ABI CellML Meeting Minutes, 6th October 2010

Present: Andrew Miller, Dougal Cowan, Mike Cooling, Tommy Yu

Apologies: Randall Britten

Last week's action items:

1) Tommy to change the cellml.org OpenCell links to latest/previous, plus redirects for older versions.

  • Not done, waiting on getting the new links to Sourceforge from Justin or someone else.

2) Justin to upload the previous versions of OpenCell onto sourceforge so Tommy can then link to them.

  • Done.

This week's agenda:

1) OpenCell development


  • Andrew: asked if Dougal has the binaries for 0.8. Dougal has the binaries for Windows and Linux. We just need to get the Mac binary, and then we can make the 0.8 release.
  • Mike: the physiome website has a link to the incorrect version of OpenCell: http://www.physiome.org.nz/cellml/tools/opencell/ . This needs to be updated.

2) CellML core specs - update


  • Andrew: has been building a reaction model (combustion of hydrogen to make water), and using this process to adjust the modules to make them work as modellers would expect.

3) CellML API - update


  • Andrew: pass-through is now working, and has been used to build correct reset rule support. This now re-starts the IDA integrator at every reset. This works with most models tested, but needs more testing.
  • Andrew: removed CellML CORBA server. This was unmaintained and not used.
  • Andrew: created test suite for CellML context, also found and fixed bugs in this.
  • Andrew: creating a new service, called TeLICeMS, the Text Language for the Input of CellML Models Service. This service is being created primarily from the code already in OpenCell for the text view, which is being moved into the API - with the input language being called TeLICeM. TeLICeMS will be able to convert between CellML models and TeLICeM formatted input models, and also convert between MathML and the math part of TeLICeM.


  • Andrew: we need people to write the reset-rule containing models that they may have been holding off on, for testing the new reset-rule support.
  • Andrew: a meeting is need to discuss how to set priorities for future development on the API, and encourage involvement from outside of Auckland in the process, now that we don't have OpenCell development to drive the API development

4) Repository contributions - update

  • No update.

5) PMR2 development - update


  • Tommy: has created a test harness, which makes it easier to add test data to the repository, and enables tests separate from Mercurial. Also wrote test cases for this.

6) Metadata


  • Mike: has been going through the material presented a few weeks ago, and adding RDF syntax to make the metadata usable. Mike will now mark up some models of interest to Edward de Bono's group using the new system, to see how it might work.


  • Mike: we need to see an implementation, that is models marked up with the metadata, in order to see how the metadata works in practice.