ABI CellML Meeting minutes 2009-08-12

Present: Dougal Cowan, Poul Nielsen, Amir Shirkhani, James Lawson, Randall Britten, Mike Cooling, David "Andre" Nickerson, Justin Marsh, Jonna Terkildsen, Andrew Miller.

Apologies: Catherine Lloyd, Peter Hunter.

Last week's action items:

1) Randall to create a tracker item to make the home page links return to the cellml.org home.

  • Done.

This week's agenda:

1) API generation of code for algebraic models (e.g. material constitutive laws for continuum mechanics).

  • Randall asked what the options are for handling this directly from the API.
  • Andrew said that in the mean time, adding an extra dummy equation (dx/dy=1 for example) is a workaround. The problem is that there is no bound variable, so the API doesn't know what to do with the model.
  • Andre said that he would like to avoid using the workaround as soon as possible, and asked that this be prioritized.

2) PMR2 update

  • Mike has some 1.1 models to play around with.
  • One of Mike's old 1.1 models has gone missing - that is, the link to the page with the model files (PMR1 hack) has broken. This is probably a quick fix, and Mike will get James to help him fix it.
  • Mike would like a separate documentation file for the model, that exists within the workspace.
  • Jonna asked if the site for old 1.1 models from PMR1 is staying - links to these have already been referenced in published papers.
  • Jonna asked if there will be a way of displaying only 1.1 models in PMR2 - Andre says that this should be part of the custom searches.
  • James can get redirects set up for the old pages (1.1 link pages) with where not migrated.

Action item 1) James to get redirects set up for the legacy 1.1 model pages that do not create dependencies on www1.cellml.org.

3) Repository contributions - update

Action item 2) James to check with others (Catherine, Jeelean etc) about any repository contributions before next week's meeting.

4) Website issues - update

  • James reports that we need to create a mailing lists page.
  • The website group will be putting up more content about the VPH day and IUPS2009.
  • There was a discussion about distributing the IUPS CellML tutorial around the ABI.

Action item 4) James to send an email to IUPS and to attempt to get feedback from tutorial attendees, both CellML and CMGUI.

5) OpenCell development - update

  • Randall suggested that there are enough new features in OpenCell for a release in August.
  • James said that snapshots have not been tested. Randall said that we do need testing done, but that we should move into release mode.
  • Justin said that the manual and tutorial will need updating.
  • Andrew said that we need to include the tree refactor as soon as possible.
  • Randall said that another option is to merge branches before release; it is probably a big job to include the revamped tree view.
  • Justin reported that the development Mac needs to be updated to 10.5. There was a discussion around which MacOS version to support - it was agreed that we will support the latest version (only), as Mozilla do.
  • Randall will look into getting a Mac mini to speed up the development process.
  • Poul is willing to do Mac testing, and James can bring in his own Mac for testing purposes.

6) CellML API - update

  • Andrew is making changes to code generation - trying out things discussed at the spec meeting - to include MALAES for infintessimal delays.
  • There is quite a bit of correspondance about the API now that we have more users.
  • James asked if an API FAQ or section of the current FAQ be useful, or perhaps more information about the API on the website in general.
  • Randall said that responding directly to enquiries is useful and important to encourage use of the API. Time invested in getting more people to understand and become familiar with the API is time well spent.
  • Randall does not know what the progress is on Java - he has not heard from Sarala.
  • Andre reported that Chris is having trouble building the API on Linux and Windows, and asked if it is possible to get binaries. He also asked if we need more VMs to support more platforms on Buildbot.
  • A breakaway was called on the API build.
  • Amir has run some basic test cases for the Python bindings.
  • Randall reported that Morgan wants a higher level service, like LibSBML. There was a discussion about Morgan's requirements.

Action item 5) Justin to look at LibSBML and try to work out what it is that we should put in our API for Morgan.

7) CellML Specs - update

  • James said that metadata was something we wanted to work on after IUPS, but that we probably need Tommy here to do it.
  • Andre said that we need to start using metadata in PMR2, and putting more effort into the SEDML side of things.
  • Poul asked if SEDML is full enough for our purposes; Andre says no, but that this is something we need to work on. Poul said that SEDML needs to be completed, and that this is something we need to push so that we can have the things we need included.

8) Additional items

  • Randall reported that the ABI brochure is being updated, and that CellML is in there. Randall will distribute this via email.
  • James asked that OpenCell sessions be put on the agenda for next week.
  • Mike asked if the Windows API build has been successful - Andrew said yes. Mike asked if Sarala or Andrew are working on the Java part - it is Sarala.
  • Justin mentioned that the Java problem is a blocker for JSim and possibly others, and might therefore be worth putting more effort into.