ABI CellML Meeting Minutes, 4th August 2010

Present: Randall Britten, Dougal Cowan, Tommy Yu, Justin Marsh

Apologies: Andrew Miller, David "Andre" Nickerson, Peter Hunter

Last week's action items:

1) Justin - Look into a script to find models that require fixing.

  • Not yet done. This action item will be handed over to Tommy for next week.

This week's agenda:

1) (Andre) Has a script been run on the repository to discover models which require fixing?


  • Tommy will run the script to find these models, as he is more involved with PMR2.

2) (Catherine) Multicellular neuronal modelling and stochastic modelling support.


  • Randall: A summer student abstract will be put together to work on this problem (large multicellular models and stochastic support). Peter Hunter also wants someone to start working on this sooner than when the summer students begin.

3) OpenCell development


  • Justin: Has made a script that runs CellML and MATLAB versions of the Saucerman model, and creates graphs to compare their output.
  • Justin: cAMP total and x graphs appear to match.
  • Randall: Other graphs do not match, because the MATLAB model has pacing which is not present in the CellML model yet.
  • Randall:

    This represents progress towards the validation of support for IDA, which is a requirement for the 0.8 release process.


  • Justin should push the working version of the Saucerman model from Geoff to the PMR2 workspace, along with the scripts for creating comparative graphs. The model should be pushed as a branch.
  • Randall: Justin to try turning off the MATLAB model pacing, and then compare results with the CellML.

Action item 1: Tommy: give push access to the Saucerman workspace to Justin.

4) CellML API - update


5) CellML core specs - update


  • Refer to agenda item 2.

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


  • Randall: Waiting to hear from Mike Cooling.

7) PMR2 development - update


  • Tommy: Has made progress on the curation metadata editor.


  • Tommy: The curation metadata editor relies on a package that will work better under Plone 4, but there are still issues with upgrading. It may require back-porting features or creating a new addon to get this working.

8) Repository contributions - update


  • Catherine: Hanne has finished SVG sessions for the signal transduction section, and is moving on to a section of her own choice.
  • Catherine: Has coded up the Vasalou and Henson 2010 model of circadian rhythms, and has fixed an error in the Bondarenko et al. 2004 cardiac cell model according to Sander Land's corrections.

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

  • Randall: Randall and Dougal held a tutorial session to start training people in OpenCell, CellML, and cmgui in preparation for the VPH tools workshop in Buenos Aires.