WBConfCall 2017-07-20-Agenda and Minutes

Agenda

Release Announcements

• maybe we can restart announcing our releases outside of staff@wormbase

WS260 Website Release

• Possibility to delay WS260 website release to Aug 25 (currently scheduled at Aug 4)?

New Datomic Widgets on Staging

• Testing needed for:
  • construct (Karen - responded)
  • interaction (Chris)
  • pcr_product (Hinxton)
  • phenotype (Chris)
  • paper (Kimberly - responded)
  • position_matrix (Raymond)
  • pseudogene (Hinxton)
  • rearrangment (Raymond, Mary Ann?)

Open Help Desk Tickets

• Need to get additional Phenotype association data into WormMine
  • Paul D. answered, but the user was looking for RNAi data in WormMine - a known issue
• Hello, I'm trying to access a paper c...
  • Karen and Paul D. answered - Karen is looking into the construct data
• Can't find the gene info reported in any of the pa...
  • Kimberly answered - need confirmation from Daniela
• Is there somewhere a good explanation of the features in the genome browser?
  • Gary answered - any more we need to do either with display or explanation?

Minutes

• On call: Adam, Chris, Daniela, Gary, Juancarlos, Karen, Kevin, Kimberly, Michael P., Paolo, Paul S., Ranjana, Raymond, Scott, Sibyl, Todd

Release Announcements

• In response to some user feedback at the worm meeting, shall we announce our releases outside of WB staff?
• Ideas:
  • Blog
    • Rotate turns on the blog?
    • Blog could link to the more detailed report of release statistics
    • Rotate authorship between Hinxton and Caltech
    • The blog post doesn't have to strictly correspond to the release date, but would record the release date for reference
  • Forum
  • Mailing lists
    • wormbase-announce
    • should resurrect the announce list
  • Website banner
• Whatever we decide, this would need to be initiated by OICR
• Suggestions for release email
  • Make the email more of a narrative with a link to the statistics, lists
  • For the narrative, capture what has been accomplished, substantially, in the latest release
    • Provisional version could be posted for comments
• How critical is it for people to know the exact date the release is made live?
  • It is important for people to cite/note versions that they searched
• Is there a REST endpoint for determining exactly when a release went live?
  • Todd will look into this; may exist, but if not, can be easily made

WS260 Website Release

• May need to be delayed for three weeks past scheduled date
• Why?
  • Datomic database was not available until yesterday
    • Datomic database is not available until after the official ACeDB release
    • Datomic has only recently been considered formally part of the production cycle
    • The web developers need a full development cycle to test Datomic, though
  • Also noticing some unresponsiveness on the website
    • Would like time to track down and address the problem
• WS261 is nearly done, though
• Should we then delay the upload for WS262 or we will be in perpetual catch-up mode
• Todd suggests we push all releases back
• Kevin proposes a slightly longer, five-week build cycle to accommodate having to build Datomic database, as well as ACeDB
  • This proposes that we move the data upload one week ahead; the overall cycle would still be eight weeks
  • One week is enough to build Datomic?
  • But there are still some problems with the data models in Datomic and we can't predict what these issues might be
• Should the release letter (currently sent out) be coordinated with the ACeDB or Datomic database build?
  • Who needs to be alerted to the release?
  • Doesn't appear to affect Raymond who use automated SOPs to check ftp site daily
  • Ranjana likes to know when the files are available for the automated description pipeline
• Matt implemented a Slack-based reporting system that reports the build stages
• The release notes could be converted to a parseable format, e.g. JSON, that allows people to mine for reports
  • Retrofit old release notes?
    • For now, won't retrofit, but if needed could be done in the future
• Summary:
  • WS260 will be delayed until August 25th
  • WS261 will be released two month after that
  • WS262 will follow the same two-month cycle, but upload will be a week earlier to begin to accommodate the five-week build cycle (may need to re-visit this)

New Datomic Widgets on Staging

• Adam needs people to test
• Testing needed for:
  • construct (Karen - responded)
  • interaction (Chris)
  • pcr_product (Hinxton)
  • phenotype (Chris)
  • paper (Kimberly - responded)
  • position_matrix (Raymond)
  • pseudogene (Hinxton)
  • rearrangment (Raymond, Mary Ann?)

Open Help Desk Tickets

• Can't find the gene info reported in any of the pa...
  • Kimberly answered - need confirmation from Daniela
  • Atomized evidence in automated descriptions
• Is there somewhere a good explanation of the features in the genome browser?
  • Gary answered - any more we need to do either with display or explanation?
  • Scott will take a look at the ticket to see what might be done here to help, e.g. tutorials

Genomic Coordinates between Releases

• Do the coordinates change between releases?
• If there's a new assembly (e.g. different Ce versions), there may be new coordinates

WormMine Update

• Paolo has WormMine at the point where new data can be added reliably
• WormMine builds are more reliable, robust, stable
• Paolo will solicit suggestions for other data to add; also feel free to contact him directly
• WS260 will have Strains
• Chris and Paolo going over RNAi data; still a few issues to be worked out here
• Chris is also discussing adding Anatomy and Phenotype ontologies so users can perform is_a descendant queries for these ontologies analogous to what can be done with GO
  • For Anatomy, will also want to include part_of searches
  • Adding new obo files is actually fairly straightforward, but Paolo is working with InterMine developers to make sure all entities associated with an ontology term can be retrieved