2017-04-04 Tuesday Team Meeting
Dundee: Will, Kenny, Jason, Jean-Marie, June, Balaji, Roger, Helen, Ola, Simon, Simone, Dominik Remote: Eleanor, David, Sebastien, Liz, Chris, Stick, Andreas,
Agenda - 2:00pm Start
Accepting minutes from last meeting
Project Timelines (2-3 minutes each)
Spaces
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Files/Formats/OME Files (Sebastien)
- CMSO mulitmot - coupling imaging and analytical data
- Followup - get experimental metadata files.
- BF- external PR from mpi. Reader addition
- OME-Files - Oxford user consuming OME files
- Minor release soon with features requested by community
- Timeline not set yet, before Dundee meeting would be nice
- JM: meeting workshop on OME-Files?
- Jason: modalities and complexities of imaging acquisition increased a lot since start of OME project.
-
Metadata (Eleanor)
- IDR meeting last week
- Submissions: biostudies submission portal. Met with biostudies.
- Analysis: use-cases discussed, good progress
- Working on two datasets, idr0026 (immunotherapy) and idr0034 (HipSci)
- Release scheduled for next week with idr0026, annotation updates and update deployment with a separate web user
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Next months work
- More datasets.
- Working with BioStudies so they can receive imaging submissions
- Upgrade to jupyter to allow whitelisting users
- Ola - upgrade the version of OMERO used in IDR to 5.3.0
- Simon - calculating WND-CHARM features on more datasets
- Proteasome analysis.
- Preparing presentation for users’ meeting.
-
OMERO 5.3.1
- 5.3.0 Release last week.
- Looking to port useful IDR features back into mainline. Thumbnailing etc.
- Matlab (Balaji) and R (Dominik) for analysis - Users’ meeting prep
- Moving more functionality to OMERO gateway - SPW features
- Jason: showing workflows using full stack, using IDR / big data
- Part of improving data-in, data-out, data-download “the straw”
- Weekly analysis meeting starting on Friday
- JM: web apps pip installable -> Douglas doing same for webtagging
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Outreach
- Josh at Janelia
- Simon and Kenny going to Ansible meeting
-
Files/Formats/OME Files (Sebastien)
Other releases/upgrades:
-
Figure
- Updating release board for using Pypi
- Looking to release on 17th April
-
Iviewer
- Working on ROI permissions
- Will: Adding ROI support to JSON API
- Aim to release first week of May
-
new website
- Started weekly meetings on Mondays
- Updating layout of OMERO section
- Currently deploying via github pages to build & host jekyll site
- JM: will eventually migrate figure.openmicroscopy.org into new site.
- Helen: more content work in progress
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Sysadmin (current board and recent PRs)
- Kenny: separate web VM for 5.3.0 on nightshade
- Need to setup SSL for logins etc.≠
- School need to update to latest Insight before server upgrade
- Specs and deployment firmed up for new nightshade on RHEL 7 VM.
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Glencoe Update (Chris)
- Pathviewer webinar at end of month
- 5.3.0 investigation for pathviewer
- Horizontal scaling with Douglas etal
- Mtools testing and new build needed for nightshade upgrade
-
Figure
User meeting update
- Workshop schedules on gdocs
- Some external workshops
- Tricky to organise 3 sessions]
- Finish with “free-for-all” depending on demand
Reverse OSAR (30-60 mins)
AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled)