren, Steven E. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

    2015-02-01

    Buildings are an integral part of our nation’s energy economy. The advancement in information and communications technology (ICT) has revolutionized energy management in industrial facilities and large commercial buildings. As ICT costs decrease and capabilities increase, buildings automation and energy management features are transforming the small-medium commercial and residential buildings sectors. A vision of a connected world in which equipment and systems within buildings coordinate with each other to efficiently meet their owners’ and occupants’ needs, and where buildings regularly transact business with other buildings and service providers (such as gas and electric service providers) is emerging. However, while the technology to support this collaboration has been demonstrated at various degrees of maturity, the integration frameworks and ecosystems of products that support the ability to easily install, maintain, and evolve building systems and their equipment components are struggling to nurture the fledging business propositions of their proponents.

  14. A comprehensive and quantitative exploration of thousands of viral genomes

    Science.gov (United States)

    Mahmoudabadi, Gita

    2018-01-01

    The complete assembly of viral genomes from metagenomic datasets (short genomic sequences gathered from environmental samples) has proven to be challenging, so there are significant blind spots when we view viral genomes through the lens of metagenomics. One approach to overcoming this problem is to leverage the thousands of complete viral genomes that are publicly available. Here we describe our efforts to assemble a comprehensive resource that provides a quantitative snapshot of viral genomic trends – such as gene density, noncoding percentage, and abundances of functional gene categories – across thousands of viral genomes. We have also developed a coarse-grained method for visualizing viral genome organization for hundreds of genomes at once, and have explored the extent of the overlap between bacterial and bacteriophage gene pools. Existing viral classification systems were developed prior to the sequencing era, so we present our analysis in a way that allows us to assess the utility of the different classification systems for capturing genomic trends. PMID:29624169

  15. Visualization analysis and design

    CERN Document Server

    Munzner, Tamara

    2015-01-01

    Visualization Analysis and Design provides a systematic, comprehensive framework for thinking about visualization in terms of principles and design choices. The book features a unified approach encompassing information visualization techniques for abstract data, scientific visualization techniques for spatial data, and visual analytics techniques for interweaving data transformation and analysis with interactive visual exploration. It emphasizes the careful validation of effectiveness and the consideration of function before form. The book breaks down visualization design according to three questions: what data users need to see, why users need to carry out their tasks, and how the visual representations proposed can be constructed and manipulated. It walks readers through the use of space and color to visually encode data in a view, the trade-offs between changing a single view and using multiple linked views, and the ways to reduce the amount of data shown in each view. The book concludes with six case stu...

  16. Relativity of Visual Communication

    Directory of Open Access Journals (Sweden)

    Arto Mutanen

    2016-03-01

    Full Text Available Communication is sharing and conveying information. In visual communication especially visual messages have to be formulated and interpreted. The interpretation is relative to a method of information presentation method which is human construction. This holds also in the case of visual languages. The notions of syntax and semantics for visual languages are not so well founded as they are for natural languages. Visual languages are both syntactically and semantically dense. The density is connected to the compositionality of the (pictorial languages. In the paper Charles Sanders Peirce’s theory of signs will be used in characterizing visual languages. This allows us to relate visual languages to natural languages. The foundation of information presentation methods for visual languages is the logic of perception, but only if perception is understood as propositional perception. This allows us to understand better the relativity of information presentation methods, and hence to evaluate the cultural relativity of visual communication.

  17. Development of Visualization Tools for ZPPR-15 Analysis

    International Nuclear Information System (INIS)

    Lee, Min Jae; Kim, Sang Ji

    2014-01-01

    ZPPR-15 cores consist of various drawer masters that have great heterogeneity. In order to build a proper homogenization strategy, the geometry of the drawer masters should be carefully analyzed with a visualization. Additionally, a visualization of drawer masters and the core configuration is necessary for minimizing human error during the input processing. For this purpose, visualization tools for a ZPPR-15 analysis has been developed based on a Perl script. In the following section, the implementation of visualization tools will be described and various visualization samples for both drawer masters and ZPPR-15 cores will be demonstrated. Visualization tools for drawer masters and a core configuration were successfully developed for a ZPPR-15 analysis. The visualization tools are expected to be useful for understanding ZPPR-15 experiments, and finding deterministic models of ZPPR-15. It turned out that generating VTK files is handy but the application of VTK files is powerful with the aid of the VISIT program

  18. VISTA - computational tools for comparative genomics

    Energy Technology Data Exchange (ETDEWEB)

    Frazer, Kelly A.; Pachter, Lior; Poliakov, Alexander; Rubin,Edward M.; Dubchak, Inna

    2004-01-01

    Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here we describe the VISTA family of tools created to assist biologists in carrying out this task. Our first VISTA server at http://www-gsd.lbl.gov/VISTA/ was launched in the summer of 2000 and was designed to align long genomic sequences and visualize these alignments with associated functional annotations. Currently the VISTA site includes multiple comparative genomics tools and provides users with rich capabilities to browse pre-computed whole-genome alignments of large vertebrate genomes and other groups of organisms with VISTA Browser, submit their own sequences of interest to several VISTA servers for various types of comparative analysis, and obtain detailed comparative analysis results for a set of cardiovascular genes. We illustrate capabilities of the VISTA site by the analysis of a 180 kilobase (kb) interval on human chromosome 5 that encodes for the kinesin family member3A (KIF3A) protein.

