computer graphics

Summary

Summary: The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.

Top Publications

  1. ncbi Java Treeview--extensible visualization of microarray data
    Alok J Saldanha
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 20:3246-8. 2004
  2. pmc Vienna RNA secondary structure server
    Ivo L Hofacker
    Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universitat Wien, Wahringerstrasse 17, A 1090 Wien, Austria
    Nucleic Acids Res 31:3429-31. 2003
  3. ncbi ACT: the Artemis Comparison Tool
    Tim J Carver
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Bioinformatics 21:3422-3. 2005
  4. pmc NCBI GEO: archive for high-throughput functional genomic data
    Tanya Barrett
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA
    Nucleic Acids Res 37:D885-90. 2009
  5. pmc BioGRID: a general repository for interaction datasets
    Chris Stark
    Ontario Cancer Institute, Princess Margaret Hospital, 610 University Avenue, Toronto, Ontario, Canada M5G 2M9
    Nucleic Acids Res 34:D535-9. 2006
  6. pmc An automated method for finding molecular complexes in large protein interaction networks
    Gary D Bader
    Samuel Lunenfeld Research Institute, MT, Sinai Hospital, Toronto ON Canada M5G 1X5, Dept, of Biochemistry, University of Toronto, Toronto ON Canada M5S 1A8
    BMC Bioinformatics 4:2. 2003
  7. pmc Dendroscope: An interactive viewer for large phylogenetic trees
    Daniel H Huson
    Center for Bioinformatics Tübingen ZBIT, Eberhard Karls Universitat Tubingen, Sand 14, 72076 Tubingen, Germany
    BMC Bioinformatics 8:460. 2007
  8. ncbi COPASI--a COmplex PAthway SImulator
    Stefan Hoops
    Virginia Bioinformatics Institute, Virginia Tech, Washington St 0477, Blacksburg, VA 24061, USA
    Bioinformatics 22:3067-74. 2006
  9. pmc The Bioperl toolkit: Perl modules for the life sciences
    Jason E Stajich
    University Program in Genetics, Duke University, Durham, North Carolina 27710, USA
    Genome Res 12:1611-8. 2002
  10. ncbi Circular genome visualization and exploration using CGView
    Paul Stothard
    Department of Biological Sciences and Computing Science, University of Alberta Edmonton, Alberta, Canada T6G 2E8
    Bioinformatics 21:537-9. 2005

Research Grants

  1. Novel Topoisomerase I Inhibitors
    MARK S CUSHMAN; Fiscal Year: 2013
  2. A Texture Analysis/Synthesis Model of Visual Crowding
    Ruth Rosenholtz; Fiscal Year: 2010
  3. PURINE METABOLISM IN TRICHOMONAS AND GIARDIA
    C Wang; Fiscal Year: 2000
  4. Virtual Reality Relapse Prevention: Alcohol Dependence
    PATRICK SHANNON BORDNICK; Fiscal Year: 2010
  5. 3D Digital Breast Phantoms For Multimodality Research
    William P Segars; Fiscal Year: 2013
  6. DESIGN AND TESTING OF DOCKING ALGORITHMS
    Brian K Shoichet; Fiscal Year: 2011
  7. CLINICAL BIOMECHANICS OF CERVICAL SPINE
    Manohar Panjabi; Fiscal Year: 1990
  8. CRYSTALLOGRAPHIC STUDIES OF HEMERYTHRIN
    RON STENKAMP; Fiscal Year: 1990
  9. IONOPHORES, TRANSPORT AND MEMBRANE STRUCTURE
    William Duax; Fiscal Year: 1980
  10. IMMUNOGLOBULINS IN MULTIPLE MYELOMA & AMYLOIDOSIS
    Allen Edmundson; Fiscal Year: 1993

Detail Information

Publications333 found, 100 shown here

  1. ncbi Java Treeview--extensible visualization of microarray data
    Alok J Saldanha
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 20:3246-8. 2004
    ..An applet version is also available that can be used on any website with no special server-side setup...
  2. pmc Vienna RNA secondary structure server
    Ivo L Hofacker
    Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universitat Wien, Wahringerstrasse 17, A 1090 Wien, Austria
    Nucleic Acids Res 31:3429-31. 2003
    ..All three services can be accessed via the Vienna RNA web server at http://rna.tbi.univie.ac.at/...
  3. ncbi ACT: the Artemis Comparison Tool
    Tim J Carver
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Bioinformatics 21:3422-3. 2005
    ..ACT is part of the Artemis distribution and is similarly open source, written in Java and can run on any Java enabled platform, including UNIX, Macintosh and Windows...
  4. pmc NCBI GEO: archive for high-throughput functional genomic data
    Tanya Barrett
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA
    Nucleic Acids Res 37:D885-90. 2009
    ..This article summarizes the GEO repository structure, content and operating procedures, as well as recently introduced data mining features. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/...
  5. pmc BioGRID: a general repository for interaction datasets
    Chris Stark
    Ontario Cancer Institute, Princess Margaret Hospital, 610 University Avenue, Toronto, Ontario, Canada M5G 2M9
    Nucleic Acids Res 34:D535-9. 2006
    ..User-customized graphs with embedded protein, gene and interaction attributes can be constructed with a visualization system called Osprey that is dynamically linked to the BioGRID...
  6. pmc An automated method for finding molecular complexes in large protein interaction networks
    Gary D Bader
    Samuel Lunenfeld Research Institute, MT, Sinai Hospital, Toronto ON Canada M5G 1X5, Dept, of Biochemistry, University of Toronto, Toronto ON Canada M5S 1A8
    BMC Bioinformatics 4:2. 2003
    ..As the size of the interaction set increases, databases and computational methods will be required to store, visualize and analyze the information in order to effectively aid in knowledge discovery...
  7. pmc Dendroscope: An interactive viewer for large phylogenetic trees
    Daniel H Huson
    Center for Bioinformatics Tübingen ZBIT, Eberhard Karls Universitat Tubingen, Sand 14, 72076 Tubingen, Germany
    BMC Bioinformatics 8:460. 2007
    ..Moreover, many programs are difficult to install or are not available for all common operating systems...
  8. ncbi COPASI--a COmplex PAthway SImulator
    Stefan Hoops
    Virginia Bioinformatics Institute, Virginia Tech, Washington St 0477, Blacksburg, VA 24061, USA
    Bioinformatics 22:3067-74. 2006
    ..Therefore, there is a big need for software tools that allow access to diverse simulation and modeling methods as well as support for the usage of these methods...
  9. pmc The Bioperl toolkit: Perl modules for the life sciences
    Jason E Stajich
    University Program in Genetics, Duke University, Durham, North Carolina 27710, USA
    Genome Res 12:1611-8. 2002
    ..We conclude with a discussion of how the open-source nature of the project has contributed to the development effort...
