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You are here: Home Community Minutes Conference Calls 2015 2015-11-10 Tuesday Team Meeting

2015-11-10 Tuesday Team Meeting

Dundee: Petr, Kenny, Mark C, Gus, Jean-Marie, Balaji, Dominik, Graeme, Colin, Helen, Will, Simon, Ola, Roger, Jason, Simone Remote: Andreas, Melissa, Josh M, Ian, Kelli, Eleanor, Sebastien B, David, Curtis, Chris, Emil, Josh B, Stick

Agenda - 2:30pm Start

  1. Accepting minutes from last meeting

    • accepted
  2. Project Timelines (2-3 minutes each)

    1. OMERO - 14:31 UK

      1. 5.2.1 (J-m)
        • new list on board for deployment testing and improving deployment documentation (especially OMERO.web)
        • Josh M will run a docker call tomorrow to help listeners assist with testing CentOS, etc.
        • Gus will help with getting-started documentation for facility managers
        • Ola: sticking to registry deadline as discussed yesterday?
          • Sebastien: possibly not
      2. Metadata (Josh M)
        • focus on pushing OMERO.tables further down the stack (perhaps model, Bio-Formats), may help with localization data, and with a workflow that Eleanor came up with
        • Jason: BBSRC 2013 proposal discusses specific heterogeneous metadata
        • Simon: populate metadata script processes files, Bio-Formats just makes sure they are included in import
        • Josh: will likely need to keep an extra “metadata” branch for breaking Bio-Formats work.
    2. Bio-Formats - 14:38 UK

      1. 5.1.6 (Melissa)
        • PRs frozen, so now testing, release probably next week, next will be 5.2.0
      2. 5.2.0 (Josh M)
        • roi folders discussion (see below)
        • create new repository for C++ reference implementation
        • CI jobs will be rearranged
        • might have to backport breaking changes to Bio-Formats metadata
    3. Registry (Sebastien) - 14:41 UK

      • working with Petr to get to good testing scenario for upgrade checks, now in good shape
    4. Glencoe Update (Chris) - 14:43 UK

      • working on ROIs and annotations
      • Stick working on issues with Python 2.7 on CentOS 6
      • path viewer release coming next month
    5. Repositories - 14:44 UK

      1. Virtual Microscope/teaching
        • no change
      2. IDR Project
        • Eleanor: working on new dataset
        • Eleanor: preparing workshop on using ontologies in IDR
        • Josh M: upgraded server but some issues
        • Simon: copied data from Cambridge
    6. Other consortium timelines (5 minutes) - 14:46 UK

      • Curtis: working on automated list of ImageJ, Fiji plugins with who is responsible for each
      • Curtis: still focus on Java3D and Java 8
      • Curtis: more ImageJ devops help coming
  3. Summary of current Folder proposal (Mark C) - 14:48 UK

    • Folders are in no more than one other Folder (tree structure)
    • any top-level object (ROI, Image, etc.) may be in any number of Folders
    • Folders may replace tag sets, perhaps even someday projects, datasets
    • what should Folders thus be called?
      • Will: folders?
      • Gus: containers? (Colin: used in the code base)
    • comments by the end of this week please
  4. Presentation on Julia by JB - 14:51 UK

    • Jean-Marie: how many people are working on it?
      • Josh B: most central core group is maybe a dozen; development/discussion is on GitHub
    • Roger: can unprivileged users install package dependencies?
      • Josh B: local installation is default (site-wide is possible)
  5. Process for operating system upgrades (Jason) - 15:23 UK

    • new operating systems do not immediately get official support from Dundee / SLS IT
    • best to consult the team before upgrading beyond what is yet supported, or may cause serious problems and block your work
    • perhaps best to initially try upgrades on non-critical machines, as do need to do it before the community hit the problems
    • perhaps best as a coherent, managed process in CI workflow to be more sure how well things still work
    • virtual machines useful for testing
  6. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled) - 15:32 UK

    • multi-modality data submitted by Alan Race (added by PW, motivated by IM)
      • Ian: discussion on ome-devel
      • Ian: how much work to put into this, when? Alan has his own Java code for reading the data.
      • Jason: commercial interest in having the format supported
      • Jason: format is like having mass-spec data for every pixel (lipids, proteins, nucleic acids, drugs, etc.), fairly sparse (masses)
      • Jason: OME-XML model lacks relevant elements, especially in acquisition
      • Emil: will open up a number (~6) other formats. Spectroscopy → Everywhere.
      • Roger: n-dimensional model could help
        • Jean-Marie: modulo c, t was indeed expected to have a limited lifetime
      • Ian: will take a look at data to get an idea of what it is
    • facility managers help/training (Seb/Gus)
      • Sebastien: session in Edinburgh
    • Jason: those on Dundee payroll should have OSAR forms to fill in, do feel free to ask if you have any questions

Done 15:47 UK

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