  19. Building 431 fire tests

    International Nuclear Information System (INIS)

    Alvares, N.J.; Beason, D.G.; Ford, H.W.; Magee, M.W.

    1977-01-01

    An extensive discussion of considerations for fire protection in the LLL mirror fusion test facility (MFTF) is presented. Because of the large volume and high bays of the building, sufficient data on fire detection is unavailable. Results of fire detection tests using controlled fire sources in the building are presented. Extensive data concerning the behavior of the building atmosphere are included. Candidate fire detection instrumentation and extinguishing systems for use in the building are briefly reviewed

  20. Dutch Building Decree

    NARCIS (Netherlands)

    Scholten, N.P.M.

    2000-01-01

    On the 1 October 1992 a change in the Dutch building legislation took effect: the revised Housing Act, the Building Decree and the technical documents related to this legislation came into force. This publication contains an English translation of the Building Decree. In order to give an idea of the

  1. Building founding method

    International Nuclear Information System (INIS)

    Tateno, Seiya; Hirako, Shizuka.

    1996-01-01

    The lower portion of a reactor building is buried at a level of a base rock. In the step of building construction, the base rock around the building is dug of keeping a construction space. The base rock present between the digging line and the building is replaced with an artificial base rock comprising aggregates and cement having a building constraining force substantially equal with that of the lower supporting base rock to obtain constraining force for the side portion of the building. The building itself is made of concrete steels. As the material for replacing the base rock between the digging line and the building, non-reinforced concrete having no steels may provide sufficient function. The burying depth is determined so as to align the surface of the base rock with the level of the base floor of the building. With such procedures, since it is not necessary to increase the area of the lower portion of the building, the amount of the materials for the building can be reduced. In addition, the earthquakes stability can be ensured without changing the shape of the building. (I.N.)

  2. Management Of Building Projects

    OpenAIRE

    Niko Majdandzic; Tadija Lovric; Vido Peric

    2006-01-01

    In this work we have shown the concept of logistic support in management in building production and in building of objects, which is realised in Enterprise resource Planning – ERP system ERPINSG, developed in Informatic firm Informatic engineering – ININ in Slavonski Brod, and in cooperation with scientists of catedra for informatics of Faculty of Mechanical Engineering and users from building firms.

  3. Concepts in Building Firesafety.

    Science.gov (United States)

    Egan, M. David

    The goal of this book is to present in a graphical format the principles of design for building firesafety. The book's more than 270 illustrations represent the core of its coverage of factors affecting fire ignition and spread in buildings, building site planning for fire suppression and occupant rescue operations, protection by building…

  4. Green Building Research Laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Sailor, David Jean [Portland State Univ., Portland, OR (United States)

    2013-12-29

    This project provided support to the Green Building Research Laboratory at Portland State University (PSU) so it could work with researchers and industry to solve technical problems for the benefit of the green building industry. It also helped to facilitate the development of PSU’s undergraduate and graduate-level training in building science across the curriculum.

  5. 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.

  6. Visualizing the Verbal and Verbalizing the Visual.

    Science.gov (United States)

    Braden, Roberts A.

    This paper explores relationships of visual images to verbal elements, beginning with a discussion of visible language as represented by words printed on the page. The visual flexibility inherent in typography is discussed in terms of the appearance of the letters and the denotative and connotative meanings represented by type, typographical…

  7. A Visual Test for Visual "Literacy."

    Science.gov (United States)

    Messaris, Paul

    Four different principles of visual manipulation constitute a minimal list of what a visually "literate" viewer should know about, but certain problems exist which are inherent in measuring viewers' awareness of each of them. The four principles are: (1) paraproxemics, or camera work which derives its effectiveness from an analogy to the…

  8. Interaction for visualization

    CERN Document Server

    Tominski, Christian

    2015-01-01

    Visualization has become a valuable means for data exploration and analysis. Interactive visualization combines expressive graphical representations and effective user interaction. Although interaction is an important component of visualization approaches, much of the visualization literature tends to pay more attention to the graphical representation than to interaction.The goal of this work is to strengthen the interaction side of visualization. Based on a brief review of general aspects of interaction, we develop an interaction-oriented view on visualization. This view comprises five key as

  9. Leadership, Literacy, and Translational Expertise in Genomics: Challenges and Opportunities for Social Work.

    Science.gov (United States)

    Werner-Lin, Allison; McCoyd, Judith L M; Doyle, Maya H; Gehlert, Sarah J

    2016-08-01

    The transdisciplinary field of genomics is revolutionizing conceptualizations of health, mental health, family formation, and public policy. Many professions must rapidly acquire genomic expertise to maintain state-of-the-art knowledge in their practice. Calls for social workers to build genomic capacity come regularly, yet social work education has not prepared practitioners to join the genomics workforce in providing socially just, ethically informed care to all clients, particularly those from vulnerable and marginalized groups. The authors suggest a set of action steps for bringing social work skills and practice into the 21st century. They propose that good genomic practice entails bringing social work values, skills, and behaviors to genomics. With education and training, social workers may facilitate socially just dissemination of genomic knowledge and services across practice domains. Increased genomic literacy will support the profession's mission to address disparities in health, health care access, and mortality. © 2016 National Association of Social Workers.

  10. KGCAK: a K-mer based database for genome-wide phylogeny and complexity evaluation.

    Science.gov (United States)

    Wang, Dapeng; Xu, Jiayue; Yu, Jun

    2015-09-16

    The K-mer approach, treating genomic sequences as simple characters and counting the relative abundance of each string upon a fixed K, has been extensively applied to phylogeny inference for genome assembly, annotation, and comparison. To meet increasing demands for comparing large genome sequences and to promote the use of the K-mer approach, we develop a versatile database, KGCAK ( http://kgcak.big.ac.cn/KGCAK/ ), containing ~8,000 genomes that include genome sequences of diverse life forms (viruses, prokaryotes, protists, animals, and plants) and cellular organelles of eukaryotic lineages. It builds phylogeny based on genomic elements in an alignment-free fashion and provides in-depth data processing enabling users to compare the complexity of genome sequences based on K-mer distribution. We hope that KGCAK becomes a powerful tool for exploring relationship within and among groups of species in a tree of life based on genomic data.

  11. The human noncoding genome defined by genetic diversity.

    Science.gov (United States)

    di Iulio, Julia; Bartha, Istvan; Wong, Emily H M; Yu, Hung-Chun; Lavrenko, Victor; Yang, Dongchan; Jung, Inkyung; Hicks, Michael A; Shah, Naisha; Kirkness, Ewen F; Fabani, Martin M; Biggs, William H; Ren, Bing; Venter, J Craig; Telenti, Amalio

    2018-03-01

    Understanding the significance of genetic variants in the noncoding genome is emerging as the next challenge in human genomics. We used the power of 11,257 whole-genome sequences and 16,384 heptamers (7-nt motifs) to build a map of sequence constraint for the human species. This build differed substantially from traditional maps of interspecies conservation and identified regulatory elements among the most constrained regions of the genome. Using new Hi-C experimental data, we describe a strong pattern of coordination over 2 Mb where the most constrained regulatory elements associate with the most essential genes. Constrained regions of the noncoding genome are up to 52-fold enriched for known pathogenic variants as compared to unconstrained regions (21-fold when compared to the genome average). This map of sequence constraint across thousands of individuals is an asset to help interpret noncoding elements in the human genome, prioritize variants and reconsider gene units at a larger scale.

  12. Visual memory and visual perception: when memory improves visual search.

    Science.gov (United States)

    Riou, Benoit; Lesourd, Mathieu; Brunel, Lionel; Versace, Rémy

    2011-08-01

    This study examined the relationship between memory and perception in order to identify the influence of a memory dimension in perceptual processing. Our aim was to determine whether the variation of typical size between items (i.e., the size in real life) affects visual search. In two experiments, the congruency between typical size difference and perceptual size difference was manipulated in a visual search task. We observed that congruency between the typical and perceptual size differences decreased reaction times in the visual search (Exp. 1), and noncongruency between these two differences increased reaction times in the visual search (Exp. 2). We argue that these results highlight that memory and perception share some resources and reveal the intervention of typical size difference on the computation of the perceptual size difference.

  13. Visual Artist or Visual Designer? Visual Communication Design Education

    OpenAIRE

    Arsoy, Aysu

    2010-01-01

    ABSTRACT: Design tools and contents have been digitalized, forming the contemporary fields of the visual arts and design. Corporate culture demands techno-social experts who understand the arts, design, culture and society, while also having a high level of technological proficiency. New departments have opened offering alternatives in art and design education such as Visual Communication Design (VCD) and are dedicated to educating students in the practical aspect of using digital technologi...

  14. Proactive building simulations for early design support

    DEFF Research Database (Denmark)

    Østergård, Torben

    important design parameters that require the most attention when seeking to improve building performance. Fast metamodels facilitate immediate feedback on design changes and reduce time-consumption related to performance assessment. Ultimately, the work described in this thesis and on buildingdesign...... that relies on thousands of simulations representing the multidimensional design space. Interactive visualizations enable decision-makers to explore, in real-time, the vast design space and identify favorable solutions which satisfy the needs of different stakeholders. Sensitivity analysis helps reveal...

  15. The Visual Dimension in Organizing, Organization, and Organization Research

    DEFF Research Database (Denmark)

    Meyer, Renate E.; Höllerer, Markus A.; Jancsary, Dennis

    2013-01-01

    and meaning construction. Building primarily on insights from the phenomenological tradition in organization theory and from social semiotics, this article sets out to consolidate previous scholarly efforts and to sketch a fertile future research agenda. After briefly exploring the workings of visuals, we...... approaches to feature visuals in research designs and to include the visual dimension in scholarly inquiry. Subsequently, we outline, in some detail, promising avenues for future research, and close with a reflection on the impact of visualization on scientific practice itself....

  16. Virtual View Image over Wireless Visual Sensor Network

    Directory of Open Access Journals (Sweden)

    Gamantyo Hendrantoro

    2011-12-01

    Full Text Available In general, visual sensors are applied to build virtual view images. When number of visual sensors increases then quantity and quality of the information improves. However, the view images generation is a challenging task in Wireless Visual Sensor Network environment due to energy restriction, computation complexity, and bandwidth limitation. Hence this paper presents a new method of virtual view images generation from selected cameras on Wireless Visual Sensor Network. The aim of the paper is to meet bandwidth and energy limitations without reducing information quality. The experiment results showed that this method could minimize number of transmitted imageries with sufficient information.

  17. Bioinformatics decoding the genome

    CERN Multimedia

    CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick

    2006-01-01

    Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

  18. Genomic research in Eucalyptus.

    Science.gov (United States)

    Poke, Fiona S; Vaillancourt, René E; Potts, Brad M; Reid, James B

    2005-09-01

    Eucalyptus L'Hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to Australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. With the sequencing of the genomes of Arabidopsis thaliana and Oryza sativa and the recent completion of the first tree genome sequence, Populus trichocarpa, attention has turned to the current status of genomic research in Eucalyptus. For several eucalypt species, large segregating families have been established, high-resolution genetic maps constructed and large EST databases generated. Collaborative efforts have been initiated for the integration of diverse genomic projects and will provide the framework for future research including exploiting the sequence of the entire eucalypt genome which is currently being sequenced. This review summarises the current position of genomic research in Eucalyptus and discusses the direction of future research.

  19. Courthouse Prototype Building

    Energy Technology Data Exchange (ETDEWEB)

    Malhotra, Mini [ORNL; New, Joshua Ryan [ORNL; Im, Piljae [ORNL

    2018-02-01

    As part of DOE's support of ANSI/ASHRAE/IES Standard 90.1 and IECC, researchers at Pacific Northwest National Laboratory (PNNL) apply a suite of prototype buildings covering 80% of the commercial building floor area in the U.S. for new construction. Efforts have started on expanding the prototype building suite to cover 90% of the commercial building floor area in the U.S., by developing prototype models for additional building types including place of worship, public order and safety, public assembly. Courthouse is courthouse is a sub-category under the “Public Order and Safety" building type category; other sub-categories include police station, fire station, and jail, reformatory or penitentiary.ORNL used building design guides, databases, and documented courthouse projects, supplemented by personal communication with courthouse facility planning and design experts, to systematically conduct research on the courthouse building and system characteristics. This report documents the research conducted for the courthouse building type and proposes building and system characteristics for developing a prototype building energy model to be included in the Commercial Building Prototype Model suite. According to the 2012 CBECS, courthouses occupy a total of 436 million sqft of floor space or 0.5% of the total floor space in all commercial buildings in the US, next to fast food (0.35%), grocery store or food market (0.88%), and restaurant or cafeteria (1.2%) building types currently included in the Commercial Prototype Building Model suite. Considering aggregated average, courthouse falls among the larger with a mean floor area of 69,400 sqft smaller fuel consumption intensity building types and an average of 94.7 kBtu/sqft compared to 77.8 kBtu/sqft for office and 80 kBtu/sqft for all commercial buildings.Courthouses range in size from 1000 sqft to over a million square foot building gross square feet and 1 courtroom to over 100 courtrooms. Small courthouses

  20. OpenBAN: An Open Building ANalytics Middleware for Smart Buildings

    Directory of Open Access Journals (Sweden)

    Pandarasamy Arjunan

    2016-03-01

    Full Text Available Towards the realization of smart building applications, buildings are increasingly instrumented with diverse sensors and actuators. These sensors generate large volumes of data which can be analyzed for optimizing building operations. Many building energy management tasks such as energy forecasting, disaggregation, among others require complex analytics leveraging collected sensor data. While several standalone and cloud-based systems for archiving, sharing and visualizing sensor data have emerged, their support for analyzing sensor data streams is primitive and limited to rule-based actions based on thresholds and simple aggregation functions. We develop OpenBAN, an open source sensor data analytics middleware for buildings, to make analytics an integral component of modern smart building applications. OpenBAN provides a framework of extensible sensor data processing elements for identifying various building context, which different applications can leverage. We validate the capabilities of OpenBAN by developing three representative real-world applications which are deployed in our test-bed buildings: (i household energy disaggregation, (ii detection of sprinkler usage from water meter data, and (iii electricity demand forecasting. We also provide a preliminary system performance of OpenBAN when deployed in the cloud and locally.

  1. Genome packaging in viruses

    OpenAIRE

    Sun, Siyang; Rao, Venigalla B.; Rossmann, Michael G.

    2010-01-01

    Genome packaging is a fundamental process in a viral life cycle. Many viruses assemble preformed capsids into which the genomic material is subsequently packaged. These viruses use a packaging motor protein that is driven by the hydrolysis of ATP to condense the nucleic acids into a confined space. How these motor proteins package viral genomes had been poorly understood until recently, when a few X-ray crystal structures and cryo-electron microscopy structures became available. Here we discu...

