WBConfCall 2015.12.03-Agenda and Minutes

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SAB (4th-5th Feb 2016, Caltech)

  • There is a page for the SAB here
  • Accommodation: should non-Caltech folks arrange their own accommodation?
  • Flying dates: should all/most be present on Weds 3rd Feb for pre-SAB activities? Ideas:
    • Project-wide planning meeting (practice talks etc)
    • Smaller working groups to discuss specific topics (add your ideas below)
  • Agenda
    • We should start thinking about one
    • Do we know the complete list of advisors yet?
  • WS253 data upload: should we postpone the upload deadline until after SAB?
    • Hinxton: yes


WormBase Survey

  • Has anyone had a chance to look over the survey results?
  • If so, are there issues in the survey results that we should address for the SAB?



  • Non-Caltech people should probably contact Sarah which will take care of arranging the accomodation for the SAB.

SAB pre-meeting

  • It would be a good idea to have a pre-SAB meeting on the 3rd, but Todd can only make the afternoon.
  • Most of Hinxton will be arriving late on the 2nd and leaving on the Sunday.
  • Discussing the Datomic migration appears to be a popular topic for the pre-SAB meeting.
  • Raymond: we should have a focus to the SAB meeting like collaborative efforts with other mods.

SAB agenda

  • Raymond: we should have a focus to the SAB meeting like collaborative efforts with other mods.
  • Todd: we should think about how we can justify our funding.
  • Chris: we need to tailor our discussions with the SAB advisors to their fields of expertese.
  • Paul Sternberg mailed a list of advisors that included: Jason Stajich, Mike Cherry (probably) and Brian Oliver.

WS253 data upload

  • Postponing the upload until after the SAB is popular. People don't want to have to rush things with Xmas and the SAB taking up their time.


  • One outstanding query about the chromosome map tool. Sybil says that she will discuss things with the Intermine developer to get a list of gene positions to quickly draw the graphs.

= WormBase Survey

  • Todd gave a quick summary of the response to the survey. The main point of concern appears to be the response to WormMine.
  • [1]
  • We should do more tutorials and outreach about WormMine.
  • There is a new user interface to Intermine coming in 2016.
  • Todd says that WormMart will be retired at the end of this month.
  • People are not using WormMart heavily.
  • It was suggested that Parasite WormMart be added to the Tolls menu on the website, but Todd explained that the new WormMine will have a range or new features that will cover what people are currently using Parasite WormMart for.

Pre-SAB discussion : Datomic

  • Adam is making great progress in getting the Datomic database ready for driving the site.
  • ACeDB will certainly be used for at least the next year.
  • It makes sense to have curation use ACeDB for the time being.
  • Discussion of how model changes would work when using Datomic.
  • Raymond would prefer to see parallel running of the two systems for some time while problems are sorted out.
  • Todd: It is not worth people sitting down and learning Datomic yet.
  • Adam described his work on Docker to help set up a local copy of the database, including the website user inteface.
  • Chris: it would be great if this could be used by WormBase end users.

Idea scratch-pad for potential pre-SAB discussion topics

  • Curation, organisation, display and querying of RNASeq data (FlyBase have moved ahead of us here)
  • Database migration
  • Deconvolution of parasitic data (could discuss cross-referencing/linking between WB and WBPS for core species, cross-searching over the two resources, etc.)