ABI CellML Meeting Minutes, 10th August, 2011

Present: Dougal Cowan, Andrew Miller, Tommy Yu, Caton Little, Poul Nielsen, Randall Britten

Apologies: David "Andre" Nickerson

Last week's action items

Action item 1: Dougal - send out an email with the cut off date for nominations, and a link to a page with current nominees.

Action item 2: Randall - email Alan Garny to see if he wants to test out the webservices.

  • Done. Alan has indicated that at the moment he can only do a small amount of testing of using webservices from OpenCOR. Nevertheless, we decided that we will publicly stage a head revision of PMR2 on an on-going basis in future, for Alan to be able to test against now, and for anyone else who wants to test any new developments.
  • Action item 1: Randall and Tommy to organise public staging of PMR2.

This week's agenda

1) Repository contributions - update

  • No update

2) PMR2 development - update


  • Tommy: continued work on OAuth plugin. The de-facto standard library has some issues that have been worked around. There is a lot of work to do on this, and it is about half-way there.
  • Tommy: Plone 4.1 is out, and 0.4 staging can begin.


  • Poul: what is the status of Thor's progress on the issue of other groups using PMR2?
  • There was a discussion about Thor's project, getting other groups to use PMR2, and keeping Tommy & Thor in contact.

3) CellML API - update


  • Andrew: working on bugs from the tracker. Provided a fix for the TeLICeMS minus/negative issue. Make install & make package now work out-of-source. Started working on documentation, which can be found on the CellML site under tools/api.


  • There was a discussion about the minus/negative issue in TeLICeMS, and the TeLICeMS grammar.
  • Poul: who had input into the grammar?
  • Andrew: it was based on discussions from tracker items and Alan Garny's input.
  • There was a discussion about TeLICeMS and how Lucian is using it.
  • Randall: filed a tracker item about MATLAB output in OpenCell 0.8, which gives incorrect arrayOffsets.

4) CellML core specs - update


  • Andrew: worked on the uncertainty spec. Contacted the people responsible for the four VPH Share exemplar modelling workflows in VPH Share WP5 (and so who will need to represent uncertainty in CellML and / or FieldML) to check that they are happy with the proposed approach. One of those groups is also responsible for tools for quantifying uncertainty as part of WP4, and so the discussion on how to ensure this is compatible with our WP5 work has also been initiated.
  • Andrew: started writing a paper on representing parameter uncertainty in CellML. This could possibly be submitted to SIAM Multiscale Modelling & Simulation.


  • Andrew: need to decide who would like to be co-authors on the uncertainty paper.
  • There was a discussion about uncertainty techniques vs. other systems.
  • Poul: this should be brought up at COMBINE - it would be good to have a common approach.

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

  • Dougal: a list of nominees who have accepted their nominations for election to the CellML editorial board can be found on the CellML site.