WebDev 2011.12.07-Agenda and Minutes

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1. Administrative Update (Todd, 5 minutes)

  • 228 still not out
    • delayed by a week - problems at oicr
  • staging 229 now
    • few more steps - done in next few hours
    • compiling flat files - watching out for id -> association counts
    • AC will push new Xapian index script
  • progress with systems

2. Update from Lincoln! (10 minutes)

  • Nothing to discuss
  • Change to VMs - feedback from TH
    • Storage upgrade this weekend (TH)
      • VMs seem stable - old vms had high cpu load doing nothing
      • improved (some transient problems)
      • changes made to several servers
      • plans to move to debian 6 (upgrade from debian 5)

3. App/UI development update (Abby; 10 minutes)

  • Protein Call Summary - see action items email from Chris
  • Xapian update
    • index common names for go_term, anatomy_term

4. GBrowse and UI development update (Xiaoqi; 10 minutes)

  • WormBase ontology browser (xshi.wormbase.org/tools/ontology_browser)
    • added descriptions
    • TH - paged results: have tabbed file download
    • number of associations per term - useful?
      • will need to retain flat files to display
      • TH: not worth effort now
  • Adding 2 new species to WS229
    • add gbrowse config for these
  • Protein call - schematic image not working
    • Catalyst::View::GD module out of date
    • will look into this more
  • Will look into interaction and orthology flat files

5. AceCouch development (Adrian; 10 minutes)

  • Couch is behaving very well now (magic?)
    • moving on to database compaction (save 10G)
    • API - works mostly, some problems moving through the tree (right, at, etc..)
      • no inherent ordering in AceCouch because of how data loaded
      • LS - right often used where col would work. Try replacing. Same with at.
      • can either restructure data going into couch or emulate right
        • try emulation

6. Crisis Management Plan (Todd; 10 minutes)

  • http://wiki.wormbase.org/index.php/Crises_Recovery_Plan
  • LS: should be moved to google doc or something independent of structure
    • on WormBase.org doc
  • companion doc: structure
  • giving access to cloud resources
  • discussion on what our policy is when things happen - rotate? shifts?

7. Open Table

  • LS: Version 1.44 of gbrowse - performance improvement, bug fixes
    • not out on cpan yet - git version
    • prefork optimum performance with gbrowse