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GMOD: Building Blocks for a Model Organism System Database

GMOD: Building Blocks for a Model Organism System Database. Lincoln Stein, CSHL. 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

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GMOD: Building Blocks for a Model Organism System Database

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  1. GMOD: Building Blocks for a Model Organism System Database Lincoln Stein, CSHL

  2. 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

  3. 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

  4. GMOD Home Page

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

  6. Apollo – BDGP & Sanger Center

  7. PubSearch – TAIR & RatDB

  8. CMap – Gramene

  9. Cmap – Multiple Maps

  10. GBrowse – WormBase

  11. GBrowse – Zoomed In

  12. GBrowse – Zoomed Way In

  13. GBrowse – Zoomed Way Way In

  14. GBrowse – Keyword Search

  15. GBrowse – Reports

  16. GBrowse – Third Party Annotations

  17. GBrowse – Multilanguage Support

  18. Extensively Customizable • End-user • Turn tracks on and off, change order, change packing & labeling attributes (stored in cookie) • Data provider • Change fonts, colors, text. • Change overview – genetic map, contigs, coverage, karyotype. • Define new tracks using simple config file. • Tinker with track appearance to hearts content.

  19. Adding a New Track (a) Create a GFF file named “deletions.gff” Chr1 targeted deletion 1293224 1294901 . . . Deletion d101k2 Chr1 targeted deletion 8239811 8241116 . . . Deletion d680k2 Chr2 targeted deletion 5866382 5866500 . . . Deletion d007k2 (b) Run the load_gff.pl script > load_gff.pl –d example_database deletions.gff Loading features… Done. 3 features loaded. (c) Add a new track “stanza” to the gbrowse configuration file [Knockout] feature= deletion glyph= span fgcolor= red key = Knockouts link = http://example.org/cgi-bin/knockout_details?$name citation= These are deletion knockouts produced by the example knockout consortium (http://example.org/knockouts.html)

  20. Extensively Extensible Plugins gbrowse CGI script Apache Web Server Glyphs Bio::Graphics library Oracle adaptor BioPerl library Flat File adaptor Bio::DB::GFF adaptor Chado adaptor Oracle MySQL/Postgres Flat Files

  21. GenBank Proxy Adaptor Bio::DB::GFF adaptor GenBank MySQL GBrowse on GenBank? GBrowse on GenBank! Plugins gbrowse CGI script Apache Web Server Glyphs Bio::Graphics library BioPerl library

  22. B. burgdorferi via GenBank proxy

  23. Who is Using GBrowse? • GMOD Members • WormBase, FlyBase, RatDB • HGMP-RC Fugu genomics group • KEGG (multiple microorganisms) • Ingenium AG (mouse) • Bristoll-Myers Squibb (drosophila) • Texas A&M University (salmonella) • Institute of Systems Biology (human)

  24. Coming Soon to www.gmod.org • Biopipe – genome annotation pipeline • Insertional mutagenesis analysis pipeline • Tree browser • Pathway browsers • Generic MOD web site framework

  25. Joining GMOD • Go to www.gmod.org • Examine software matrix • Find a project or suggest new one • Contact Scott Cain: cain@cshl.org • Or mail gmod-dev@lists.sourceforge.net

  26. Credits CSHL Adrian Arva Shuly Avraham Scott Cain Ken Clark Allen Day BDGP Nomi Harris Suzanna Lewis Chris Mungall John Richter ShengQiang Shu Colin Weil EBI Michele Clamp Stephen Searle Carnegie Institute Sue Rhee Danny Yoo Harvard David Emmert Stan Letovsky http://www.gmod.org

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