5/8/06 Scott Cain Stein Lab Retreat, 2006 GMOD Update Progress since last year  Software releases  Notable new users  Schema enhancements  New GMOD.

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Presentation transcript:

5/8/06 Scott Cain Stein Lab Retreat, 2006 GMOD Update Progress since last year  Software releases  Notable new users  Schema enhancements  New GMOD website/Demo site Plans for the coming year  Software releases  Cooperative agreements  modENCODE  Website/Demo site improvements

5/8/06 Scott Cain Stein Lab Retreat, 2006 Software Releases GBrowse (Lincoln Stein) Apollo (Mark Gibson & Nomi Harris) CMap (Ben Faga and Ken Clark) gmod (alpha) (Scott Cain) LuceGene (a lucene based gbrowse adaptor) (Don Gilbert) FlashGViewer (Simon Twigger) blastGraphic (Developers at SGD)

5/8/06 Scott Cain Stein Lab Retreat, 2006 Notable Users ParameciumDB NESCent Gramene (for the HS instructional grant) Over 150 organizations use GMOD software

5/8/06 Scott Cain Stein Lab Retreat, 2006 Schema improvements GODB bridge—can now run AmiGO on Chado (Allen Day) Cleaner separation of genotypes and phenotypes; should make it easier for evolutionary biologists (Chris Mungall) Greatly improved loading tools (over release) (Scott Cain)

5/8/06 Scott Cain Stein Lab Retreat, 2006 New GMOD Web/Demo Site migrated to brebiou from SourceForge.net  Running Drupal CMS Obtained a new demo server (gmod.cshl.edu); currently running a yeast comparative genome database with turnkey, gbrowse, cmap, apollo, and biomart (See poster tomorrow or Thursday(?))

5/8/06 Scott Cain Stein Lab Retreat, 2006 To Do: Software releases GBrowse 1.65: fixes since 1.64 (RSN) GBrowse 1.66: templates (2 nd half 2006) gmod 0.01 (RSN) GMODTools (?, Don Gilbert) gmod-ware (Eric Just at DictyBase) Turnkey (?, Allen Day & Brian O'Connor) CMap 0.16? (RSN) BioPipe (Olivier Arnaiz)

5/8/06 Scott Cain Stein Lab Retreat, 2006 Cooperative Agreements NESCent: Next GMOD meeting there on June Ian Holmes group for GBrowse-AJAX

5/8/06 Scott Cain Stein Lab Retreat, 2006 modENCODE Submitting a joint grant with UCSC to provide a data center for worm/fly ENCODE projects using a chado database and GMOD tools.

5/8/06 Scott Cain Stein Lab Retreat, 2006 Web/Demo Site Improvements I'm pretty happy with the website, but is anybody else? Will run a poll and ask for suggestions. Need to continue to add docs and FAQs. For Demo site:  Add more databases ('reference implementations')  Stabilize turnkey  Provide an 'editable' database to allow Apollo edits?  Make a unified css  Migrate to gmod.cshl.edu?