WebDev 2010.05.19-Agenda and Minutes

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1. Administration update (Todd; 5 minutes)

  • almost all services now migrated to OICR
  • servers giving good performance
  • leaner architecture

2. modENCODE status (Xiaoqi; 10 minutes)

  • slow software, try 2.08 version (LS)
  • test in dev
  • try MySQL optimization

3. Biomart progress (Abby; 10 minutes)

  • Biomart WS210 building, slow
  • Port 80 for the Biomart site -- problematic; works with 8080
  • To discuss issues with folks @ OICR, esp. Joseph.

4. WS214 status & WS215 pipeline goals (Norie; 10 minutes)

  • position matrix restore for WS214
  • for WS215: GFF-MySQL, additional ontology search data

5. API progress (Xiaoqi, Norie, Todd, 5 minutes)

  • Strains, Interactions developed and tested; working on Anatomy_ontology, Gene_ontology, Person (NBC)
  • DB connectivity, evidence method (XS)
  • Variation (nearly done) and Paper (25%) (TH)

6. Open table

Aligner and exact search problem in gbrowse2 (Abby)

Made changes to Bio::Graphics::Browser2::Region.pm

  • wasn't searching through automatic classes for exact search - failing for Bio::DB::GFF.
  • changed in dev, aligner and exact search work there

Search demo (Abby)

http://dev.wormbase.org:9010/ --home page

http://dev.wormbase.org:9010/search/gene/lin-5* --multiple hit example

If there's time and/or you want explanations of code I added:

  • Search box triggers action to Search controller:


  • Controller accesses Search object from API:



  • Search object returns list of Search::Result objects:


  • results.tt2 template renders the Search::Result objects: