GMOD Update

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 bridgecan 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?