  2. Green Buildings and Health.

    Science.gov (United States)

    Allen, Joseph G; MacNaughton, Piers; Laurent, Jose Guillermo Cedeno; Flanigan, Skye S; Eitland, Erika Sita; Spengler, John D

    2015-09-01

    Green building design is becoming broadly adopted, with one green building standard reporting over 3.5 billion square feet certified to date. By definition, green buildings focus on minimizing impacts to the environment through reductions in energy usage, water usage, and minimizing environmental disturbances from the building site. Also by definition, but perhaps less widely recognized, green buildings aim to improve human health through design of healthy indoor environments. The benefits related to reduced energy and water consumption are well-documented, but the potential human health benefits of green buildings are only recently being investigated. The objective of our review was to examine the state of evidence on green building design as it specifically relates to indoor environmental quality and human health. Overall, the initial scientific evidence indicates better indoor environmental quality in green buildings versus non-green buildings, with direct benefits to human health for occupants of those buildings. A limitation of much of the research to date is the reliance on indirect, lagging and subjective measures of health. To address this, we propose a framework for identifying direct, objective and leading "Health Performance Indicators" for use in future studies of buildings and health.

  3. The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes

    KAUST Repository

    Bracken-Grissom, Heather

    2013-12-12

    Over 95% of all metazoan (animal) species comprise the invertebrates, but very few genomes from these organisms have been sequenced. We have, therefore, formed a Global Invertebrate Genomics Alliance (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site () has been launched to facilitate this collaborative venture.

  4. Commercial Buildings Characteristics, 1992

    Energy Technology Data Exchange (ETDEWEB)

    1994-04-29

    Commercial Buildings Characteristics 1992 presents statistics about the number, type, and size of commercial buildings in the United States as well as their energy-related characteristics. These data are collected in the Commercial Buildings Energy Consumption Survey (CBECS), a national survey of buildings in the commercial sector. The 1992 CBECS is the fifth in a series conducted since 1979 by the Energy Information Administration. Approximately 6,600 commercial buildings were surveyed, representing the characteristics and energy consumption of 4.8 million commercial buildings and 67.9 billion square feet of commercial floorspace nationwide. Overall, the amount of commercial floorspace in the United States increased an average of 2.4 percent annually between 1989 and 1992, while the number of commercial buildings increased an average of 2.0 percent annually.

  5. Between Two Fern Genomes

    Science.gov (United States)

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

  6. Causes of genome instability

    DEFF Research Database (Denmark)

    Langie, Sabine A S; Koppen, Gudrun; Desaulniers, Daniel

    2015-01-01

    function, chromosome segregation, telomere length). The purpose of this review is to describe the crucial aspects of genome instability, to outline the ways in which environmental chemicals can affect this cancer hallmark and to identify candidate chemicals for further study. The overall aim is to make......Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome's integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus...

  7. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  8. Visual acuity test

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/003396.htm Visual acuity test To use the sharing features on this page, please enable JavaScript. The visual acuity test is used to determine the smallest ...

  9. The Visual System

    Medline Plus

    Full Text Available ... to blinding eye diseases, visual disorders, mechanisms of visual function, preservation of sight, and the special health problems and requirements of the blind.” ... Clinical Studies Publications Catalog Photos ...

  10. Topological Methods for Visualization

    Energy Technology Data Exchange (ETDEWEB)

    Berres, Anne Sabine [Los Alamos National Lab. (LANL), Los Alamos, NM (United Stat

    2016-04-07

    This slide presentation describes basic topological concepts, including topological spaces, homeomorphisms, homotopy, betti numbers. Scalar field topology explores finding topological features and scalar field visualization, and vector field topology explores finding topological features and vector field visualization.

  11. The Visual System

    Medline Plus

    Full Text Available ... National Eye Institute’s mission is to “conduct and support research, training, health information dissemination, and other programs with respect to blinding eye diseases, visual disorders, mechanisms of visual function, preservation of sight, ...

  12. The Visual System

    Medline Plus

    Full Text Available ... NIH), the National Eye Institute’s mission is to “conduct and support research, training, health information dissemination, and other programs with respect to blinding eye diseases, visual disorders, mechanisms of visual function, preservation of ...

  13. Visualization of Social Networks

    NARCIS (Netherlands)

    Boertjes, E.M.; Kotterink, B.; Jager, E.J.

    2011-01-01

    Current visualizations of social networks are mostly some form of node-link diagram. Depending on the type of social network, this can be some treevisualization with a strict hierarchical structure or a more generic network visualization.

  14. Visual Control of Locomotion

    National Research Council Canada - National Science Library

    Loomis, Jack M; Beall, Andrew C

    2005-01-01

    The accomplishments were threefold. First, a software tool for rendering virtual environments was developed, a tool useful for other researchers interested in visual perception and visual control of action...

  15. MIPS plant genome information resources.

    Science.gov (United States)

    Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

    2007-01-01

    The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

  16. Introgression Browser: High throughput whole-genome SNP visualization

    NARCIS (Netherlands)

    Aflitos, S.A.; Sanchez Perez, G.F.; Ridder, de D.; Fransz, P.; Schranz, M.E.; Jong, de J.H.S.G.M.; Peters, S.A.

    2015-01-01

    Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not

  17. Introgression browser: high-throughput whole-genome SNP visualization

    NARCIS (Netherlands)

    Alves Aflitos, S.; Sanchez-Perez, G.; de Ridder, D.; Fransz, P.; Schranz, M.E.; de Jong, H.; Peters, S.A.

    2015-01-01

    Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not

  18. Faustoviruses: Comparative genomics of new Megavirales family members

    Directory of Open Access Journals (Sweden)

    Samia eBenamar

    2016-02-01

    Full Text Available An emerging interest for the giant virus discovery process, genome sequencing and analysis has allowed an expansion of the number of known Megavirales members. Using the protist Vermamoeba sp. as cell support, a new giant virus named Faustovirus has been isolated. In this study, we describe the genome sequences of nine Faustoviruses and build a genomic comparison in order to have a comprehensive overview of genomic composition and diversity among this new virus family. The average sequence length of these viruses is 467,592.44 bp (ranging from 455,803 bp to 491,024 bp, making them the fourth largest Megavirales genome after Mimiviruses, Pandoraviruses and Pithovirus sibericum. Faustovirus genomes displayed an average G+C content of 37.14 % (ranging from 36.22% to 39.59% which is close to the G+C content range of the Asfarviridae genomes (38%. The proportion of best matches and the phylogenetic analysis suggest a shared origin with Asfarviridae without belonging to the same family. The core-gene-based phylogeny of Faustoviruses study has identified four lineages. These results were confirmed by the analysis of amino acids and COGs category distribution. The diversity of the gene composition of these lineages is mainly explained by gene deletion or acquisition and some exceptions for gene duplications. The high proportion of best matches from Bacteria and Phycodnaviridae on the pan-genome and unique genes may be explained by an interaction occurring after the separation of the lineages. The Faustovirus core-genome appears to consolidate the surrounding of 207 genes whereas the pan-genome is described as an open pan-genome, its enrichment via the discovery of new Faustoviruses is required to better seize all the genomic diversity of this family.

  19. Smart buildings: Energy efficient conditioning of building occupants

    NARCIS (Netherlands)

    Zeiler, W.; Houten, van M.A.; Boxem, G.; Vehler, R.; Verhoeven, M.; Fremouw, M.

    2009-01-01

    To further optimize energy performance of buildings, intelligent building control offers new possibilities. Intelligent Software Agents (ISA) can be implemented at different levels of building automation. Individual agents for individual climate control for each user of the building in combination

  20. Visual explorer facilitator's guide

    CERN Document Server

    Palus, Charles J

    2010-01-01

    Grounded in research and practice, the Visual Explorer™ Facilitator's Guide provides a method for supporting collaborative, creative conversations about complex issues through the power of images. The guide is available as a component in the Visual Explorer Facilitator's Letter-sized Set, Visual Explorer Facilitator's Post card-sized Set, Visual Explorer Playing Card-sized Set, and is also available as a stand-alone title for purchase to assist multiple tool users in an organization.

  1. Creativity, visualization abilities, and visual cognitive style.

    Science.gov (United States)

    Kozhevnikov, Maria; Kozhevnikov, Michael; Yu, Chen Jiao; Blazhenkova, Olesya

    2013-06-01

    Despite the recent evidence for a multi-component nature of both visual imagery and creativity, there have been no systematic studies on how the different dimensions of creativity and imagery might interrelate. The main goal of this study was to investigate the relationship between different dimensions of creativity (artistic and scientific) and dimensions of visualization abilities and styles (object and spatial). In addition, we compared the contributions of object and spatial visualization abilities versus corresponding styles to scientific and artistic dimensions of creativity. Twenty-four undergraduate students (12 females) were recruited for the first study, and 75 additional participants (36 females) were recruited for an additional experiment. Participants were administered a number of object and spatial visualization abilities and style assessments as well as a number of artistic and scientific creativity tests. The results show that object visualization relates to artistic creativity and spatial visualization relates to scientific creativity, while both are distinct from verbal creativity. Furthermore, our findings demonstrate that style predicts corresponding dimension of creativity even after removing shared variance between style and visualization ability. The results suggest that styles might be a more ecologically valid construct in predicting real-life creative behaviour, such as performance in different professional domains. © 2013 The British Psychological Society.

  2. Visual attention and stability

    NARCIS (Netherlands)

    Mathot, Sebastiaan; Theeuwes, Jan

    2011-01-01

    In the present review, we address the relationship between attention and visual stability. Even though with each eye, head and body movement the retinal image changes dramatically, we perceive the world as stable and are able to perform visually guided actions. However, visual stability is not as

  3. Visualizing Matrix Multiplication

    Science.gov (United States)

    Daugulis, Peteris; Sondore, Anita

    2018-01-01

    Efficient visualizations of computational algorithms are important tools for students, educators, and researchers. In this article, we point out an innovative visualization technique for matrix multiplication. This method differs from the standard, formal approach by using block matrices to make computations more visual. We find this method a…

  4. Big Data Visualization Tools

    OpenAIRE

    Bikakis, Nikos

    2018-01-01

    Data visualization is the presentation of data in a pictorial or graphical format, and a data visualization tool is the software that generates this presentation. Data visualization provides users with intuitive means to interactively explore and analyze data, enabling them to effectively identify interesting patterns, infer correlations and causalities, and supports sense-making activities.

  5. Genotype call for chromosomal deletions using read-depth from whole genome sequence variants in cattle

    DEFF Research Database (Denmark)

    Mesbah-Uddin, Md; Guldbrandtsen, Bernt; Lund, Mogens Sandø

    2018-01-01

    We presented a deletion genotyping (copy-number estimation) method that leverages population-scale whole genome sequence variants data from 1K bull genomes project (1KBGP) to build reference panel for imputation. To estimate deletion-genotype likelihood, we extracted read-depth (RD) data of all...

