ABI CellML Meeting Minutes, 15th September 2010


Last week's action items

1) Mike will put up the presentation on metadata, amended based on comments received in the meeting.

  • Done.

2) Tommy will publicise the tracker item [about URL shortening] and encourage people to give feedback.

  • Tommy has publicised the tracker item, but so far there has been no discussion.
  • Randall: go ahead with the plan discussed at last week's meeting.

3) Randall will send this correspondence [about the CellML converter from Dan Beard] on to Andrew.

  • Done.

4) Andrew to look at whether toplevel piecewise models work properly with IDA.

  • Piecewise equations require a fix, and Andrew is going to try a method to get them working. There was a discussion about how to get piecewise working under IDA.

This week's agenda

1) CellML API - update


  • Andrew: has spent most of the time trying to get integrator to restart, in order to provide IDA support for piecewise equations to support reset rules.
  • Justin: discovered that a test for the API is not 64bit clean.

2) OpenCell development


  • Justin: OpenCell is ready to be bundled up and tested.
  • Justin: fixed a few small bugs that were causing a test to fail (graph trace issues when switching between models).


  • Dougal: can do Windows and Linux testing for OpenCell.

3) CellML core specs - update


  • Andrew: working on the ModML reaction generator, which is very close to being finished. The next step is to make and test some models.


  • Randall: the Beard group have a database of reactants and reaction rates, which may be useful. They also have a database of MATLAB snippets.

4) Metadata specifications (general, citations, graphing, simulation, other) - update

  • No update.

5) Repository contributions - update

  • No update.

6) PMR2 development - update


  • Tommy: continuing to refactor, exposures and workspaces now fully separated. Working on Plone menus.
  • Tommy: has begun the paper submission process.
  • Andrew: BMC Bioinformatics said that we should include (?). This has now been included, and will be re-submitted this evening. The new complex-provenance diagram is now included.

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

  • Andre: summer studentships are now organised. There are a number of studentships (FieldML etc.) which did not get students.