2010.05 OICR WebDev Meeting

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Meeting summary


  • Abby: built WS205, migrated to new biomart machine


  • Abby: might be some configuration problems with Apache
  • TH: setting up as subdomain, virtual host

Development Update Pipeline

  • Norie: added support for mirroring pre-prepared GFF mysql databases fom Sanger


  • Continue update to WS214
  • GFF MySQL code to be tested with WS215


  • Xiaoqi: migrated current modENCODE data to production
  • Emailed dev list
  • Added caveat


  • Need to copy over configuration stanzas to production configuration files
    • GBrowse-1.70
    • GBrowse-2.03


  • Debugged various plugin issues
  • SequenceDumper.pm and FastaDumper.pm issues


  • add initial landmark config
  • set up GBrowse 1.x @ OICR and update proxy
  • XQ: Ensure feature parity between GB1/GB2
  • Resolve preservation of track selection prefs problem
  • TH: Karyotype hosting?
  • resolve keyword searching issue (ie unc-9)
  • Sanger: nucleosome data


  • TH: migrate wiki, forums, blog
    • added subdomains
    • update urchin tracking
    • updated proxy config
    • added 301 redirects
    • update index.html
  • TH: added analytics for subdomains
  • TH: Cleaned up calendar on Wiki; embedded google calendar; added events


  • TH: modify hostnames to reflect purpose
  • TH: backups/crises recovery plan
  • TH : wormbase infrastructre doc
  • migrate aceserver
    • wb-blast
    • perl 5.10.1
    • modules
    • acedb
  • TH: set up QA/QC testing schedule
  • Set up dev environment for new site


Database Connectivity

  • Xiaoqi: converting from lock based method to one checking status
  • Xiaoqi: code done next week or so.


  • Standardized data structure
  • Expanded class coverage
  • Norie working on additional classes


  • TH: prioritize order in which classes/pages should be converted.
    • Gene (NdlC)
    • Protein (XQ)
    • Variation (TH)
    • Sequence (XQ)
    • Person (TH)
    • Paper (XQ)
    • Strain (NdlC)



  • TH:to establish dev environment

Visit goals

  • Benchmarks
  • Tests
  • Documentation
  • Sanger Databases
  • Issue Tracker issues
  • OICR aceserver