2018-06-19

Dundee: Will, Petr, Simon, Mark, Kenny, Riad, June, Jason

Remote: Josh, Seb, Chris, Andreas, Jean-marie, Melissa, Emil, David, Wilma, Liza

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• Summer epics

  • Monitoring (Simon)

    • Prometheus running locally, deciding deployment strategy

    • pub-omero “test case, demo-like” being monitored, agent

      installed

    • Deploy of prometheus to kubernetes monitoring demo this week

    • Downtime to be arranged for Nightshade next week to allow

      install and restart

  • Formats (Seb)

    • Bio-Formats 5.9.0: minor release i.e. including reader fixes

      with no memoization breakages. Candidate for inclusion in OMERO 5.4.7

    • KLB reader (IDR dataset): ongoing progress on the reading of

      the format. Initial work on orthogonal projections promising. Looking into the complete multi-dimensional image next. Test a 1TB file next.

    • Pyramid TIFF: pushed to an upcoming minor release of

      Bio-Formats. Current limitation is the Java writing.

  • TOPIM

    (Board, JM)

    • Plan is to use:

      • Users meeting workshop (import section replaced by

        slides) (data idr0021)

      • Orbit-OMERO. Good progress see

        g.doc for steps. To be shown to Manuel Stritt (data SVS under downloads.openmicroscopy.

        • Demo planned.
      • CellProfiler (notebook) plate from idr0002

    • Infra:

      • No answer cf network i.e. tadpole (issue with pytables)

        vs outreach

      • Running a production server on tadpole is becoming

        problematic

        • JRS: Mac Minis == bad place to be - becoming barely

          usable

        • 4G modem is the backup option

      • Intel NUCs as an alternative

      • (Linux) Laptop potentially an option, portability

        priority

  • Import (Mark)

    • Background: at present importing 1000s of files at once is

      slow

    • Dom: opened simplified UI for large imports

    • Mark: Reviewed detail of server-side import process with

      focus on noting duration of substeps. Next to implement simple benchmarking code for reporting on performance of imports.

    • Riad: investigating “skip=thumbs” UI for insight

• Glencoe

  • Preparing for a 200 student educational deployment, includes

    microservice improvements and load testing

  • Developing/documenting organisational policies for workflows

    (e.g. how security issues are handled)

• Community

  • Meetings at EBI:

    • July 2 PM: HCA/IDR

    • July 3 AM: BioStudies/IDR

    • Involves full-stack discussions

    • Dovetailing outreach work with

      http://itr.openmicroscopy.org/

  • HCA (Josh)

    • Picking short-term goals.

    • NB: use of

      zarr (issue) and xarray (issue)

    • Looking for a format that can support unregistered tiled

      images without restricting freedom of HCA developers to make changes to their processing workflows

    • Proposing to develop an interoperable validation compliance

      tool based on BioFormats

    • HCA has a very strong Python (imaging) community

    • Matterbridge (interoperable chat)

      • Matterbridge app supports up to NxN interchange of

        multiple chat platforms

      • New #gitter room on slack is incoming-only (to slack,

        from gitter)

      • Could be a useful tool for tracking external slack

        channels

  • World tour being planned

1. AOB

(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)

• A word about PRs

  • JRS: process was devised when we had fewer external inputs
• Another (ci-master) Jenkins downtime Wed late afternoon circa 1630

  (UK)

• Update on OME Team Contracts & Grants

  • Several grant applications in progress (rough ETA Sept)

  • UKRI is investing in long-term research infrastructure (one of

    which is OME)

1. Main Topic

(20-25 minutes plus 15 minutes questions max)