  10. ncbi Circular genome visualization and exploration using CGView
    Paul Stothard
    Department of Biological Sciences and Computing Science, University of Alberta Edmonton, Alberta, Canada T6G 2E8
    Bioinformatics 21:537-9. 2005
    ..AVAILABILITY: CGView (the standalone application, library or applet), sample input, sample maps and documentation can be obtained from http://wishart.biology.ualberta.ca/cgview/ CONTACT: david.wishart@ualberta.ca...
  11. pmc VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology
    Zhenjun Hu
    Center for Advanced Genomic Technology, Program in Bioinformatics, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 37:W115-21. 2009
    ..Both algorithms take account of network topology (i.e. correlations between genes based on various sources of evidence). VisANT is freely available at http://visant.bu.edu...
  12. pmc STRING: a database of predicted functional associations between proteins
    Christian von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 31:258-61. 2003
    ..The database predicts functional interactions at an expected level of accuracy of at least 80% for more than half of the genes; it is online at http://www.bork.embl-heidelberg.de/STRING/...
  13. ncbi BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
    Steven Maere
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology VIB, Ghent University, Technologiepark 927, B 9052, Ghent, Belgium
    Bioinformatics 21:3448-9. 2005
    ....
  14. ncbi affylmGUI: a graphical user interface for linear modeling of single channel microarray data
    James M Wettenhall
    Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville 3050, Australia
    Bioinformatics 22:897-9. 2006
    ..Output of the analysis (tables and figures) can be exported to an HTML report. The GUI provides user-friendly access to state-of-the-art methods embodied in the Bioconductor software repository...
  15. pmc DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
    Ioannis Xenarios
    UCLA DOE Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, PO Box 951570, UCLA, Los Angeles, CA 90095 1570, USA
    Nucleic Acids Res 30:303-5. 2002
    ..Tools have been developed that allow users to analyze, visualize and integrate their own experimental data with the information about protein-protein interactions available in the DIP database...
  16. pmc Tools for the automatic identification and classification of RNA base pairs
    Huanwang Yang
    Department of Chemistry and Chemical Biology, Rutgers University, NJ 08854 8087, USA
    Nucleic Acids Res 31:3450-60. 2003
    ..rutgers.edu/services/. The application RNAMLview can also be downloaded from this site. The 2D diagrams produced by RNAview are available for RNA structures in the Nucleic Acid Database (NDB) at http://ndbserver.rutgers.edu/atlas/...
  17. ncbi Graph-based analysis and visualization of experimental results with ONDEX
    Jacob Köhler
    Division of Biomathematics and Bioinformatics, Rothamsted Research, AL5 2JQ Harpenden, UK
    Bioinformatics 22:1383-90. 2006
    ..Software tools are needed to automate this task which at present is labor-intensive and requires considerable informatics and biological expertise...
  18. pmc The CGView Server: a comparative genomics tool for circular genomes
    Jason R Grant
    Department of Agricultural, Food and Nutritional Science, University of Alberta, Canada
    Nucleic Acids Res 36:W181-4. 2008
    ..The CGView Server can be accessed at http://stothard.afns.ualberta.ca/cgview_server/..
  19. pmc VANTED v2: a framework for systems biology applications
    Hendrik Rohn
    Leibniz Institute of Plant Genetics and Crop Plant Research IPK, Corrensstr 3, 06466 Gatersleben, Germany
    BMC Syst Biol 6:139. 2012
    ..Networks provide a basis for the integration, analysis and visualization of multi-omics experimental datasets...
  20. pmc KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats
    Clemens Wrzodek
    Center for Bioinformatics Tuebingen, University of Tuebingen, 72076 Tubingen, Germany
    Bioinformatics 27:2314-5. 2011
    ..g. MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those...
  21. pmc PDBsum: summaries and analyses of PDB structures
    R A Laskowski
    Department of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
    Nucleic Acids Res 29:221-2. 2001
    ..Numerous links take the user to related sites. PDBsum is updated whenever any new structures are released by the PDB and is freely accessible via http://www.biochem.ucl.ac.uk/bsm/pdbsum...
  22. pmc Presenting and exploring biological pathways with PathVisio
    Martijn P van Iersel
    Department of Bioinformatics, BiGCaT Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, The Netherlands
    BMC Bioinformatics 9:399. 2008
    ..The GenMAPP MAPP file format is replaced by GPML, a new XML file format that provides seamless exchange of graphical pathway information among multiple programs...
  23. pmc HMM Logos for visualization of protein families
    Benjamin Schuster-Böckler
    Department of Mathematics and Computer Science, Freie Universitat Berlin, Germany
    BMC Bioinformatics 5:7. 2004
    ..Profile Hidden Markov Models (pHMMs) are a widely used tool for protein family research. Up to now, however, there exists no method to visualize all of their central aspects graphically in an intuitively understandable way...
  24. ncbi limmaGUI: a graphical user interface for linear modeling of microarray data
    James M Wettenhall
    Division of Genetics and Bioinformatics, Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville, 3050, Australia
    Bioinformatics 20:3705-6. 2004
    ..limmaGUI is available for most platforms on the which R runs including Windows, Mac and most flavors of Unix...
  25. pmc SuperPose: a simple server for sophisticated structural superposition
    Rajarshi Maiti
    Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada
    Nucleic Acids Res 32:W590-4. 2004
    ..The SuperPose web server is freely accessible at http://wishart.biology.ualberta.ca/SuperPose/...
  26. ncbi OPM: orientations of proteins in membranes database
    Mikhail A Lomize
    College of Literature, Science and the Arts, University of Michigan, Ann Arbor, MI 48109 1065, USA
    Bioinformatics 22:623-5. 2006
    ..All coordinate files with the calculated membrane boundaries are available for downloading...
  27. pmc jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web
    Samuel A Smits
    Department of Biological Sciences, San Jose State University, San Jose, California, United States of America
    PLoS ONE 5:e12267. 2010
    ..We propose a novel approach for publishing interactive phylogenetic trees...
  28. pmc KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor
    Jitao David Zhang
    Division of Molecular Genome Analysis, German Cancer Research Center DKFZ, INF 580, Heidelberg, Germany
    Bioinformatics 25:1470-1. 2009
    ..While valuable graph tools have been implemented in R/Bioconductor, to our knowledge there is currently no software package to parse and analyze KEGG pathways with graph theory...
  29. pmc 3did Update: domain-domain and peptide-mediated interactions of known 3D structure
    Amelie Stein
    Institute for Research in Biomedicine, Barcelona Supercomputing Center, c Baldiri Reixac 10 12, 08028 Barcelona, Spain
    Nucleic Acids Res 37:D300-4. 2009
    ..A web-based tool to query 3did is available at http://3did.irbbarcelona.org...
