ABI CellML Meeting Minutes, 21st September 2011

Present: Dougal Cowan, Tommy Yu, David "Andre" Nickerson, Alan Garny, Randall Britten, Peter Hunter, Caton Little

Last week's action items:

Action item 1: Dougal - make a news item for PMR2 staging, take down nominations item.

  • Done.

This week's agenda:

1) Status on rule-based modelling in CellML - Alan


  • Alan: Elisavet Soumaka (from Daryl Shanley's team in Newcastle) has indirectly asked if it is possible to do rule-based modelling with CellML.
  • Andrew: it is possible in 1.1 using infinitesimal delays.
  • Randall: this has not been fully tested.
  • There was a discussion about test cases for rule-based modelleing and what the Newcastle group is using to run CellML models.
  • Peter: it is well worth keeping in touch with them as an important user group, keeping up to date with what they want to do.
  • Alan: will get back to them with the current situation - that this should be possible with the API at the moment, or they could wait for OpenCOR.

2) CellML website front page


  • News items have been added for the PMR2 staging and API release.

3) CellML core specs - update


  • Randall: has anyone read Andrew's 1.2 draft?
  • There was a discussion about the draft.
  • Andrew: has looked at how the API for 1.2 could be prototyped, looked into a Haskell prototype.
  • Peter: what is the timeframe of the 1.2 API?
  • Andrew: it is a major re-write.
  • Peter: will stochastic support be added to 1.1 or do we wait for 1.2? Andrew: already implemented in 1.1 but not widely tested.
  • Alan: could stochastic modelling be done in 1.0, which many people are using? Andrew: yes.
  • There was a discussion about Andrew's uncertainty paper.
  • There was a discussion about the major features of CellML 1.2.

4) CellML API - update


  • Andrew: 1.10 has been released, and a fix made where the install file needed updating for CMake.
  • Andrew: cleaning up documentation. Will eventually move all Plone-based docs to doxygen to prevent duplication for easier maintenance. Doxygen has been split out by API version.
  • Alan & Andre: we need a doxygen page for "latest" that always shows the latest trunk docs.
  • There was a discussion about documentation links.
  • Andrew: cleaning up old tracker items. Python exceptions issue (tracker item 3054) is fixed.
  • Andrew: have been helping Alan get the API working.
  • Alan: The API now works in OpenCOR on all three platforms .


  • There was a discussion about what Alan plans to develop in OpenCOR over the next four weeks.
  • Alan: probably to open, run, and graph output of a CellML model.
  • Peter: keep in touch with Herbert Sauro about SED-ML developments.
  • Randall: what are the most important features of OpenCOR in Alan's view?
  • Alan:
    • editing - first the raw XML, then COR-like view, then some other views.
    • simulation - probably the first goal for OpenCOR while in Auckland.
    • analysis - requiring libraries created by other groups such as Jim Bassingthwaighte's.
    • metadata annotation - using ontologies. A lot of work.
  • Peter: we need to be working with Bernard de Bono and Sarala etc on this. Also, we need to incorporate existing annotation tools such as Saint and or SemSim.
  • Andre: ideally we should be building models from the annotations, rather than annotating models.
  • Alan: will come up with a road map for OpenCOR development.
  • Randall: OpenCell is the only tool that can currently use the SVG sessions. Andre pointed out that if SVG diagrams used annotation rather that OpenCell specific JavaScript, it would be easier to support them in other software systems.
  • There was a discussion about future SVG session support or replacement.
  • Andre: the metadata spec is available, we just need someone to annotate some models using it.
  • Peter: Alan should talk to Mike Cooling about the metadata spec.

5) PMR2 development - update


  • Tommy: more testing, fixed bug where raw code was being rendered with decorations. Have been playing with the Python bindings, and created a buildout using the API.


  • Tommy: when should the 0.4 release happen?
  • There was a discussion about testing of the staging and the release.
  • Alan: comments on the PMR2 - categories could be split into 3 columns. Number of models in each category would be useful. User download counts for models would be nice. It would be good to have user comments and ratings for models.
  • There was a discussion about PMR2 improvements.
  • Alan: would like to try the basics of webservices in OpenCOR while in Auckland.
  • Alan: there are Mercurial plugins for Qt.
  • There was a discussion about Hg issues, PMR2 security, etc.

Action item 1: Tommy - follow up with Gareth about getting a certificate.

  • Alan: what happened to curation flags to replace stars?
  • Tommy: this stalled after Catherine and James left. There are some documents including some models Catherine flagged to test the system.

Action item 2: Tommy - add mailto link to Dougal to the curation portlet on exposure pages for reporting model problems.

6) Repository contributions - update


  • Andre: fixed Luo Rudy 1994.