2016-02-02 Tuesday Team Meeting
Dundee: Kenny, Mark, Petr, Dominik, Colin, June, Simon, Will, Jean-Marie, Balaji, Roger, Jason, Simone Remote: Eleanor, Josh M, Sebastien B, Gus, Ian, Kelli, David, Harald, Melissa, Andreas, Josh B, Wilma, Emil, Stick, Chris
Agenda - 2:30pm Start
Accepting minutes from last meeting
- accepted
Project Timelines (2-3 minutes each)
Spaces - 14:31 UK
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Mainline (J-m)
- Ice 3.6: server/client now working. Further testing required for 3.5 client-3.6 server compatibility
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Download from web update. (Josh)
- If a download is very fast then gevent will fall over killing workers.
- Short-term fix: limit downloads feed of nginx (effectively down to FastCGI speeds)
- Long-term fix: shoot for using asynchronous workers
- configuration on cowfish does work for everybody
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Focus on deployment docs and generation.
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improving documentation for various OMERO installs
- making it easier for people to reconstruct them for testing
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improving documentation for various OMERO installs
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Model (Sebastien)
- good meeting last week
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Mark: initial Folder model now merged to regions devspace
- Folders are a strict tree, but ROIs may be in multiple Folders
- Folders can be created and ROIs put in them from the CLI
- working on making graph operations Folder-aware
- server available that Insight can connect to
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Dominik working on client-side
- initial version seems to recognize folders
- some testing tomorrow
- still on course for mid-February m1 BF, end-of-February m1 OMERO
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Roger is working on C++ transforms
- Roger: now making them work with OME-TIFF reader and writer, that should be done soon
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David is working on code generation
- David: also working on transforms in bug-fixing
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Metadata (Josh)
- Simon getting WND-CHARM working on IDR
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getting plates through BF out of IDR without bringing it down
- perhaps using hadoop
- somewhat pushed work on getting metadata out etc.
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big analysis (presentation next week)
- Simone: presentation is about a way to run distributed WND-CHARM on hadoop
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Jason: got several large datasets in IDR, need to make them available for analysis
- whether their scripts are run on IDR
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... or by downloading data to their end with features, etc. already calculated
- not raw data downloaded, but maybe thumbnails, links to original data
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Mainline (J-m)
Other releases/upgrades: - 14:44 UK
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Figure
- Will: tiny bug-fixes
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FLIMfit/OPT (Ian)
- migration to new build system looks promising
- working on downloading for localization
- look at getting localization data into OMERO.tables
- talking to superresolution community, about files to work with
- still unanswered questions about OMERO for mass spec
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ImageJ
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Josh: commented on uploading results from ImageJ to OMERO for bulk annotation
- will be increasing interesting in that kind of thing
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Josh: commented on uploading results from ImageJ to OMERO for bulk annotation
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Learning
- nothing new
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Sysadmin
- nothing new
-
Figure
Glencoe Update (Chris) - 14:48 UK
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first set of PathViewer bugs/idiosyncrasies
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related to how Insight writes ROIs to the server, not matching schema
- need to decide how to work with some of these fields set by Insight
- Jean-Marie: definitely can believe issues with polygon, polyline, etc.
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some units issues with marshalling
- affects electron microscopy data
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related to how Insight writes ROIs to the server, not matching schema
-
first set of PathViewer bugs/idiosyncrasies
Topic: team communication (Jason) - 14:52 UK
- Drafting a blog entry regarding reducing support for OMERO.server on Windows
- Any new platform will come with changes -- some good or bad, depending on beholder
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Not using Slack beyond today, not yet paid-for to be depended on for use by us
- actually shut down openmicroscopy demo
- feel free to create your own world in Slack but don’t fracture work communication
- but is possible that everybody may decide that we shouldn’t live without it
- Need to actually try out solutions for a while to properly evaluate them
- Go back to Jabber for now, continue to get work done
- Certainly open to other suggestions
- Need to define requirements (especially work-related!)
- Having IRC be more visible has been interesting
- Jean-Marie: best to bear release schedule in mind when considering when to try alternatives
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Simone: we have had a quick look at gitter, has some nice features
- Colin: free version is user-limited to 25
- Josh: feedback to chat feedback board
AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled) - 15:03 UK
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Jason: June and I doing a lot on the annual users’ meeting, trying to sort out rooms, etc.
- June: likely meeting dates at end of May, start of June
- also working on grant stuff
- Jean-Marie: talking with Andrea, Tuesday to Friday
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Jason: June and I doing a lot on the annual users’ meeting, trying to sort out rooms, etc.
Done 15:05 UK