  30. pmc The UCSC Genome Browser Database: update 2006
    A S Hinrichs
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz UCSC, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 34:D590-8. 2006
    ..These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/...
  31. ncbi Ultra-fast FFT protein docking on graphics processors
    David W Ritchie
    INRIA Nancy Grand Est, LORIA, 615 rue du Jardin Botanique, 54506 Vandoeuvre les Nancy, France
    Bioinformatics 26:2398-405. 2010
    ..Developing very fast protein docking tools will be useful for studying large-scale PPI networks, and could contribute to the rational design of new drugs...
  32. pmc GoMiner: a resource for biological interpretation of genomic and proteomic data
    Barry R Zeeberg
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Biol 4:R28. 2003
    ..The first is a tree-like structure analogous to that in the AmiGO browser and the second is a compact, dynamically interactive 'directed acyclic graph'. Genes displayed in GoMiner are linked to major public bioinformatics resources...
  33. ncbi GSEA-P: a desktop application for Gene Set Enrichment Analysis
    Aravind Subramanian
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Bioinformatics 23:3251-3. 2007
    ..AVAILABILITY: GSEA-P 2.0 is freely available for academic and commercial users and can be downloaded from http://www.broad.mit.edu/GSEA..
  34. ncbi Visualizing genomes: techniques and challenges
    Cydney B Nielsen
    British Columbia Cancer Agency, Genome Sciences Centre, Vancouver, Canada
    Nat Methods 7:S5-S15. 2010
    ....
  35. pmc Editing, validating and translating of SBGN maps
    Tobias Czauderna
    Leibniz Institute of Plant Genetics and Crop Plant Research IPK Gatersleben, Martin Luther University of Halle Wittenberg, Halle, Germany
    Bioinformatics 26:2340-1. 2010
    ..However, to increase the use of SBGN, tools for editing, validating and translating SBGN maps are desirable...
  36. pmc Evaluation of clustering algorithms for protein-protein interaction networks
    Sylvain Brohée
    Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Universite Libre de Bruxelles, CP 263, Campus Plaine, Bd, du Triomphe, B 1050 Bruxelles, Belgium
    BMC Bioinformatics 7:488. 2006
    ..In this paper we present a comparative assessment of four algorithms: Markov Clustering (MCL), Restricted Neighborhood Search Clustering (RNSC), Super Paramagnetic Clustering (SPC), and Molecular Complex Detection (MCODE)...
  37. pmc WebGestalt: an integrated system for exploring gene sets in various biological contexts
    Bing Zhang
    Graduate School in Genome Science and Technology, University of Tennessee Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Nucleic Acids Res 33:W741-8. 2005
    ..Exploration of all the 48 gene sets using WebGestalt is available for the public at http://genereg.ornl.gov/webgestalt/wg_enrich.php...
  38. ncbi Cytoscape: a community-based framework for network modeling
    Sarah Killcoyne
    Institute for Systems Biology, Seattle, WA, USA
    Methods Mol Biol 563:219-39. 2009
    ..It also describes the development of a plugin used to investigate a particular research question in systems biology and walks through an example analysis using Cytoscape...
  39. pmc TreeDyn: towards dynamic graphics and annotations for analyses of trees
    François Chevenet
    Laboratoire de Génétique et Evolution des Maladies Infectieuses, UMR CNRS IRD 2724, IRD, 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
    BMC Bioinformatics 7:439. 2006
    ..Consequently, a tedious manual analysis and post-processing of the tree graphics are required if one needs to use external information for displaying or investigating trees...
  40. pmc The generic genome browser: a building block for a model organism system database
    Lincoln D Stein
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11790, USA
    Genome Res 12:1599-610. 2002
    ..GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org...
  41. ncbi Visualization for genomics: the Microbial Genome Viewer
    Robert Kerkhoven
    Centre for Molecular and Biomolecular Informatics, University of Nijmegen, P O Box 9010, 6500 GL Nijmegen, The Netherlands
    Bioinformatics 20:1812-4. 2004
    ..Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection...
  42. ncbi The Systems Biology Graphical Notation
    Nicolas Le Novère
    EMBL European Bioinformatics Institute, Hinxton, UK
    Nat Biotechnol 27:735-41. 2009
    ..We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling...
  43. ncbi CFinder: locating cliques and overlapping modules in biological networks
    Balázs Adamcsek
    Department of Biological Physics, Eotvos University, Pázmány P stny 1A, H 1117 Budapest, Hungary
    Bioinformatics 22:1021-3. 2006
    ..Availability: CFinder (for Windows, Linux and Macintosh) and its manual can be downloaded from http://angel.elte.hu/clustering. Supplementary information: Supplementary data are available on Bioinformatics online...
  44. pmc Regulatory sequence analysis tools
    Jacques van Helden
    Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Universite Libre de Bruxelles, Campus Plaine, CP 263, Bld du Triomphe, B 1050 Bruxelles, Belgium
    Nucleic Acids Res 31:3593-6. 2003
    ..RSAT currently holds >100 fully sequenced genomes and these data are regularly updated from GenBank...
  45. pmc The KEGG databases at GenomeNet
    Minoru Kanehisa
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 30:42-6. 2002
    ..The KEGG databases are updated daily and made freely available (http://www.genome.ad.jp/kegg/)...
  46. pmc Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome
    Jodi E Hirschman
    Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305 5120, USA
    Nucleic Acids Res 34:D442-5. 2006
    ..Detailed lists are accessible through SGD's Advanced Search tool (http://db.yeastgenome.org/cgi-bin/search/featureSearch), and all the data presented on this page are available from the SGD ftp site (ftp://ftp.yeastgenome.org/yeast/)...
  47. ncbi GPU computing for systems biology
    Lorenzo Dematté
    CoSBi Centre, Italy
    Brief Bioinform 11:323-33. 2010
    ..In this paper, we review some recent efforts in exploiting the processing power of GPUs for the simulation of biological systems...
  48. ncbi Dynamic exploration and editing of KEGG pathway diagrams
    Christian Klukas
    Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany
    Bioinformatics 23:344-50. 2007
    ....
  49. pmc MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes
    Stephane Cruveiller
    Génoscope UMR CNRS 8030, Atelier de Génomique Comparative, 2 rue Gaston Cremieux, F 91006 Evry, France
    Nucleic Acids Res 33:W471-9. 2005
    ..The MICheck website is accessible at the following address: http://www.genoscope.cns.fr/agc/tools/micheck...
  50. pmc Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion
    Martin Christen Frølund Thomsen
    Center for Biological Sequence Analysis, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Nucleic Acids Res 40:W281-7. 2012
    ..The output from the server is a sequence logo and a PSSM. Seq2Logo is available at http://www.cbs.dtu.dk/biotools/Seq2Logo (14 May 2012, date last accessed)...
