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You are here: Home Community Minutes Conference Calls 2016 2016-03-08 Tuesday Team Meeting

2016-03-08 Tuesday Team Meeting

Dundee: Jean-Marie, Dominik, Petr, June, Helen, Chris, (15:22) Mark, Will, Gus Remote: Josh, Seb, Stick, Colin, Kelli, Melissa, David, Eleanor, Liza, Roger, David

Agenda - 3:00pm Start

  1. Accepting minutes from last meeting

  2. Project Timelines (2-3 minutes each)

    1. Spaces

      1. Mainline (J-m)

        • Front-facing work on the metadata front, incl. Tagging & search
        • Support for Ice 3.6. Still waiting on release from ZeroC. Will have our CI infrastructure & doc in place for when that happens. (Possible to build from source regardless)
        • Few cards to add.
        • Helen: nothing particular on the doc front
          • Old Ice 3.6 PR that could be resurrected.
          • Several deployment/installation issues that were moved from docs-comms.
        • J-m: need mechanism to test all the scripts, similar to update of all the webapps.
        • J-m: to-be-combined with 5.1.9
        • Seb: within roughly 1 month. Batch of bugfixes among the last before 5.2.0. Board & trac cleaned. Melissa left as owner only when concretely on her radar. < 2 dozen unassigned. Annotated by Melissa. Candidates (though not blockers) for 5.1.9.
          • 9 unassigned
        • J-m: 5.2.3 targeted for the end of April.
      2. Model (Sebastien)

        • 5.2.0-m3 -- bug fixes (before backporting to 5.1.9) as well as DB changes based on the design issues
        • Finish client-side work based on Dom’s changes as well as defining the API for folders (incl. Export, Graphs, etc.)
        • Start ramping up on the documentation so it’s not all last minute.
        • Keep using the regions devspace for m3; hopefully move to the mainline afterwards.
      3. Metadata (Josh)

        • Hardware adjustments on IDR infrastructure - Metadata52 offline
        • Deadline (Mar 14) to get WND-CHARM feature calculations working
        • Server EBI migration hopefully mid-April. Impact on URLs
        • Eleanor: attended CMSO remotely. Linking screen compounds. Gathering information on recording information about studies (ISATab)
        • JM: linking? Eleanor: some studies (Broad) don’t have names. Looked into unique IDs for compounds. Might have metadata tags.
        • Report on CMSO & thoughts on OME-Files (+10 min) (at the end)
    2. Other releases/upgrades:

      1. Figure
        • J-m: No movement at the moment. Few bug fixes.
        • Would like to push a release due to Pillow version bump.
      2. FLIMfit/OPT (Ian)
        • FLIMfit 5.2 RC delayed by problems with Windows build - OSX version looks good.
        • Ideally time release to follow (very shortly) BF 5.1.9
        • Helen: Gus has a card regarding email.
        • Petr: got an email from Ian regarding improving the scenario.
        • Seb: good to have a driving card since the board is closed. Cost of maintaining infrastructure.
      3. ImageJ
        • Discussion on tables tabled.
      4. Learning: see last week’s report re: demo.
      5. Sysadmin
        • Few lessons about upgrading OMERO servers. Result: doc PRs to benefit the community
        • General system cleanup / configuration (based on ansible) underway.
        • Ice 3.6 will likely live on beluga (with * DNS)
        • Need some downtime for regions-ci. Seb: discussions tomorrow may be the perfect window.
    3. Glencoe Update (Chris) - 15:21 UK

      • Planning the next stages of OMERO fixes. Mostly in web arena, especially with a focus on metadata on images and the querying thereof.
      • Neither of the clients are good at finding things (they currently focus on aggregating and structuring for display). Work to focus on API as well as UI/querying.
      • Previously an issue with PathViewer, but more of an issue now with the greater web infrastructure.
      • Focusing attention as well on very large datasets in Bio-Formats (taking a significant portion of Melissa’s time)
  3. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled)

    • Dundee meeting (June): working on registration. Nothing immediate.
    • Kenny/Simon: Floss UK next week (TWR). Presentation? Like to do a lightning talk if possible.
    • CMSO report
      • MultiMOT Grant for bringing together 6 workgroups: building standard organization, implementing it, performing wetlab experiments, writing document according to the standards, performing analysis and storing in a repository
      • OME role: Bio-Formats
      • Meeting was about the standard organization
      • Minimal Requirements (+ Controlled vocabulary) w/ Eleanor
      • Formats & API
      • Started from a single concept encompassing everything (from experiment to analysis). Moved back to individual components/boxes.
      • Experimental covered by ISA-tab
      • Narrowed down to Positions / working towards a format specification that OME could support
      • Looking at Eleanor’s IDR model of metadata
      • Work towards defining extension points in the model that could address problems similar to the Micro-Manager JSON thread for e.g. tabular data etc
      • Mark: role of ExternalInfo/LSID? (Never seen anyone use them). PDF link from Jason Josh: how to link the files? Currently use UUID in every file. CMSO: use a server to resolve the linking.
      • Chris: pb with ExternalInfo is relevance given its infinite scope. Using it to link to other systems. But can’t have multiple step resolution, can’t rely on external resolution.
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