  6. An integrated map of genetic variation from 1.092 human genomes

    DEFF Research Database (Denmark)

    Abecasis, Goncalo R.; Auton, Adam; Brooks, Lisa D.

    2012-01-01

    By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination ...

  7. Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system

    NARCIS (Netherlands)

    Speth, D.R.; Zandt, M.H. in 't; Guerrero Cruz, S.; Dutilh, B.E.; Jetten, M.S.M.

    2016-01-01

    Partial-nitritation anammox (PNA) is a novel wastewater treatment procedure for energy-efficient ammonium removal. Here we use genome-resolved metagenomics to build a genome-based ecological model of the microbial community in a full-scale PNA reactor. Sludge from the bioreactor examined here is

  8. Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project

    OpenAIRE

    Dunlap, Jay C.; Borkovich, Katherine A.; Henn, Matthew R.; Turner, Gloria E.; Sachs, Matthew S.; Glass, N. Louise; McCluskey, Kevin; Plamann, Michael; Galagan, James E.; Birren, Bruce W.; Weiss, Richard L.; Townsend, Jeffrey P.; Loros, Jennifer J.; Nelson, Mary Anne; Lambreghts, Randy

    2007-01-01

    A consortium of investigators is engaged in a functional genomics project centered on the filamentous fungus Neurospora, with an eye to opening up the functional genomic analysis of all the filamentous fungi. The overall goal of the four interdependent projects in this effort is to acccomplish functional genomics, annotation, and expression analyses of Neurospora crassa, a filamentous fungus that is an established model for the assemblage of over 250,000 species of nonyeast fungi. Building fr...

  9. Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium

    DEFF Research Database (Denmark)

    Freschi, Luca; Jeukens, Julie; Kukavica-Ibrulj, Irena

    2015-01-01

    The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of Pseudomonas genome evolution, antibiotic resistance and virulence genes. Metadata, including genomic and phenotypic data for each isolate of the collection, are a...... implicated in human and animal infections, understand how patients become infected and how the infection evolves over time as well as identify prognostic markers for better evidence-based decisions on patient care....

  10. De novo assembly of human genomes with massively parallel short read sequencing

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Zhu, Hongmei; Ruan, Jue

    2010-01-01

    genomes from short read sequences. We successfully assembled both the Asian and African human genome sequences, achieving an N50 contig size of 7.4 and 5.9 kilobases (kb) and scaffold of 446.3 and 61.9 kb, respectively. The development of this de novo short read assembly method creates new opportunities...... for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way....

  11. Modelling the probability of building fires

    Directory of Open Access Journals (Sweden)

    Vojtěch Barták

    2014-12-01

    Full Text Available Systematic spatial risk analysis plays a crucial role in preventing emergencies.In the Czech Republic, risk mapping is currently based on the risk accumulationprinciple, area vulnerability, and preparedness levels of Integrated Rescue Systemcomponents. Expert estimates are used to determine risk levels for individualhazard types, while statistical modelling based on data from actual incidents andtheir possible causes is not used. Our model study, conducted in cooperation withthe Fire Rescue Service of the Czech Republic as a model within the Liberec andHradec Králové regions, presents an analytical procedure leading to the creation ofbuilding fire probability maps based on recent incidents in the studied areas andon building parameters. In order to estimate the probability of building fires, aprediction model based on logistic regression was used. Probability of fire calculatedby means of model parameters and attributes of specific buildings can subsequentlybe visualized in probability maps.

  12. Residential and commercial buildings

    Energy Technology Data Exchange (ETDEWEB)

    Svendsen, Svend; Furbo, S.

    2012-11-15

    Low-energy buildings can make a major contribution to general sustainable development by providing a solution to problems related to the use of fossil fuels. The EPBD (EU Directive on Energy Performance of Buildings) requirements that by 2020 new building shall be constructed to use nearly zero energy, and no fossil fuels, can be accomplished by combining low-energy buildings with renewable energy via low-temperature district heating in cities and suburbs, and via heat pumps for low-density settlements. Based on experience with passive houses, low-energy buildings meeting the energy performance requirements of 2020 are expected to cost only a few percent more than conventional buildings. The very large and rapid changes needed in the energy performance of buildings is a challenge for the building sector, but one that can be overcome by better methods of developing products and designing, constructing and operating buildings. Simulation-based analysis and optimisation, and considerations of durability, will be important here. Building may thus be transformed from an experience-based sector to one based on knowledge and research, with high-quality sustainable products and good business opportunities. (Author)

  13. Integration and Visualization of Epigenome and Mobilome Data in Crops

    OpenAIRE

    Robakowska Hyzorek, Dagmara; Mirouze, Marie; Larmande, Pierre

    2016-01-01

    International audience; In the coming years, the study of the interaction between the epigenome and the mobilome is likely to give insights on the role of TEs on genome stability and evolution. In the present project we have created tools to collect epigenetic datasets from different laboratories and databases and translate them to a standard format to be integrated, analyzed and finally visualized.

