Difference between revisions of "WBConfCall 2020.11.05-Agenda and Minutes"

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  Does anyone have anything else for WS280 consideration.
  Does anyone have anything else for WS280 consideration.
== Social Hour? ==
=== Social Hour? ===
== Help Desk ==
== Help Desk ==

Revision as of 17:21, 5 November 2020


  • Welcome to new starter at Hinxton, Archana Singh

WormBase Webinars

  • Anything to discuss after the 1st webinar?

Lessons/Things for next time:

  • Turned off private chat and sound notifications when people join or leave the meeting.
  • Staff should provide full name in the Zoom.
  • Mute all participants but give "co-host" privilege to WB staff members.
  • As "co-hosts" you will be able to unmute yourself.
  • Meeting URL to all registrants 72-48 hours ahead of time (2-3 business days). Since the next webinar is on Monday 9am, it should go out on Wed. or Thurs.
  • Reminder to be sent on Friday evening.
  • Is it possible to have a public-contribute, moderated wiki page for protocols?

Proposal: Tie WormBase releases to the Alliance release schedule

The Alliance makes approximately quarterly data releases. We propose to tie WormBase releases to the Alliance schedule. WormBase releases would precede each Alliance release by (for example) one month. This would allow time to vet the release, deliver data to the Alliance, etc.


  • Further moves WormBase towards integration with the Alliance.
  • Allows for easier synchronized release notation (eg, "WB281-AGR 4.x.x")
  • Reduces WormBase specific effort by one release per annum, which can be redirected to Alliance work.


  • Further slows the given WormBase release cycle.

Release Coordination

  • WS279 released anything for follow-up
Analysis data from CalTech

  • WS280 Release schedule.
  • Two options

1) One more production cycle late 2020 - early 2021 extended because of holiday/site shutdown period.

13th Nov 2020 - Models freeze (2 weeks to adopt this schema version). Need time for models integration see below.
27th Nov 2020 - Data upload to Hinxton
30th Nov 2020 - Acedb production 4 weeks Plus 1 week Datomic migration
15th Jan 2021 - Hinxton production FTP/S3 (Allowing for holiday period and site shutdown)
18th Jan 2021 - OICR staging cycle begins
etc. etc.

2) Have a pause in production to do additional development. Hinxton VEP pipeline integration, Caltech ??

27th Nov 2020 - Models freeze
     Dec 2020 - Data uploaded to Hinxton any time prior to the holidays
04th Jan 2021 - Acedb production 4 weeks Plus 1 week Datomic migration
05th Feb 2021 - Hinxton production FTP/S3 
08th Feb 2021 - OICR staging cycle begins
etc. etc.

WS280 Models can be prepared for either schedule:

3 Changes PD aware of in development:

1) Molecular change additions for Variation::Molecular_change to allow for WB to switch to using VEP inline with AGR data providers (Mark)
2) Simple Species additions for papers and provenance (Kimberly/Paul)
3) SO_term tag addition to fix production bug with loading the processed SO_term file from SO consortia (Paul)
4) To be proposed: new tag in the Relations Ontology class to capture the exact text string to be used in GO GAF 2.2 files (Kimberly/Michael P)

Does anyone have anything else for WS280 consideration.

Social Hour?

Help Desk

  • Please take a look at GitHub issue #7971 and help user
    • I'm looking for specific strains of c. elegans that have calcium sensitive gfp in specific neuron types (DAergic, GABAergic, etc) but I don't know how to filter down to the meaningful strains using the search tool.


Help Desk

User Webinars

  • Will improve upon the past webinar
  • Juancarlos will send the reminder e-mails today and on Sunday, a day before the meeting

Protocol pages for WormBase

  • There has been interest in a protocols collection from users
  • Perhaps have a Wiki page to allow users to add protocols but moderated by WB
  • What about the community worm forum, users to ask questions here, but need something more organized is better
  • How much personnel time is needed? Recruit someone from the community to moderate the page--do protocols work, are the reagents available, and so on.
  • What do other MODs have? Think about in terms of Alliance
  • WormBook page:http://www.wormbook.org/toc_wormmethods.html, this is WB's page, which we can udpate, let users update this and we moderate
  • We can act as brokers for Bioprotocols and protocos I/O fo r
  • Versioning for protocols would be good

Communications to Users

  • Google has a 500 e-mail limit/day, so the outreach e-mail has limitations
  • Todd will take a look, might need to use a e-mail sending service

Tie WormBase releases to the Alliance

  • Sync releases to Alliance?
  • Looks good to funding agencies, easier syncing of data to Alliance, lets us use that effort to do Alliance work
  • Alliance has about 3 releases/year
  • Our Users would have to wait for new data
  • Alliance plans to do data only updates more frequently, possibly data update monthly
  • Maybe users not dialed in too much to the update schedule
  • ZFIN updates everyday
  • Short term take a hit, but have an infrastructure to update data faster
  • Gene sets change every release, so have to do the recomputes, but in the interim we do a lightweight build to update curation data from Caltech
  • OICR will still have to do a full release
  • Model changes have been light, but the web release still takes the same time
  • Plan how much work it would be for Hinxton for a monthly data build