WormBase-Caltech Weekly Calls

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Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

GoToMeeting link: https://www.gotomeet.me/wormbase1

2018 Meetings






June 7, 2018

Alliance literature pipeline working group

  • Has anyone gotten back to Carol Bult about WB/Textpresso membership in the group? Not yet
  • Paul & Kimberly can join; Kimberly will sit in on group meetings

SPELL migration

  • SGD put SPELL into the cloud; will give us code to set up WB SPELL in cloud
  • Want to have common interface but two instances (yeast & worm)
  • Worm data in SPELL may be more complicated than the yeast data (different species, platforms, meta data, etc.)
  • Mike Cherry proposed to use GTEx to replace SPELL. (www.gtexportal.org)
  • Trying to get GTEX to have same functionality as SPELL

Progress report

  • Wen can generate numbers of changes since last year
  • 5-year progress report coming up (for funding agencies)
  • Want a progress report-like document to give to SAB in July
  • WS259 - WS265

Paper author name

Lab class

  • Lab data is not clean/consistent; has gotten messy
  • Cecilia trying to clean it up
  • There is conflicting data from lab class, author class, and person class
  • Currently there is a ~redundant curation pipeline; considering pulling person info into lab class
  • When looking at lab page, if there is a problem with a person's info, changes would be made (requested) in the person class, not the lab class
  • Cecilia will contact labs to ask about correctness of information
  • Can have a discussion with Ann and Aric at CGC

How many C. elegans genes have "good" knockouts?

  • Paul giving talk next week, wants to report
  • Chris will look into
  • Mitani did 1,000 deletions in last year

Server logs

  • SimpleMine logs are all coming from Amazon; will need to ask Todd about SimpleMine usage (from AWS stats?)

Migration of lab data

  • Data for labs was coming from Name Server (in Hinxton) - Comment:[PD] Not coming from the Name Server, geneace was the only source of Lab data prior to handover.
  • Now Paul D has stopped curating lab info - Comment:[PD] Build config has been updated to take the majority of lab data from citace rather than geneace
  • Now that Cecilia is curating, will pull lab info from Postgres