  14. Hierarchical Sets: Analyzing Pangenome Structure through Scalable Set Visualizations

    DEFF Research Database (Denmark)

    Pedersen, Thomas Lin

    2017-01-01

    of hierarchical sets by applying it to a pangenome based on 113 Escherichia and Shigella genomes and find it provides a powerful addition to pangenome analysis. The described clustering algorithm and visualizations are implemented in the hierarchicalSets R package available from CRAN (https...

  15. Green Building Tools for Tribes

    Science.gov (United States)

    Tribal green building tools and funding information to support tribal building code adoption, healthy building, siting, energy efficiency, renewable energy, water conservation, green building materials, recycling and adaptation and resilience.

  16. Recent updates and developments to plant genome size databases

    Science.gov (United States)

    Garcia, Sònia; Leitch, Ilia J.; Anadon-Rosell, Alba; Canela, Miguel Á.; Gálvez, Francisco; Garnatje, Teresa; Gras, Airy; Hidalgo, Oriane; Johnston, Emmeline; Mas de Xaxars, Gemma; Pellicer, Jaume; Siljak-Yakovlev, Sonja; Vallès, Joan; Vitales, Daniel; Bennett, Michael D.

    2014-01-01

    Two plant genome size databases have been recently updated and/or extended: the Plant DNA C-values database (http://data.kew.org/cvalues), and GSAD, the Genome Size in Asteraceae database (http://www.asteraceaegenomesize.com). While the first provides information on nuclear DNA contents across land plants and some algal groups, the second is focused on one of the largest and most economically important angiosperm families, Asteraceae. Genome size data have numerous applications: they can be used in comparative studies on genome evolution, or as a tool to appraise the cost of whole-genome sequencing programs. The growing interest in genome size and increasing rate of data accumulation has necessitated the continued update of these databases. Currently, the Plant DNA C-values database (Release 6.0, Dec. 2012) contains data for 8510 species, while GSAD has 1219 species (Release 2.0, June 2013), representing increases of 17 and 51%, respectively, in the number of species with genome size data, compared with previous releases. Here we provide overviews of the most recent releases of each database, and outline new features of GSAD. The latter include (i) a tool to visually compare genome size data between species, (ii) the option to export data and (iii) a webpage containing information about flow cytometry protocols. PMID:24288377

  17. Python data visualization cookbook

    CERN Document Server

    Milovanovic, Igor

    2013-01-01

    This book is written in a Cookbook style targeted towards an advanced audience. It covers the advanced topics of data visualization in Python.Python Data Visualization Cookbook is for developers that already know about Python programming in general. If you have heard about data visualization but you don't know where to start, then this book will guide you from the start and help you understand data, data formats, data visualization, and how to use Python to visualize data.You will need to know some general programming concepts, and any kind of programming experience will be helpful, but the co

  18. Visualization system on ITBL

    International Nuclear Information System (INIS)

    Suzuki, Yoshio

    2004-01-01

    Visualization systems PATRAS/ITBL and AVS/ITBL, which are based on visualization software PATRAS and AVS/Express respectively, have been developed on a global, heterogeneous computing environment, Information Technology Based Laboratory (ITBL). PATRAS/ITBL allows for real-time visualization of the numerical results acquired from coupled multi-physics numerical simulations, executed on different hosts situated in remote locations. AVS/ITBL allow for post processing visualization. The scientific data located in remote sites may be selected and visualized on a web browser installed in a user terminal. The global structure and main functions of these systems are presented. (author)

  19. Investigating the presence of hazardous materials in buildings

    International Nuclear Information System (INIS)

    Gustitus, D.A.; Blaisdell, P.M.

    1996-01-01

    Environmental hazards in buildings can be found in the air, on exposed surfaces, or hidden in roofs, walls, and systems. They can exist in buildings in solid, liquid, and gaseous states. A sound methodology for investigating the presence of environmental hazards in buildings should include several components. The first step in planning an investigation of environmental hazards in buildings is to ascertain why the investigation is to be performed. Research should be performed to review available documentation on the building. Next, a visual inspection of the building should be performed to identify and document existing conditions, and all suspect materials containing environmental hazards. Lastly, samples of suspect materials should be collected for testing. It is important to sample appropriate materials, based on the information obtained during the previous steps of the investigation. It is also important to collect the samples using standard procedures. Pollutants of concern include asbestos, lead, PCBs, and radon

  20. Visual Semiotics & Uncertainty Visualization: An Empirical Study.

    Science.gov (United States)

    MacEachren, A M; Roth, R E; O'Brien, J; Li, B; Swingley, D; Gahegan, M

    2012-12-01

    This paper presents two linked empirical studies focused on uncertainty visualization. The experiments are framed from two conceptual perspectives. First, a typology of uncertainty is used to delineate kinds of uncertainty matched with space, time, and attribute components of data. Second, concepts from visual semiotics are applied to characterize the kind of visual signification that is appropriate for representing those different categories of uncertainty. This framework guided the two experiments reported here. The first addresses representation intuitiveness, considering both visual variables and iconicity of representation. The second addresses relative performance of the most intuitive abstract and iconic representations of uncertainty on a map reading task. Combined results suggest initial guidelines for representing uncertainty and discussion focuses on practical applicability of results.