WBConfCall 2013.03.21-Agenda and Minutes

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Deadline for model changes (Wen)

Caltech find it hard to check data

  • Currently only a week between models tagging (Hinxton) and upload.
    • Big model changes/multiple model changes cause problems
    • Encountered lots of problem for WS237
  • Propose that model changes can be finalized one month before the data upload.

HX proposal

To give a 3 week window rather than 1.

Wednesday before the current "Proposal Deadline" call = New deadline for proposals

  • Models should have bee tested by Proposing curators
  • programmers/curators responsible for dumping data and producing upload databases should have been contacted by proposing curator and pipelines should be on the way to being developed for next phase

Thursday Conference call

  • Pre-tagged models in place
  • Summary of models for next release


  • Models testing
    • Hinxton incorporate changes/retractions to proposed models
    • Caltech test/implement citace production code

Thursday Conference call

  • Final tagged models in place
  • Summary of changes in models since last call (Model retractions/changes)

1 week to produce final upload databases (If no modifications from the pre-tagged models then the upload should be ready??)

Models strategy.png

Website release schedule/testing (Todd)

IWM (Karen)

What are the plans?


Model changes deadline


  • Caltech finds it tight


  • Give 3 weeks rather than 1.
  • Hinxton has model proposal deadline, make file available right away
  • Still release final, **final** models one week before deadline


  • seems fine
  • okay for Hinxton?


  • will refuse large changes closer to deadline


  • Agreed

website release schedule (Todd)


  • make things more transparent - development/testing process
  • working this out project-wide
  • Website:
    • development time for new release
    • add testing time
    • Added 'Under testing' label
    • close tickets you think are done
    • diagram available later today

IWM plans (Karen)


  • co-host wiki-pathways session
  • what are the other sessions going to look like?
    • workshop talks? tutorials? room?


  • increase presence
    • more than workshop/couple talks
  • Do 2 workshops on both days
    • day 1: overview & new data, data mining
    • day 2: data mining, wiki-pathways
  • getting space might be hard

Workshop: data mining:

  • JD, intro to intermine
  • any ways to access data from WB
  • ftp, queries, etc


  • coordinate with intermine -- modmine talk?
  • ppl agree that this should be one workshop
  • will contact intermine group, keep PS updated


  • modmine will limit extent of datasets included?


  • pass out sheet with all WB activities during meeting
  • add ad-hoc groups
  • greater visibility, get more feedback

Workshop: Overview:

  • Hinxton coordinate
  • curator led
  • need volunteers - talk on interests/data types
  • all curators interested will email Kevin today with topics

Workshop: Introduction - for complete newbs

  • we should have one - PS


  • April 12 deadline
  • 6min plenary talk?
    • introduce all the workshops/meeting presence
  • plenary talk - Kevin


  • all display our own posters?
  • Have them all up around the booth/helpdesk
  • human disease, spell, pathways, gene expression, website, others
    • decide on topics next few weeks

Site updates


  • QA/QC
    • please test new species/new genome browser tracks
  • begin caching next week
  • JD- intermine, very close to having working mine up


  • Raymond & Chris - fixed gene interaction table dumping script
  • cleaning up ghost objects around
    • cleaner database soon
    • dump citace and reload and check again? -PD
  • Ranjana, looking into omim errors with Wen - today
    • seen some in gene objects in db_info -PD
  • Chris: questions for Kevin
    • rnai mappings - doing coding genes now
    • finalize mapping for transcriptome rather than genome? ideas...


  • Variation - about to receive 800000 new polymorphisms from Moerman group
    • consolidation, lots of redundancy
    • variation will be associated with several strains
  • Raymond: implications in phenotype curation
    • annotate phenotype to allele in context of strain
  • outstanding list of sets to add
    • next release WS238
    • what data are we bringing in? what are users looking for?


no outstanding issues - #978 just came in