WebDev 2013.06.03-Agenda and Minutes

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Review minutes of 31 May 2013 (all; 5 minutes)

Administrative notes (TH; 5 minutes)

IWM - next week look through presentations

    • prepare slides and share with comrades

schedule time (Friday meeting?) to review presentations as a group.

Discuss WS238 development status (all; 10 minutes)

  • GBrowse work
  • finished most issues

Pre-baking site

  • faster with data
    • found slow widgets - target for optimization
    • found errors (ncRNAs - sequences, others)

GBrowse - JB

  • Kevin looked at all the tracks
    • mostly good except for things Kevin is reporting
    • elegans ESTs -> problem with aggregator?, not sure
    • config he wrote is good - but work wasn't very coordinated
      • Kevin finished work
  • automate the test - retrieve gbrowse image files, diff the image (imagemagik)

Define WS238/WS239 objectives (all; 10 minutes)

Bit of a breather before WS239.

  • expand test suite - current tests obsolete (JB)
    • also GBrowse testing
  • optimization - some ares are more computationally intensive (AC)
    • change our pre-baking strategy to generate slowest first
    • have logs of bugs/times
  • improving error handling, reporting
    • make it easier to trap errors - where/why?
  • REST api
    • documentation on web
      • needs formatting
    • adopt standards
  • Graph databases comparison

Discuss Intermine progress; define critical blocking issues (JD; 10 minutes)

Main blocker: server issues (running out of resources)

    • 2nd server should be up soon
    • many issues are hinging on the new built

Asking curators for descriptions, summary view.

  • Will we have time to address all these issues before IWM?

What features will we demo at IWM?

  • templates (use cases)
    • available on alpha mine
    • make an effort to standardize grammar/format of descriptions/names (ask Chris?)
  • some features may have to be taken out of the beta release


  • header/footer - next week
  • login - revisit next week
    • if not feasible,


  • acceptance tests - look at this next week

Discuss mobile app (AC; 10 minutes)

  • Antonio Marino - GSoC
    • unable to attend today's call due to prior commitments, but will attend future calls
  • WormBase/website-mobile on github

Upcoming milestones (TH; 5 minutes)


  • begin exploration of genome browser options (JB)
    • tough call to find a good alternative (GBrowse is very feature complete)
    • most other browsers, flashier, but not as feature rich
    • Genome Maps - from Spain (suggestion from LS)
  • reignite discussion of possible backends for website (AC, JB, TH)
    • may want to engage build team
    • graph databases meetup
  • adopt PM tool for clearer tracking of tasks, milestones and resources (TH)
    • formalize time management (239)


  • community survey (AC, TH)
    • collect more feedback
  • complete cloud migration (TH)
  • full launch of intermine with WS240 (JD)

Open Table