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
Accepting minutes from last meeting
- accepted
Project Timelines (2-3 minutes each)
OMERO - 14:31 UK
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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
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Ola: sticking to registry deadline as discussed yesterday?
- Sebastien: possibly not
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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.
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5.2.1 (J-m)
Bio-Formats - 14:38 UK
Registry (Sebastien) - 14:41 UK
- working with Petr to get to good testing scenario for upgrade checks, now in good shape
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
Repositories - 14:44 UK
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Virtual Microscope/teaching
- no change
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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
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Virtual Microscope/teaching
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
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
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what should Folders thus be called?
- Will: folders?
- Gus: containers? (Colin: used in the code base)
- comments by the end of this week please
Presentation on Julia by JB - 14:51 UK
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Jean-Marie: how many people are working on it?
- Josh B: most central core group is maybe a dozen; development/discussion is on GitHub
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Roger: can unprivileged users install package dependencies?
- Josh B: local installation is default (site-wide is possible)
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Jean-Marie: how many people are working on it?
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
AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled) - 15:32 UK
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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.
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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
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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
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multi-modality data submitted by Alan Race (added by PW, motivated by IM)
Done 15:47 UK