  51. pmc ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes
    Ivan Ovcharenko
    Genome Biology Division and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
    Nucleic Acids Res 32:W280-6. 2004
    ..The interconnection of the ECR Browser with other DNA sequence analysis tools creates a unique portal for studying and exploring vertebrate genomes...
  52. ncbi CytoscapeRPC: a plugin to create, modify and query Cytoscape networks from scripting languages
    Jan J Bot
    Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
    Bioinformatics 27:2451-2. 2011
    ..This enables them to access Cytoscape functionality and visualize their data interactively without leaving the programming environment with which they are familiar...
  53. pmc TreeVector: scalable, interactive, phylogenetic trees for the web
    Ralph Pethica
    Computer Science Department, University of Bristol, Bristol, United Kingdom
    PLoS ONE 5:e8934. 2010
    ..Traditional techniques of plotting phylogenetic trees focus on rendering a single static image, but increases in the production of biological data and large-scale analyses demand scalable, browsable, and interactive trees...
  54. pmc ePMV embeds molecular modeling into professional animation software environments
    Graham T Johnson
    Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Structure 19:293-303. 2011
    ....
  55. ncbi The contourlet transform: an efficient directional multiresolution image representation
    Minh N Do
    Department of of Electrical and Computer Engineering, Coordinated Science Laboratory, Beckman Institute, University of Illinois, Urbana, IL 61801, USA
    IEEE Trans Image Process 14:2091-106. 2005
    ..Index Terms-Contourlets, contours, filter banks, geometric image processing, multidirection, multiresolution, sparse representation, wavelets...
  56. pmc Type 2 diabetes genetic association database manually curated for the study design and odds ratio
    Ji Eun Lim
    Department of Biomedical Engineering, School of Medicine, Kyung Hee University, Seoul, Korea
    BMC Med Inform Decis Mak 10:76. 2010
    ..In this study, a user-friend database of type 2 diabetes genetic association of manually curated information was constructed...
  57. pmc Real-time 4D signal processing and visualization using graphics processing unit on a regular nonlinear-k Fourier-domain OCT system
    Kang Zhang
    Department of Electrical and Computer Engineering, The Johns Hopkins University, 3400 N Charles Street, Baltimore, MD 21218, USA
    Opt Express 18:11772-84. 2010
    ..This technique is highly cost-effective and can be easily integrated into most ultrahigh speed FD-OCT systems to overcome the 3D data processing and visualization bottlenecks...
  58. pmc Savant Genome Browser 2: visualization and analysis for population-scale genomics
    Marc Fiume
    Department of Computer Science, University of Toronto, Ontario, Canada M5S 2E4
    Nucleic Acids Res 40:W615-21. 2012
    ..The Savant Genome Browser is freely available (open source) at www.savantbrowser.com...
  59. ncbi On representation of proteins by star-like graphs
    Milan Randić
    National Institute of Chemistry, Ljubljana, Slovenia
    J Mol Graph Model 26:290-305. 2007
    ..We describe several graph invariants, mostly extracted from distance matrices of star-like graphs, which can serve as protein descriptors. The approach is illustrated on strand A of the human insulin...
  60. pmc SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny
    Derek Wilson
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK
    Nucleic Acids Res 37:D380-6. 2009
    ..The database, models and associated scripts are available for download from the ftp site...
  61. pmc An integrated software system for analyzing ChIP-chip and ChIP-seq data
    Hongkai Ji
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA
    Nat Biotechnol 26:1293-300. 2008
    ....
  62. pmc EPIBLASTER-fast exhaustive two-locus epistasis detection strategy using graphical processing units
    Tony Kam-Thong
    Max Planck Institute of Psychiatry, Munich, Germany
    Eur J Hum Genet 19:465-71. 2011
    ..Our method allows for exhaustive and rapid detection of significant SNP pair interactions without imposing significant marginal effects of the single loci involved in the pair...
  63. pmc SEARCHPKS: A program for detection and analysis of polyketide synthase domains
    Gitanjali Yadav
    National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
    Nucleic Acids Res 31:3654-8. 2003
    ..SEARCHPKS can be accessed at http://www.nii.res.in/searchpks.html...
  64. ncbi FANMOD: a tool for fast network motif detection
    Sebastian Wernicke
    Institut fur Informatik, Friedrich Schiller Universität Jena Ernst Abbe Platz 2, 07743 Jena, Germany
    Bioinformatics 22:1152-3. 2006
    ..Additional benefits of FANMOD are the ability to analyze colored networks, a graphical user interface and the ability to export results to a variety of machine- and human-readable file formats including comma-separated values and HTML...
  65. pmc Dalliance: interactive genome viewing on the web
    Thomas A Down
    Wellcome Trust CRUK Gurdon Institute, Cambridge CB2 1QN, UK
    Bioinformatics 27:889-90. 2011
    ..All data is fetched using the established distributed annotation system (DAS) protocol, making it easy to customize the browser and add extra data...
  66. pmc NCI: A server to identify non-canonical interactions in protein structures
    M Madan Babu
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nucleic Acids Res 31:3345-8. 2003
    ..In addition, the user can view the RasMol image highlighting the interactions in the protein structure and download the RasMol script. The NCI server is available at: http://www.mrc-lmb.cam.ac.uk/genomes/nci/...
  67. ncbi Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis
    Claire L Wilson
    Paterson Institute for Cancer Research, Manchester M20 4BX, UK
    Bioinformatics 21:3683-5. 2005
    ..Simpleaffy also offers fast implementations of popular algorithms for generating expression summaries and detection calls...
  68. pmc Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format
    Michael N Edmonson
    National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Bioinformatics 27:865-6. 2011
    ....
  69. pmc A large scale analysis of information-theoretic network complexity measures using chemical structures
    Matthias Dehmer
    Institute for Bioinformatics and Translational Research, UMIT, Hall in Tyrol, Austria
    PLoS ONE 4:e8057. 2009
    ..Generally, a high uniqueness is an important and desirable property when designing novel topological descriptors having the potential to be applied to large chemical databases...
  70. pmc MaGe: a microbial genome annotation system supported by synteny results
    David Vallenet
    Atelier de Génomique Comparative, CNRS UMR8030, 2 rue Gaston Cremieux, 91057 Evry, Cedex, France
    Nucleic Acids Res 34:53-65. 2006
    ..In addition, MaGe allows for annotation curation and exploration of already published genomes from various genera (e.g. Yersinia, Bacillus and Neisseria). MaGe can be accessed at http://www.genoscope.cns.fr/agc/mage...
  71. pmc Gene set analysis exploiting the topology of a pathway
    Maria Sofia Massa
    Department of Statistical Sciences, University of Padova, Via C, Battisti 241, Padova, Italy
    BMC Syst Biol 4:121. 2010
    ..Although pathways maps carry important information about the structure of correlation among genes that should not be neglected, the currently available multivariate methods for gene set analysis do not fully exploit it...
