ABI CellML Meeting Minutes, 1st September 2010

Present: Randall Britten, Justin Marsh, David (Andre) Nickerson, Tommy Yu, Andrew Miller (minute-taker)

Last week's action items

Last week's action item 1: Catherine: ask Peter and Poul if there is any funding for open access for the application note - Don't know if this has been done.Randall mentioned that there might be some PBRF funding which can be used for this. Andrew is waiting for final confirmation from Peter as it turned out the cost was higher than previously thought.

Last week's action item 2: Tommy: get confirmation from everyone that draft is OK, and get all the requirements for submission organised. Tommy has now heard back from everyone. Andrew noted that, on the other paper (the revision history / DVCS repositories paper), he is still waiting to hear back from Alan.

Last week's action item 3: Andre: send Catherine a link on how to tunnel in to Litmus. This has been done.

Repository contributions

No repository contributions mentioned this week.



  • Tommy has been working on a feature suggested by Andre.
  • In addition, he has been working on the layout of PMR2, to make the structure of the code clearer. Eventually, exposures & workspaces will be in different packages.


  • Andre noted that the ICSB tutorial that included a demonstration of PMR2 has been cancelled. However, Andre is still working on documenting PMR2.

Core specifications - ModML


  • Andrew has been working on a module to allow reactions support in ModML, by translating from a system of 'reactions' (any set of processes on entities) to a DAE model with units. He has been working on code which allows the use of a large database of processes and entities, with only some specific entities with values (and possibly instructions to clamp particular entities to zero), with the model iteratively picking the processes and entities which are relevant to the model. This allows modellers to have a large database of processes and having only those which are applicable appear in the model.

Core specifications - CellML 1.2


  • Randall noted that it has been a while since we last looked at support for infinitesimally delayed variables, and that while code generation works, there is a need to go back and look into whether the code works numerically with IDA now.

Metadata specifications

No update was given this week.



  • Justin has been working on using ndiff to allow for the validation of numerical results with a tolerance. He noted that there are still minor problems, which he is working on fixing.
  • Andrew has been working on Python support, and now has basic calls into the API from Python working.


  • Andrew plans to add support for accessing the API extensions from within Python this week.
  • Andrew noted that these changes to the CellML API could allow new features for PMR2, as it will allow it to access the API directly from in Python. There were several possibilities discussed, including allowing for numerical integrations to be performed on the server, and improved code generation support where the user can provide their own CeLEDS definition.



  • Justin has been trying to work out why OpenCell doesn't work for Catherine on Mac. He is not sure why yet, and his efforts have been hampered by the limited number of Macs he has access to to try things on - especially ones running 10.5 as Catherine has. There was a discussion of which computers he could test OpenCell on.