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

Last week's action items:

1) Tommy to remove link to legacy repository (PMR0).
  • Done.
2) Tommy to change PCEnv instances to OpenCell in PMR2.
  • Not done, carries over
Action item 1) Tommy to change PCEnv instances to OpenCell in PMR2.

3) Tommy to allow editing of sub-exposure titles
  • Functionality finished but not exposed yet.
4) Dougal to take Catherine through PMR2 usage (including Mercurial).
  • Done.
5) James to complete the migration manifest files.
  • Done.
6) Randall to create a tracker item for PMR2 deployment.

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.
Action item 2) Everyone to read Matt's email on the Saint/annotation issue.

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.
Action item 3) Everyone to send their various tutorials to Dougal.
  • 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?
Action item 4) Andrew to write up the requirements for building Python bindings.