  72. pmc An ontology for cell types
    Jonathan Bard
    Department of Biomedical Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh, EH8 9XD, UK
    Genome Biol 6:R21. 2005
    ..The ontology is freely available at http://obo.sourceforge.net/ and can be viewed using standard ontology visualization tools such as OBO-Edit and COBrA...
  73. ncbi CARHTA GENE: multipopulation integrated genetic and radiation hybrid mapping
    Simon de Givry
    INRA, Biométrie et Intelligence Artificielle Génétique Cellulaire, BP 27, 31326 Castanet Tolosan Cedex, France
    Bioinformatics 21:1703-4. 2005
    ..Dedicated heuristics for framework mapping are also included. CAR(H)(T)A GENE: can be used as a C++ library, through a shell command and a graphical interface. The XML output for companion tools is integrated...
  74. pmc Bioimage informatics: a new area of engineering biology
    Hanchuan Peng
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
    Bioinformatics 24:1827-36. 2008
    ....
  75. pmc Human immunodeficiency virus type 1, human protein interaction database at NCBI
    William Fu
    Southern Research Institute, Frederick, MD 21701, USA
    Nucleic Acids Res 37:D417-22. 2009
    ..The database is also tightly linked to other databases through Entrez Gene, enabling users to search for an abundance of information related to HIV pathogenesis and replication...
  76. ncbi The use of visual analogue scales to assess motivation to eat in human subjects: a review of their reliability and validity with an evaluation of new hand-held computerized systems for temporal tracking of appetite ratings
    R J Stubbs
    Rowett Research Institute, Bucksburn, Aberdeen, UK
    Br J Nutr 84:405-15. 2000
    ..However, subjects appear to exhibit a significantly more constrained use of the scale when using the EARS relative to the P&P. For this reason it is recommended that the two techniques are not used interchangeably...
  77. ncbi Crystal structures explain functional properties of two E. coli porins
    S W Cowan
    Department of Structural Biology, University of Basel, Switzerland
    Nature 358:727-33. 1992
    ..The structures explain at the molecular level functional characteristics and their alterations by known mutations...
  78. pmc WEBnm@: a web application for normal mode analyses of proteins
    Siv Midtun Hollup
    Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgt 55, N 5008 Bergen, Norway
    BMC Bioinformatics 6:52. 2005
    ..NMA relies on the hypothesis that the vibrational normal modes having the lowest frequencies (also named soft modes) describe the largest movements in a protein and are the ones that are functionally relevant...
  79. pmc The Pfam protein families database
    Alex Bateman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 30:276-80. 2002
    ..New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource...
  80. pmc A comparison of phylogenetic network methods using computer simulation
    Steven M Woolley
    Computational Biology Program, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS ONE 3:e1913. 2008
    ....
  81. pmc Binding MOAD, a high-quality protein-ligand database
    Mark L Benson
    Bioinformatics Graduate Program, Biophysics Research Division, University of Michigan, Ann Arbor, MI 48109, Torrey Path LLC, Ann Arbor, MI 48104, USA
    Nucleic Acids Res 36:D674-8. 2008
    ..Ligands have additional chemical data, allowing for cheminformatics mining. Lastly, logins are no longer necessary, and Binding MOAD is freely available to all at http://www.BindingMOAD.org...
  82. ncbi Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex
    P D Jeffrey
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Nature 376:313-20. 1995
    ..These changes activate the kinase by realigning active site residues and relieving the steric blockade at the entrance of the catalytic cleft...
  83. pmc Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data
    Richard J S Baerends
    Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
    Genome Biol 5:R37. 2004
    ..The compiled version of Genome2D is freely available for academic or non-profit use from http://molgen.biol.rug.nl/molgen/research/molgensoftware.php...
  84. ncbi Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks
    Adriano V Werhli
    Biomathematics and Statistics Scotland, Edinburgh, UK
    Bioinformatics 22:2523-31. 2006
    ..We use both laboratory data from cytometry experiments as well as data simulated from the gold-standard network. We also compare passive observations with active interventions...
  85. pmc Tilescope: online analysis pipeline for high-density tiling microarray data
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Genome Biol 8:R81. 2007
    ..The program is designed with a modular, three-tiered architecture, facilitating parallelism, and a graphic user-friendly interface, presenting results in an organized web page, downloadable for further analysis...
  86. ncbi Multiple Alignment of protein structures and sequences for VMD
    John Eargle
    Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, 607 South Mathews Avenue, Urbana, IL 61801, USA
    Bioinformatics 22:504-6. 2006
    ..It is implemented as a plugin for VMD (Visual Molecular Dynamics), which is distributed by the NIH Resource for Macromolecular Modeling and Bioinformatics at the University of Illinois...
  87. pmc IPAVS: Integrated Pathway Resources, Analysis and Visualization System
    Pradeep Kumar Sreenivasaiah
    School of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology, Gwangju 500 712, Korea
    Nucleic Acids Res 40:D803-8. 2012
    ..The integrated datasets in IPAVS are made available in several standard data formats that can be downloaded. IPAVS is available at: http://ipavs.cidms.org...
  88. ncbi BicOverlapper: a tool for bicluster visualization
    Rodrigo Santamaría
    Departamento de Informática y Automática, Pz de Los Caídos S N, 37008 Salamanca, Spain
    Bioinformatics 24:1212-3. 2008
    ..The technique is based on a force-directed graph where biclusters are represented as flexible overlapped groups of genes and conditions...
  89. pmc The design and evaluation of a graphical display for laboratory data
    David T Bauer
    University of Virginia, Charlottesville, Virginia, USA
    J Am Med Inform Assoc 17:416-24. 2010
    ..The effect of this novel display on physicians' interpretation of data was investigated...
  90. ncbi Cactus graphs for genome comparisons
    Benedict Paten
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California, USA
    J Comput Biol 18:469-81. 2011
    ..Supplementary Material is available at www.liebertonline.com/cmb ...
  91. pmc MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation
    Huabin Hou
    Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou 325035, China
    Nucleic Acids Res 38:W732-6. 2010
    ..MagicViewer is freely available at http://bioinformatics.zj.cn/magicviewer/...
  92. pmc Connections between classical and parametric network entropies
    Matthias Dehmer
    Institute for Bioinformatics and Translational Research, UMIT, Hall in Tirol, Austria
    PLoS ONE 6:e15733. 2011
    ..The inequalities established in this paper relating classical and parametric measures lay a foundation for systematic classification of entropy-based measures of graph complexity...
  93. pmc MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data
    Zhengwei Zhu
    Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093, USA
    Bioinformatics 29:122-3. 2013
    ..This viewer is easy to use on all computer systems with modern web browsers and requires no software installation...
  94. pmc Real-time GPU-based 3D Deconvolution
    Marc A Bruce
    Stanford Immunology, Stanford University, Stanford, California 94305, USA
    Opt Express 21:4766-73. 2013
    ..This software provides a low-cost and rapid way to improve the accuracy of 3D microscopic images obtained by any method...
  95. ncbi MGV: a generic graph viewer for comparative omics data
    Stephan Symons
    Center for Bioinformatics Tubingen, Faculty of Science, University of Tubingen, 72076 Tubingen, Germany
    Bioinformatics 27:2248-55. 2011
    ..Especially, it is necessary to compare biological models with measured data. This allows the identification of new models and new insights into existing ones...
  96. ncbi POLYVIEW: a flexible visualization tool for structural and functional annotations of proteins
    Aleksey A Porollo
    Children s Hospital Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
    Bioinformatics 20:2460-2. 2004
    ..POLYVIEW may be used for automated generation of pictures with structural and functional annotations for publications and proteomic on-line resources...
  97. pmc Drawing explicit phylogenetic networks and their integration into SplitsTree
    Tobias H Kloepper
    Center for Bioinformatics ZBIT, Tubingen University, Sand 14, 72076 Tubingen, Germany
    BMC Evol Biol 8:22. 2008
    ..It contains a wide variety of methods for the import/export, calculation and visualization of phylogenetic information. The software is developed in Java and implements a command line tool as well as a graphical user interface...
  98. ncbi A matrix approach to tomographic reconstruction and its implementation on GPUs
    F Vazquez
    Deptartment of Computer Architecture, University of Almeria, 04120 Almeria, Spain
    J Struct Biol 170:146-51. 2010
    ..In combination with GPU computing, the matrix approach for WBP exhibits a significant acceleration factor compared to the standard implementation...
  99. pmc EvolView, an online tool for visualizing, annotating and managing phylogenetic trees
    Huangkai Zhang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics BIG, Chinese Academy of Sciences CAS, No 7 Beitucheng West Road, Chaoyang District, 100029 Beijing, PR China
    Nucleic Acids Res 40:W569-72. 2012
    ..To make EvolView easy to use, it is equipped with an intuitive user interface. With a free account, users can save data and manipulations on the EvolView server. EvolView is freely available at: http://www.evolgenius.info/evolview.html...
  100. pmc Online detector response calculations for high-resolution PET image reconstruction
    Guillem Pratx
    Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
    Phys Med Biol 56:4023-40. 2011
    ..75 mm hot spheres in air, the variation in reconstructed sphere size was 0.5 mm RMS for the shift-invariant model, compared to 0.07 mm RMS for the shift-varying model...
  101. ncbi Accelerating reaction-diffusion simulations with general-purpose graphics processing units
    Matthias Vigelius
    FIT Centre for Research in Intelligent Systems, Monash University, Clayton, Victoria, Australia
    Bioinformatics 27:288-90. 2011
    ..Our SSA exploits GPGPU architecture to achieve a performance gain of two orders of magnitude over the fastest existing implementations on conventional hardware...

Research Grants62

  1. Novel Topoisomerase I Inhibitors
    MARK S CUSHMAN; Fiscal Year: 2013
    ..the fundamental forces stabilizing the inhibitor/enzyme/DNA ternary complexes through medicinal chemistry, computer graphics molecular modeling, molecular mechanics, ab initio quantum mechanics, and biochemical studies...
  2. A Texture Analysis/Synthesis Model of Visual Crowding
    Ruth Rosenholtz; Fiscal Year: 2010
    ..Thus, Dr. Rosenholtz will attack the problem of crowding through a useful synthesis of computer graphics, computer vision, and psychophysics...
  3. PURINE METABOLISM IN TRICHOMONAS AND GIARDIA
    C Wang; Fiscal Year: 2000
    ..requires a consortium of researchers in biochemistry, pharmacology, molecular biology, structural biology, computer graphics and organic synthesis to work together...
  4. Virtual Reality Relapse Prevention: Alcohol Dependence
    PATRICK SHANNON BORDNICK; Fiscal Year: 2010
    ..VRRP will combine computer graphics with sensory input devices including: tracking devices, visual head mounted displays (HMD), scents and ..
  5. 3D Digital Breast Phantoms For Multimodality Research
    William P Segars; Fiscal Year: 2013
    ..The normal background anatomy of the phantoms will be constructed using state-of-the-art computer graphics techniques based on this unique data...
  6. DESIGN AND TESTING OF DOCKING ALGORITHMS
    Brian K Shoichet; Fiscal Year: 2011
    ..A Model Binding Site for Testing Scoring Functions in Molecular Docking Interactive computer graphics available through the RBVI are key to visualizing and evaluating how well docking calculations have ..
  7. CLINICAL BIOMECHANICS OF CERVICAL SPINE
    Manohar Panjabi; Fiscal Year: 1990
    ..Detaialed and quantified three-dimensional anatomy, using computer graphics; computer graphics (2) Biomechanics...
  8. CRYSTALLOGRAPHIC STUDIES OF HEMERYTHRIN
    RON STENKAMP; Fiscal Year: 1990
    ..Models of the redox complex between hemerythrin and cytochrome b5, generated and analyzed using computer graphics and energy minimization techniques, will allow investigation of elements involved in and controlling ..
  9. IONOPHORES, TRANSPORT AND MEMBRANE STRUCTURE
    William Duax; Fiscal Year: 1980
    ..Using computer graphics and force field energy calculations (1) solid state data concerning complexed and uncomplexed forms of ..
  10. IMMUNOGLOBULINS IN MULTIPLE MYELOMA & AMYLOIDOSIS
    Allen Edmundson; Fiscal Year: 1993
    ..7-A resolution, in combination with interactive computer graphics. When crystallized in deionized water (orthorhombic form), the Mcg dimer assumes a signficanctly different 3-..
  11. COMPUTER-WORKSTATION/NETWORK-SERVER TO LINK NIH INVESTIG
    WILLIAM RYMER; Fiscal Year: 1992
    ..This advanced technology will make possible the development of three-dimensional (3D) computer graphics models of the musculoskeletal system, which will significantly enhance our studies of movement control...
  12. CONNECTIONS OF THE LIMBIC SYSTEM AND HYPOTHALAMUS
    LARRY SWANSON; Fiscal Year: 2005
    ..of experimental neuroanatomical methods in the rat are designed to explore this hypotheses: (1) A systematic computer graphics atlas/database of LHA differentiation based on connections and in situ hybridization-related mRNA expression ..
  13. PREDICTION METHODS; HEMOLYTIC TOXINS & PLASMIN KRINGLES
    MARTHA TEETER; Fiscal Year: 1993
    ..The prediction method is based on computer graphics modeling combined with in vacuo global energy minimization with AMBER...
