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GMOD Update

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. Software Releases. GBrowse (Lincoln Stein)

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GMOD Update

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  1. 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

  2. Software Releases • GBrowse (Lincoln Stein) • Apollo (Mark Gibson & Nomi Harris) • CMap (Ben Faga and Ken Clark) • gmod 0.003 (alpha) (Scott Cain) • LuceGene (a lucene based gbrowse adaptor) (Don Gilbert) • FlashGViewer (Simon Twigger) • blastGraphic (Developers at SGD)

  3. Notable Users • ParameciumDB • NESCent • Gramene (for the HS instructional grant) • Over 150 organizations use GMOD software

  4. 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 0.003 release) (Scott Cain)

  5. New GMOD Web/Demo Site • www.gmod.org 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(?))

  6. To Do: Software releases • GBrowse 1.65: fixes since 1.64 (RSN) • GBrowse 1.66: templates (2nd 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)

  7. Cooperative Agreements • NESCent: Next GMOD meeting there on June 29-30 • Ian Holmes group for GBrowse-AJAX

  8. modENCODE • Submitting a joint grant with UCSC to provide a data center for worm/fly ENCODE projects using a chado database and GMOD tools.

  9. 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 www.gmod.org to gmod.cshl.edu?

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