WBConfCall 2017-07-20-Agenda and Minutes

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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

Minutes

  • On call: Adam, Chris, Daniela, Gary S., Gary W., 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

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
  • Other new datasets, e.g. gene classes, expanded variation dataset, have been loaded and it would be really helpful to create new templates as these datasets come in
    • Tie new templates into Blog posts to help introduce more people to data mining with InterMine
  • Also, embed templates, programmatically, into the respective widgets to give people access to be pre-canned queries
    • Build an InterMine widget that could be included anywhere?
      • This was done at an InterMine workshop some time ago and it fairly straightforward
    • These could be really helpful for retrieving long lists of data, e.g. all genes with lethal phenotypes
  • Are single gene queries better served from Datomic?
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