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You are here: Home Community Minutes Conference Calls 2016 2016-11-29 Tuesday Team Meeting

2016-11-29 Tuesday Team Meeting

Dundee:Petr, J-m, Mark, Roger, Jason, Graeme, Balaji, June, Simone, Gus, Helen, Dom, Ola, Chris, David Walker Remote: Sebastien, Josh, Eleanor, Andreas, Melissa, David, Emil, Will (14:15+)

Dundee:Petr, J-m, Mark, Roger, Jason, Graeme, Balaji, June, Simone, Gus, Helen, Dom, Ola, Chris, David Walker Remote: Sebastien, Josh, Eleanor, Andreas, Melissa, David, Emil, Will (14:15+)

Agenda - 2:00pm Start

  1. Accepting minutes from last meeting

  2. Project Timelines (2-3 minutes each)

    1. Spaces
      1. Files/Formats/OME Files (Sebastien)
        1. Full rebuild of C++ binaries due to libtiff secvuln 1 First time; good test. Went well.
        2. Bio-Formats 5.3.0: closing last milestone
          1. Tiling: need final set of fixes & unit tests (samples, etc)
          2. Options: good to have final review and get it in tomorrow to start driving use cases
        3. OME-Files 0.3.0 to focus on extending current support for heterogeneous metadata
          1. Related to upcoming MULTIMOT meeting (Dec 12/13)
          2. Discussing Roger’s proposal at the meeting tomorrow
        4. Roger: have fixes for transform issues
      2. Metadata (Josh)
        1. Jason: IDR paper out
        2. More below.
      3. OMERO 5.3.0
        1. 5.3.0-m6 available (OMERO+jpegxr)
          1. Jason: write to the lists? Was originally requested on IRC (#ome)
          2. Seb: would need to associate all the caveats
          3. Jason: another group in Australia
          4. J-m: could contact a few directly.
          5. Chris: danger of confusion
        2. Work on testlib to make integration tests possible in other repositories
        3. Discussion Thursday 10 UK on proposed deprecations (sharing, etc)
        4. Plan for upgrading nightshade to CentOS 7 so C6 can be dropped
        5. Java 1.8 bump will require testing for MATLAB. Do workarounds exist?
          1. Chris: recognizing other ecosystems.
      4. Outreach
        1. neubias deadline end of the week
        2. mmc2017 Abstract submission opened
    2. Other releases/upgrades: 14:17 UK
      1. Figure
        1. Number of cleanup PRs (other web apps as well)
      2. Learning
        1. Holiday down time
      3. Sysadmin
        1. Cowfish getting RAM’ed
        2. Suggestion to have another OpenStack training dedicated to production (features like snapshots etc). Potentially in the context of nightshade.
      4. Website redevelopment/redesign (Liza)
      5. Smuggler (Montpellier)
      6. viewer
        1. Rename issue short list prefix OMERO.: discovery, vision, view, phase, imageviewer (IV)
    3. Glencoe Update (Chris)
      1. David Walker: PhD student involved with the NPSC project.
      2. Trying to finish a few issues before beginning scalability work.
      3. Elasticsearch experiment:
        1. Not yet highly installable
        2. Has pointed to a number of undocumented features
      4. Final contractual details before commencing Read Only Phase II, Service Routing work
  3. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled)

  4. walkthrough of the IDR by Josh

    1. The Mega-scenario
      1. Deployment
      2. Infrastructure repo too complex for newcomers. Not a good starting point but contains deployment sources
        1. IDR/deployment as the entry point
        2. Spinning up IDR deploys 8-9 instances at once
          1. Single proxy (nginx + ssh), 2 servers (1 for analysis) with 2 databases
          2. Deployment of IDR 0.3.1 will involve spinning the whole stack and switching IP addresses. No downtime
          3. Identical stack copy at UoD. Good place for experimentation
      3. EuroBioImaging encountered issue with caching. PhenoImageShare also walked images and collecting thumbnails
        1. Need to keep system up and running for others
      4. 0.3.2: rendering. Requires tools to check everything has been updated.
      5. IDR landing page (Jekyll)
        1. Includes virtual analysis environments. IDR notebooks capture and make IDR work available. Includes IPNBs to reproduce figures in paper.
      6. Walk through of mapr
      7. Future - search (combining searches e.g. images with certain gene plus phenotype, images in screenX with no annotation), import/background annotating, making use of feature data
      8. Jason: “mini-IDRs” for testing. J-m: similar to request from training.
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