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 0.003 (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 0.003

release) (Scott Cain)

5/8/06

Scott Cain

Stein Lab Retreat, 2006

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(?))

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 (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)

5/8/06

Scott Cain

Stein Lab Retreat, 2006

Cooperative Agreements

NESCent: Next GMOD meeting there on June 29-

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