ABI CellML Meeting Minutes, 1st of June, 2011

Present: Dougal Cowan, Tommy Yu, Mike Cooling, David "Andre" Nickerson, Randall Britten, Poul Nielsen

Last week's action items:

Action item 1: Dougal - update the models that Alan has problems with.

  • In progress.

Action item 2: Dougal - Look at a solution to the imported models lack of descriptions.

  • Solution was decided - a change to the default workspace page with more information

Action item 3: Dougal - look at mediawiki as a solution for the ABI software "book".

  • MediaWiki appears to provide all the required features.

This week's agenda:

1) HARMONY report


  • Tommy: highlight was speaking with Camille from EBI (who is building their new repository software) about PMR2. Had a discussion about user access control issues, and how PMR2 can provide for these requirements.
  • Poul: The EBI group is reluctant to use PMR2 because of Python, they use Java.
  • There was a discussion about access control features of PMR2.
  • Tommy: the SBML hackathon was enlightening. Used libsbml Python bindings to create a simple SBML viewer - libsbml is straightforward to use.
  • Randall: we could put SBML models up on PMR2 using a simple SBML viewer.
  • Andre: the reactome project has curators for pathways, we could try to get them to help with curating our pathway models. An XML diff tool is being developed by Ron Henkel, University of Rostock, which can be used to filter history. There is a lot of work being done on ontologies, using them to generate SBGN diagrams and pathway merging.
  • Andre: it would be good to try to get CellML to be one of the core standards for COMBINE.
  • Mike: we should try to have a strong presence at COMBINE in Heidelberg in early September. Mike will go, Poul might be able to attend some of it, and Andre will try to go.

2) CellML API - update


  • Andrew: made another release candidate, fixed the missing file issue.
  • Mike: the RC works on Windows, but there is an issue with libxml2. A specific Windows dll should be provided, or clear instructions given.
  • Randall: some more extensive examples and tests would be good, such as a numerical integration example.
  • Andrew: working 10 hours a week on CellML API maintenance.
  • Andrew: looked into crashes in Wine.


  • There was a discussion about Windows testing issues and machines/VMs for this.


  • Randall: the release should be made, including clear instructions about libxml2.

3) CellML core specs - update


  • Andrew: working on a spec for uncertain parameters, a way of representing uncertain parameters. Starting on SED-ML support


  • There was a discussion about xpath and imports in CellML - only exposing top-level to the SED-ML, vs. using some sort of virtual document or "flattening" method.

4) PMR2 development - update


  • Tommy: exposure rollover form has been fixed. A bug to do with the description field has been fixed. Broken navigation listing for workspace logs has been fixed.

5) Repository contributions - update


  • Dougal: have been working on the Friel group models, and need some assistance from the team.
  • Randall: Peter suggested a classical model section in the repository, with classic ODE examples. These would be a useful teaching resource.
  • Randall: Ting has been experimenting with using PMR2 to store the OpenCMISS tests.
  • There was a discussion about result storage and numerical comparison.
  • Randall: need to store a canonical result set to compare to.

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

  • Tommy: demonstrated the new features of PMR2 - the new math view, sub-repo navigation, and the CellML-simulator view.