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

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

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

4. GMOD Home Page

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

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 u End-user –Turn tracks on and off, change order, change packing & labeling attributes (stored in cookie) u 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 Apache Web Server gbrowse CGI script BioPerl library Bio::DB::GFF adaptor Chado adaptor MySQL/Postgres Plugins Bio::Graphics library Oracle Oracle adaptorFlat File adaptor Flat Files Glyphs

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

22. B. burgdorferi via GenBank proxy

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

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

25. Joining GMOD u Go to www.gmod.org u Examine software matrix u Find a project or suggest new one u Contact Scott Cain: cain@cshl.org –Or mail gmod-dev@lists.sourceforge.netgmod-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 http://www.gmod.org EBI Michele Clamp Stephen Searle Carnegie Institute Sue Rhee Danny Yoo Harvard David Emmert Stan Letovsky