ABI CellML Meeting Minutes, 8th December 2010

Present: Dougal Cowan, Mona Zhu, Amy You, Andrew Miller, David "Andre" Nickerson, Tommy Yu, Randall Britten, Poul Nielsen

Last week's action items:

1) Randall to get in touch with Alan to discuss the TeLICeMS service and text input in OpenCell (from 2 weeks ago).

  • Done: Alan thought the suggested ideas about more fine-grained conversion sounded good.

This week's agenda:


1) Use of RSS feeds for monitoring tracker items versus use of Bugzilla's default CC list feature. (Randall)


  • Randall: It is possible to use the RSS feeds of tracker searches instead of default CCs to allow people to keep track of certain areas of the tracker.
  • Andre: Every component or category should have a default CC, tracker users need to know that someone is looking at the tracker items they create. People can contact the CCs directly if they need to.
  • Poul: It is important to have a real person to contact. We can discuss who the contacts for the repository can be next week with Peter.
  • Randall: we need to sort out who is taking over from James, Catherine and Justin.
  • There was a discussion about how to assign default CCs, and how to organize the tracker components for the repository.
  • Andre: we should have a single tracker component for repository models, as the categories are wrong or models can fit into more than one.
  • There was an extensive discussion about how to categorize repository model tracker items, and the pros and cons of discarding the fine-grained categories.

2) Repository contributions - update


  • Mona: finished first 1.1 model - Houart et al. 1999. 1 error remains.
  • Dougal: exposed models for Mike Cooling - bugbuster, systems model tutorial, electrecoblu.

3) PMR2 development - update


  • Tommy: refactored and fixed a couple of test cases, and submitted the paper rebuttal.

4) CellML API - update


  • Andrew: working on TeLICeMS. Can now serialize CellML to TeLICeMS, and parse TeLICeMS to CellML. Round tripping is working with a few minor exceptions. There still seems to be a memory leak which is hard to track down. Next step is to create automatic round-tripping shell scripts.
  • Dougal: The CellML API survey received ethics approval and is now up on-line.


  • Randall: can we help out Lucian with the API?
  • Andrew: Lucians problems seem to be with XULRunner - it may be easier for us to help him convert his code to not use XULRunner.
  • Poul: it is important that we can help out people like Lucian who are trying to use the API.

Action item 1: Andrew to look into converting Lucian's code to no longer use XULRunner.

  • Amy: got examples working on Linux.
  • There was a discussion of Amy's project, and tracker item 2798.
  • Randall: OpenCell 0.8 seems to generate MATLAB code with arrays starting at 0 instead of 1.
  • Andrew: has had correspondence from people interested in using OpenCell in teaching. Alan is interested in helping them out.

5) CellML core specs - update


  • Andrew: ModML. Still working on Rice model. Discovered more errors in the ModML coded version of the model, and now getting very similar results to the CellML model. The ModML is based on the MATLAB version, which is slightly different to the CellML version.

6) Time permitting: Updates or additional items from volunteering attendees


  • Andrew: encyclopedia article. Adding links to the CellML API & tools pages is already done.
  • There was a discussion as to whether everyone is happy to now send this off.
  • Andre: still needs to read the latest version.