ABI Meeting minutes 2009-05-13
Present: Dougal Cowan, Randall Britten, Mike Cooling, Andrew Miller, Peter Hunter, Poul Nielsen, James Lawson, Tommy Yu
Apologies: Catherine Lloyd
3) Tommy to allow editing of sub-exposure titles
1) Update on Newcastle SAINT-CellML annotation system.
2) PMR2 update
3) Repository contributions - update
4) Website redesign - update
5) OpenCell development - update
6) CellML API - update
7) CellML Specs - update
8) Time permitting - updates or additional items from volunteering attendees
Apologies: Catherine Lloyd
Last week's action items:
1) Tommy to remove link to legacy repository (PMR0).- Done.
- Not done, carries over
3) Tommy to allow editing of sub-exposure titles
- Functionality finished but not exposed yet.
- Done.
- Done.
- Done; tracker item 1770.
This week's agenda:
1) Update on Newcastle SAINT-CellML annotation system.
- James would like to see continued collaboration on this and asked if much progress has been made.
- Mike has received questions on user requirements.
- Poul reported that Matt has replied to the mailing list.
- Poul asked how urgent Sarala's reservations are; will taking the initial approach preclude later taking Sarala's approach?
- James and Poul don't see how the initial approach could preclude Sarala's.
- Poul suggested waiting for Sarala and then having a discussion about this.
- There was an extensive discussion about annotation of multiple imports of the same component into CellML 1.1 models.
- Andrew suggested a possible method where parts of an imported component have generic properties that are annotated in the connection. (?)
- There was discussion about the ways that imported components might be usefully annotated.
- Randall said that it would be useful to have a summary of this discussion available.
- Mike suggested that examples be built of 1.1 models that import such components, to try different annotation scheme on in order to figure out what works.
- Poul said that Sarala should be updated on ideas from this discussion.
- Randall said that the Newcastle group seem to have succeeded with the Java bindings.
- Mike will email Morgan about this.
- Poul said that there will be a post-grad from UCSD here for 2 months (arriving in 6 weeks) who might be able to work on the Python bindings.
2) PMR2 update
- Tommy reported that release candidate 1 is up on VPSlink.
- Randall asked if there is a local instance yet - Tommy said no, but he will put one up.
- Peter said that ITS should be able to provide what we need for PMR2 within a day.
- Randall suggested that Tommy and Peter S can talk directly.
- Randall suggested that Tommy set up a stress/load test for PMR2.
3) Repository contributions - update
- James has been making a few curation status updates.
- Peter asked if we have a plan to deal with units updates.
- James said that he will be fixing models that fail validation due to units issues by hand.
- Peter said that we should have a plan to deal with this, as it is not good for the reputation of the repository to have the current situation.
- Randall suggested running the validation script, and fixing the problems that are found.
- Peter said that we should aim to have the problems dealt with by IUPS. Updating the curation status to say which models have the problems is a good first step.
- Randall suggested first marking all the models that fail validation, and then hand picking the ones to fix.
- Peter asked when the new curation flags will be in PMR2.
- Tommy said that we have not yet defined what the flags will be. The facility for them exists in PMR2, however.
4) Website redesign - update
- James reported that Gareth has made available a light CMS (ModX) with static HTML versions of the pages for the new website, in order to enable rapid template development and tweaking.
- Tommy reported that he has already offered to create Plone 3 skins from Gareth's templates and put them up on the staging instance on James' machine. Tommy can do more work on Plone 3 skins, now that PMR2 is in the RC stage.
- Peter said that this is a CellML community issue, not an ABI issue - therefore we should take Gareth off the job.
5) OpenCell development - update
- Andrew has been refactoring the tree view. There is now a single file that describes the appearance of the tree view, so we can now add things such as metadata editing etc.
6) CellML API - update
- Andrew reported that he has been looking at a bug report filed by Alan Garny, where one of Jonna's models runs extremely slowly. This seems to be something we can fix.
- Randall asked Andrew if it is worth working on this.
- Andrew said that this would be quite a lot of work, but is possible.
- Randall is keen to get this fixed, in order to keep Jonna happy as she gives good feedback on OpenCell.
7) CellML Specs - update
- James has been working on the metadata specs, and brought up the issue of naming sub-exposure pages. It is possible to use a DC title to name variants, or separate models from the same publication.
8) Time permitting - updates or additional items from volunteering attendees
- Peter brought up the need to get working on the IUPS workshop handouts.
- Randall asked where the handouts from the summer workshop are.
- Peter suggested that we pull everything we have together and have a meeting about it.
- Poul asked if Dougal wants his CellML talks - Dougal said yes.
- James said that we need a place to put posters, presentations, etc - some of these could be made publicly viewable.
- Poul asked what resources Amir (from UCSD) will need to be able to start building the Python bindings - can he put Amir in touch with Andrew and Justin to see how much assistance he will need?