  14. NEURAL MECHANISMS OF SIZE PERCEPTION
    John Allman; Fiscal Year: 2001
    ..In another test of the influence of the visual context, we will create a virtual laboratory in the form of a computer graphics model of our actual experimental set- up...
  15. RETIREMENT,LEISURE & OLD ADULTS--DEVELOPMENT DISABILITIE
    Martin Sheehan; Fiscal Year: 2000
    ..The program will combine text-based information, video (narrative and simulations), computer graphics, and audio (voice, music, and sound effects) in a self- paced interactive CD-ROM training format Program ..
  16. RETINOID-BINDING PROTEINS
    PER PETERSON; Fiscal Year: 1992
    ..between the two proteins using, in succession, antipeptide antibodies, site-directed mutagenesis and computer graphics modeling. The RBP-site interacting with a cell surface receptor will be identified by a similar approach...
  17. Virtual Relaxation Environment for Chronic Back Pain
    Libby Tannenbaum; Fiscal Year: 2004
    ..Virtual reality (VR) environments combine computer graphics with sensory input devices including tracking devices, visual head mount displays, and directional audio ..
  18. BIOMECHANICAL BASIS FOR THE TREATMENT OF SLEEP APNEA
    Richard Schwab; Fiscal Year: 2000
    ..Regional compliance of the airway and surrounding soft tissues will be measured. Customized computer graphics-based volumetric image analysis and display methods provide for objective quantitation of the image data...
  19. ENZYME-ACTIVATED IRREVERSIBLE INHIBITORS OF PROTEASES
    John Katzenellenbogen; Fiscal Year: 1990
    ..what chemical species are involved and what residue is the site of alkylation; furthermore, we will utilize computer graphics- molecular modeling to rationalize relationships between inactivator structure and inactivating efficiency ..
  20. COMPUTER-DRIVEN PHASE-DIFFERENCE CRT HAPLOSCOPE
    STEVEN PANISH; Fiscal Year: 1990
    ..The primary goal will be development of user-friendly applications programs for semi-automated clinical strabismus screening and orthoptics...
  21. 3-D ANALYSIS OF LEFT VENTRIULAR REGIONAL WALL MOTION
    R Clark; Fiscal Year: 1990
    This project involves the development of an easy to use, computer graphics based software package which will allow users to fully analyze regional wall motion in the left ventricle in three dimensions...
  22. Data-driven Real-Time Surgical Simulation from Reality-based Soft-tissue Models
    JAYDEV DESAI; Fiscal Year: 2009
    ..of BRG by addressing problems in bioengineering and bringing biomechanical engineering, surgery, and computer graphics together to solve compelling surgical training problems...
  23. A 3D DVD Atlas of Human Development
    MICHAEL HULTNER; Fiscal Year: 2002
    ..then animated and rendered to create didactic video presentations of the embryonic form in full-motion 3D computer graphics. Motion graphic overlays are then added to create a 3D labeling system...
  24. INTERACTIVE MULTIMEDIA CD ROM FOR SOCIAL SKILLS IN ADHD
    ELIZABETH GOLDSWORTHY; Fiscal Year: 2000
    ..By using the latest computer graphics and media capabilities, it is possible to develop a training program with components that approximate the ..
  25. Virtual Reality Cannabis Cue Exposure Assessment System
    Patrick Bordnick; Fiscal Year: 2004
    ..Virtual reality exposure (VRE) combines computer graphics with sensory input devices including: tracking devices, visual head mounted displays (HMD), and directional ..
  26. SPEECH PERCEPTION STUDIES BIMODAL AND DEVELOPMENTAL
    LYNNE BERNSTEIN; Fiscal Year: 1990
    ..Work on Project IV will also include development of training and testing protocols using computer graphics. Protocols will be developed to train and test children on bimodal speech perception schemes...
  27. ADAPTATION OF THE VOR TO MAXIMIZE GAIN CHANGES
    Erik Viirre; Fiscal Year: 2000
    ..We have developed an immersive computer graphics environment designed for visual-vestibular interaction research...
  28. THREE DIMENSIONAL CT COLONOGRAPHY
    Christopher Beaulieu; Fiscal Year: 2007
    ..Our goals are to provide improved computer graphics and computer aided diagnosis technology and to establish interpretation practices that will maximize polyp ..
  29. CAD/CAM FOR DENTAL RESTORATIONS
    Dianne Rekow; Fiscal Year: 1992
    ..on recent technologic advances in robotics, three-dimensional vision systems, stereophotogrammetry, computer graphics, and computer integrated engineering...
  30. IRIS MODEL 4D220 VGX WORKSTATION
    Suse Broyde; Fiscal Year: 1991
    Funds are sought for an IRIS Model 4D220 VGX Computer Graphics Workstation and accessories from Silicon Graphics Computer Systems...
  31. Communicating probabilities through interactive computer graphics
    Rita Kukafka; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  32. BIOMEDICAL RESEARCH SUPPORT
    Donald Brown; Fiscal Year: 1991
    ..the structure, dynamics, and function of biomolecules and their interactions with drugs are applying for computer graphics equipment which they will share...
  33. INTEGRATED 3D DISPLAY OF MR, CT, AND PET IMAGES
    David Levin; Fiscal Year: 1993
    ..Specifically, spatial integration will be achieved by using computer graphics to create 3-D renditions of brain anatomy or function from each modality...
  34. Virtual-Endoscopic Reporter for Lung-Cancer Assessment
    William Higgins; Fiscal Year: 2001
    ..The 3D Reporter draws upon recent innovations in virtual endoscopy, image processing, and computer graphics. This Phase-I project's aims are as follows: (1) prototype the 3D Reporter's main interactive visualization ..
  35. MOLECULAR CONFORMATION, COMPARISON AND INTERACTION
    Michael Connolly; Fiscal Year: 1991
    ..This is not the case for interactive superposition of two structures on a color computer graphics screen. It is therefore necessary to develop automatic computer algorithms for molecular comparison...
  36. ELECTROTACTILE DISPLAY OF COMPUTER GRAPHICS FOR BLIND
    KURT KACZMAREK; Fiscal Year: 2001
    ..The increasing use of computer graphics and pictorial displays (such as the Apple Macintosh and Microsoft Windows environments) presents a major ..
  37. SYNTHETIC COLLAGENASE INHIBITORS
    Robert Gray; Fiscal Year: 1990
    ..design and synthesis of new peptide inhibitors using conformational analysis, x-ray crystallography and computer graphics techniques coupled both with potency data for currently available compounds as well as newly acquired ..
  38. INTERACTIVE COMPUTER GRAPHICS FOR TEENAGE SEX EDUCATION
    R Avent; Fiscal Year: 1993
    ....
