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

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

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

GMOD Home Page

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

Apollo – BDGP & Sanger Center

PubSearch – TAIR & RatDB

CMap – Gramene

Cmap – Multiple Maps

GBrowse – WormBase

GBrowse – Zoomed In

GBrowse – Zoomed Way In

GBrowse – Zoomed Way Way In

GBrowse – Keyword Search

GBrowse – Reports

GBrowse – Third Party Annotations

GBrowse – Multilanguage Support

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.

Adding a New Track (a) Create a GFF file named “deletions.gff” Chr1 targeted deletion Deletion d101k2 Chr1 targeted deletion Deletion d680k2 Chr2 targeted deletion 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 = citation = These are deletion knockouts produced by the example knockout consortium (

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

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

B. burgdorferi via GenBank proxy

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)

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

Joining GMOD u Go to u Examine software matrix u Find a project or suggest new one u Contact Scott Cain: –Or mail

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