ABI CellML Meeting Minutes, 8th September 2010

Status: Draft

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

Apologies: Justin Marsh

Last week's action items



Mike gave a presentation on the work he has been doing on the metadata specifications. Action Item 1: Mike will put up the presentation on metadata, amended based on comments received in the meeting.



  • Tommy has split the exposure code into its own package. This will help with the process of writing better unit tests.
  • Andrew has submitted the paper on Revision History Aware Repositories.


  • There is a need to move forward with the shorter URL proposal. There is already a tracker item on this; Tommy plans to give people another week to comment on the proposal on the tracker.

    Action item 2: Tommy will publicise the tracker item and encourage people to give feedback.

Core specifications


  • Andrew has continued work on the reactions module for use in ModML.
  • Randall has had correspondence several months ago from Dan Beard requesting feedback on his CellML converter. Action item 3: Randall will send this correspondence on to Andrew.
  • Randall reported that Mark Hanna, as part of his fourth year project on delayed differential equations, has written a script which recognises a particular pattern in the CeLEDSExporter generated Python and converts it into a form that can be used with the PyDDE solver. He has identified a model for which this works. This model has a constant delay, and does not require historical data from prior to the start time of the model.

Repository contributions


  • Andre has made an HTML style exposure collating the kidney related models in the repository.



  • Andrew has tested Python support and it now seems to work properly. All extension modules should be accessible.
  • Andre reported a problem with out of directory builds with Python support, which Andrew has now been fixed.
  • Andrew has added a new flag to configure, --with-libxml2, which allows the path to xml2-config to be specified, to meet the needs of the OpenCMISS project. However, Andre noted that the problem is that OpenCMISS comes with a packaged xml2-config which provides wrong values, and so this is inadequate to make it work. There was some discussion as to whether this was a problem that should be fixed in OpenCMISS or in the CellML API.
  • Andrew has been working on a cron job to regularly update the Sourceforge CellML API documentation. It currently works off the latest version. Consensus was that it was good to have this. Randall suggested that we could move later move the documentation into version specific subdirectories to support this. This will probably mean not putting the documentation in the toplevel directory.
  • Randall reported on Justin's progress from an e-mail: Justin has been working on narrowing down a problem in the release candidate, where when the model is switched in the Model List on the left, the update isn't reflected on the graphing control.


  • Action item 4: Andrew to look at whether toplevel piecewise models work properly with IDA.
  • Mike asked about when the handover of OpenCell development from Auckland to Oxford will occur. The date has yet to be finalised.