tags: Tuesday —

2025-04-22

Attending: Will, Josh, Dom, Petr, Khaled, J-m, Melissa, Kyle, Frances, Chris, Andreas, Chris MacLeod, Jason, Erin, Seb,

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

(2-3 minutes each)

• IDR Frances:
  • prod127 ongoing, estimate release end of month
  • Updating download instructions for various studies
• OMERO
  • QA not working - DNS issue? - solved
  • no web meeting last week (holiday)
• Bio-Formats Melissa
  • Repository tests updates: Promising infrastructure in place. Nightly running time of about 4 hours on all the data with logs comparable to those from Jenkins. Logs uploaded to s3, including times for various batches of tests.
  • Should be able to start merging PRs by end of the week
  • JM: Great!
  • Seb: need to decide on format of logs. E.g. 1 zip etc. depends on how we want to consume them
  • currently viewable at https://open.quiltdata.com/b/bf-testing-results/tree/2025-04-22/
  • Josh: might be some permissions issues on some files
    • 4.7 TB of test data in total
    • Testing same testing bash script in Munster, but running much slower.
  • Seb: doesn’t have to be only Glencoe running this. Scripts etc are managed via Github. Full curated data repository only available to Glencoe and OME (current statu quo).
  • Seb: tests don’t need to be super-fast, as long as they run “overnight”. E.g. max of ~7hrs.
• NGFF
  • Zarr spec 3.1 “tagged”. https://github.com/zarr-developers/zarr-extensions being prepared now.
    • Next step will be re-vamping ZEP0000
    • Can now register extensions
  • 0.6.dev1 in the works: https://github.com/joshmoore/ngff/commit/878e15c550b4b71a3b0d7e690ce64dd91d963ca6
    • sample data: https://imagesc.zulipchat.com/#narrow/channel/328251-NGFF/topic/Transforms.20examples.20for.20RFC-5
    • some bugs around RFC-6
    • schema naming, e.g. coordinateTransformations.schema vv coodinate_transformation.schema
• GerBI
  • Josh: Workshop package: galaxy, ELN etc to deploy on Hive for workshops
• Glencoe
  • meetings coming up (see previous notes)
• Community
  • OME About Pages (Jason):
    • e.g., Teams, Commercial
    • Feedback please on anything that needs fixing?
  • BINA OME Meeting Update
    • expect ~60 attendees
    • Program
    • Janelia, Allen etc attending
    • Follow-up hackathon at Broad (1 day)

AOB

- April 29, BINA OME Meeting, several people out.

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

Main Topic

(20-25 minutes plus 15 minutes questions max)