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The GMOD Project

The GMOD Project. Lincoln Stein Cold Spring Harbor Laboratory. FRANCIS HARRY COMPTON CRICK 1916-2004. The GMOD Project. Lincoln Stein Cold Spring Harbor Laboratory. What’s a MOD?. Model Organism Database Repository for reagents Stocks, vectors, clones Genetic & physical maps

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The GMOD Project

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  1. The GMOD Project Lincoln Stein Cold Spring Harbor Laboratory

  2. FRANCIS HARRY COMPTON CRICK 1916-2004

  3. The GMOD Project Lincoln Stein Cold Spring Harbor Laboratory

  4. What’s a MOD? • Model Organism Database • Repository for reagents • Stocks, vectors, clones • Genetic & physical maps • Large-scale data sets • Genome • EST sets, microarray results, 2-cell hybrid interactions • Literature • Ontologies & Nomenclature • Meetings, announcements

  5. Example MOD: WormBase

  6. Gene

  7. Genome

  8. Comparative Genomics

  9. Functional Genomics

  10. Citation

  11. Demand for CuratedDatabases is High • Actinomycetes • Barley • Chlamydia • Cow • HIV • Honeybee • Paramecium • Planaria • Plasmodia • Pseudomonas • Staphylococci • Schistosoma • Soybean • Tetrahymena • Volvox

  12. The GMOD Project • Portable, open source software to support model organism databases • Multiple MODs involved • Worm, fly, yeast, mouse, arabidopsis, rat, monocot, fugu, E. coli • Funded by NIH as of June 2002 • Programmers, coordinator, quarterly meetings http://www.gmod.org

  13. Modular Applications The GMOD Pyramid Modular Schema Open Source DBMS & Middleware

  14. genetic maps liter- ature genome A MOD Construction Set map browser map editor Appplication Layer annotation pipeline genome browser genome editor citation browser citation editor Bioperl BioJava BioPython Middleware Layer genomes maps citations Database Layer

  15. Chado – Modular Schema • Common schema for use by MODs • Ontology Driven • Small number of generic tables driven by a controlled vocabulary • Evidence-Savvy • Extensible • A collection of application-driven modules

  16. www.gmod.org

  17. Chado Genbank BioPipe Other Formats Other Formats Other Formats Genome Management Gbrowse (web site) Apollo (desktop) loaders

  18. Genome Annotationand Visualization

  19. Apollo – BDGP/Sanger

  20. Adding a Transcript

  21. Apollo Exon Editor

  22. Apollo Macrosynteny Viewer

  23. Apollo Microsynteny Viewer

  24. Chado Genbank BioPipe Genome Management Gbrowse (web site) Apollo (desktop) bioperl

  25. GBrowse – Low Magnification

  26. Zoom – Medium Magnification

  27. Zoom – High Magnification

  28. Zoom – Highest Magnification

  29. Sequence dumps & other reports

  30. Extensively Customizable

  31. DAS: Gbrowse on UCSC

  32. DAS: Gbrowse on EnsEMBL

  33. DAS: Gbrowse on both

  34. Distributed GBrowse Gbrowse 2 Gbrowse 3 Gbrowse 1 My Gbrowse

  35. Embeddable Embedding Capable

  36. Internationalizable

  37. Genetic, Sequenceand Physical MapManagement

  38. CMap: Map Comparisons

  39. Metabolic PathwayVisualization &Management

  40. Pathway Tools - SRI

  41. Citation Managementand Searching

  42. PubSearch/PubFetch

  43. Pattern recognition & Markup engine TextPresso Db Search Interface TextPresso - WormBase PDFs

  44. Future Attractions

  45. Interaction Browser

  46. Turnkey Website

  47. Known GMOD Users Agricultural Biotechnology Center, Hungary BAWI, S. Korea Baylor College of Medicine Biocrates GmbH, Innsbruck Brandeis University Bristol-Meyers Squibb British Columbia Centre for Diseaes Control CIRAD, France CSIRO, Australia Cambridge University (multiple labs) Center for Genomics & Bioinformatics, Stockholm Centre de Genetique Moleculaire, CNRS Cold Spring Harbor Laboratory (multiple labs) Compugen Concordia University, Canada Cornell Medical School Cornell University DNA Landmarks, Inc. Donald Danforth Plant Sciences Center Duke University (multiple labs) EMBL, Heidelberg Faculdade de Medicina de Ribeirão Preto FlyBase Foundation for Research and Technology, Crete Fundação Hemocentro, Sao Paolo Genoscope, France GrainGenes Harvard University Hospital for Sick Kids, Toronto Illinois Institute of Technology Incyte Corporation Inpharmatica, Ltd. Institute for Systems Biology, Seattle Institute of Molecular and Cell Biology, Singapore International Rice Research Institute, Phillipines John Innes Centre KEGG Kansas State University Karolinska Institute Kennedy Krieger Institute Lawrence Berkeley Laboratories Marine Biological Laboratories, Woods Hole Massachusetts Institute of Technology (multiple labs) Mayo Institute McGill University Meat Animal Research Center, University of Nebraska

  48. Known GMOD Users Open Informatics Consulting Corp. Oxagen Corp. Pasteur Institute, Paris Pioneer Corporation QIAGEN Operon Corp. RIKEN (multiple labs) RatDB Regulome, Inc. Rhobio (Bayer CropScience SA & Biogemma joint venture) Rigshospitalet, Copenhagen Rockefeller University Roslin Institute, Edinburgh Russian Academy Medical Sciences Serono International Corp, Geneva Simon Frasier University South Africa National Bioinformatics Institute Southern Illinois University St. Jude Children's Research Hospital, Memphis Stowers Institute for Medical Research Texas A&M (multiple labs) The Institute for Genome Research Tulane University University California Davis University of Arizona (multiple labs) University of British Columbia University of California Santa Barbara University of Georgia (multiple labs) University of Minnesota University of Muenster University of New South Wales, Australia University of Oklahoma (multiple labs) University of Pennsylvania (multiple labs) University of Southern California University of Texas University of Toronto University of Virginia University of Washington Universität Giessen Université de Liège, Belgium Wageningen Universiteit & Researchcentrum, Netherlands Washington University at St. Louis (multiple labs) WormBase deVGen, Belgium

  49. Find out more about GMOD • Go to www.gmod.org • Examine software matrix • Find a project you’re interested in • Contact project leader • Or contact Scott Cain: cain@cshl.org • Or mail gmod-dev@lists.sourceforge.net

  50. Credits Broad Institute Michele Clamp Carnegie Institute Sue Rhee Danny Yoo CSHL Adrian Arva Shuly Avraham Scott Cain Ken Clark Allen Day Xiaokang Pan BDGP Nomi Harris Suzanna Lewis Chris Mungall John Richter ShengQiang Shu Colin Weil MCW Simon Twigger UCLA Allen Day Brian O’Connor Harvard David Emmert Stan Letovsky Caltech Eimear Kenny Hans-Michael Muller SRI International Peter Karp http://www.gmod.org

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