WebDev 2009.12.09-Agenda and Minutes

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1. Administrative Update (Todd, 10 minutes)

  • Scheduling for next weeks -- regular call 12/16; 12/23; 01/06; -- off 12/30
  • Development deadline -- 12/16

2. Discuss WS209 update status (Norie; 10 minutes)

  • GFF and acedb steps mostly complete
  • Anticipate being complete Friday
  • Changes from Michael
  • Todd will install MySQL 5.1 to match databases from Michael
  • Cleaned up display for the updated disease search

3. GBrowse2 Progress (Abby & Xiaoqi; 10 minutes)


  • links provided below
  • some gene models feature doesn't link properly to details page
  • library conflict occasionally dogs work
  • gbrowse_details need some debugging for some tier III features
  • standardization of displays well underway
  • footer issue
  • toggle header


  • imbedded images, necessary functionalities that enable them to work will be released soon: LS
  • inclusion of protein motif?

Tier I:


http://dev.wormbase.org/db/gb2/gbrowse/c_elegans_gmap/ <-- Does not work in dev or live


Tier II:






Tier III:





  • Nbrowse -- what to do given new db requirements. TH: Grant read-only access to the world for nbrowse db; will contact Mark.

4. Define SAB Goals (All; 10 minutes)

  • GBrowse II Rollout
  • Tier II/Tier III handling
    • some file downloads not working
    • check genome browser linkings
    • matrix needs populating by SAB meeting time -- careful assessment of genome handling
    • we need direct links to Gbrowsers
    • AC still working with config files
    • Gbrowse updated in CPAN
  • Site 2.0 demo

5. WormBase 2.0 installation issues (All; 10 minutes)

  • Questions?
  • AC got test 1 to work, 2nd part not working (starting the test server) -- check hard coded path in config file
  • TH: Report issues on the tracker
  • 5.10.1 required; 5.10.0 has weird bug which is difficult to unravel -- TH to post test script vs. 5.10.0

6. Open Table