  39. INTELLIGENT MAPPING OF GENE EXPRESSION PROFILES
    Yue Wang; Fiscal Year: 2002
    ..A novel integration of information theory and computer graphics will permit (1) an automatic identification and modeling of biomarker clusters, (2) a probabilistic ..
  40. INTELLIGENT MAPPING OF GENE EXPRESSION PROFILES
    Yue Wang; Fiscal Year: 2000
    ..A novel integration of information theory and computer graphics will permit (1) an automatic identification and modeling of biomarker clusters, (2) a probabilistic ..
  41. Virtual Reality Cue Exposure for Drug Addiction: Smoking
    Patrick Bordnick; Fiscal Year: 2002
    ..Virtual reality exposure (VRE) combines computer graphics with sensory input devices including: tracking devices, visual head mounted displays (HMD), and directional ..
  42. PHYSICIAN-COMPUTER INTERACTION USING GRAPHICS AND SPEECH
    Edward Shortliffe; Fiscal Year: 1990
    ..We accordingly propose a staged research plan to study the way computer graphics can be bused to constrain the possible meanings of an utterance, thereby promoting physician-computer ..
  43. METALLOPROTEIN STRUCTURE AND DESIGN
    ELIZABETH GETZOFF; Fiscal Year: 2001
    ..structure determination, spectroscopy, protein engineering, theoretical and computational approaches, and computer graphics with experimental testing of functional hypotheses by metalloprotein design...
  44. CARDIAC MYOFIBER MORPHOGENESIS IN MOUSE, MONKEY, & MAN
    John Prothero; Fiscal Year: 1991
    ..semiautomated photomicrography, manual digitization, automatic coordinate reassembly, interactive 3-D computer graphics reconstructions, graphics file editing, image production and archiving...
  45. 6TH BIOPHYSICAL DISCUSSION--BIOPHYSICS & RECOMBINANT DNA
    Stephen White; Fiscal Year: 1992
    ..species, the innovative use of mutagenesis to test specific hypotheses, and modeling built on computation or computer graphics as compared with the need for more accurate three-dimensional molecular structures...
  46. SODIUM-CALCIUM EXCHANGE IN VASCULAR SMOOTH MUSCLE
    MOHAMMED MATLIB; Fiscal Year: 1992
    ..and digital imaging microscopy, and the contractile state will be assessed by utilizing an interactive computer graphics system to measure cell length...
  47. VIRTUAL DENTAL PATIENT
    Ralph DeLong; Fiscal Year: 2001
    ..specific aims: (1) incorporate the soft and hard tissue of the dental arches into virtual 3-D images using computer graphics; (2) bring the imaged arches into the correct clinical relationship; (3) add animation to reproduce the ..
  48. SYNTHESIS OF NEW ANTIHIV AGENTS RELATED TO COSALANE
    Mark Cushman; Fiscal Year: 2000
    ..These efforts are being assisted by computer graphics molecular modeling of hypothetical ligand-protein complexes, as well as by analysis of the available ..
  49. MINORITY HIGH SCHOOL STUDENT RESEARCH APPRENTICE PROGRAM
    CHING CHUNG CHOU; Fiscal Year: 1992
    The application requests funds for the purchase of a computer graphics system to be used primarily by those research groups in the Department of Chemistry and Biochemistry whose research interests are in the areas of mechanistic ..
  50. In-Car Technology to Alert Attention-Imparied Drivers
    Matthew Rizzo; Fiscal Year: 2009
    ..The research team members are experts in human factors engineering, neurology, biostatistics, computer graphics, and cognitive science...
  51. Advanced Computational Methods for the Virtual Heart
    Ravi Samtaney; Fiscal Year: 2005
    ..to solve a variety of problems in areas of nonlinear physics, turbulence, fluid and magnetohydro dynamics, computer graphics and computational endocrinology...
  52. MODELING OPIOID RECEPTOR STRUCTURE/FUNCTION
    David Ferguson; Fiscal Year: 1999
    ..formulated from the most recent structural information on G-protein coupled receptors using interactive computer graphics and predictive techniques based on homology...
  53. Virtual Reality Skills Training: Nicotine Dependence
    Patrick Bordnick; Fiscal Year: 2005
    ..VRST combines computer graphics with sensory input devices including: tracking devices, visual head mounted displays (HMD), and directional ..
  54. HAPTIC DISPLAY OF COMPUTER GRAPHICS FOR THE BLIND
    Paul Hooper; Fiscal Year: 1990
    The increasing use of computer graphics and pictoral displays (and the increasing resolution for the displays) poses a major problem for blind computer users...
  55. BIOMEDICAL RESEARCH SUPPORT GRANT
    Grant Morrow; Fiscal Year: 1991
    The creation of a cardiovascular shared instrument image analysis and computer graphics facility at the Johns Hopkins University School of Medicine (JHSM) is proposed...
  56. COMPUTATIONAL GRAPHICS FOR BIOCHEMISTRY
    JOSEPH KRAUT; Fiscal Year: 1992
    ..the structure, dynamics and function of biomolecules and their interactions with drugs are applying for computer graphics equipment which they will share...
  57. COMPUTER GRAPHICS EQUIPMENT
    Douglas Turner; Fiscal Year: 1991
    ..Intra- molecular distance estimates from NOESY data will be used to constrain energy minimization programs to determine the three-dimensional structure of biomolecules in solution...
  58. REAL-TIME VLSI CHIP FOR 3-D SURFACE RENDERING FOR CT & M
    KENDALL PRESTON; Fiscal Year: 1991
    ..e., instantaneous presentation of any three dimensional view upon demand of the user, requires expensive computer graphics workstations...
  59. MOLECULAR STRUCTURE IN SOLUTION-A FEASIBILITY STUDY
    Irwin Kuntz; Fiscal Year: 1993
    ..These methods will use computer graphics, structural databases, and pattern recognition; 4) Developing a complete package of algorithms for ..
  60. SILICON GRAPHICS-4D240GTX GRAPHICS COMPUTER WORKSTATION
    Godfrey Pearlson; Fiscal Year: 1991
    ..group of federally-funded researchers with strong collaborative ties to access expensive state of the art computer graphics technology for 3 dimensional volume rendering of brain images...
  61. VISUALIZATION AND IMAGE ANALYSIS FOR 3-D ULTRASOUND
    George Stetten; Fiscal Year: 1999
    ..The proposed approach is twofold. (l) To explore computer graphics volumetric and surface rendering techniques that preserve the content of the data for the human observer...
  62. Computational Methods for Transcriptional Mapping of Eukaryotic Genomes
    Charles Delisi; Fiscal Year: 2009
    ..GABA is the major inhibitory neurotransmitter in the central nervous system (CNS), and plays a key role in CNS development and disease. ..