ABI CellML Meeting Minutes, 14th September 2011

Present: Dougal Cowan, Randall Britten, David "Andre" Nickerson, Caton Little, Tommy Yu, Andrew Miller

Last week's action items:

Action item 1: Dougal - put these news items up.

  • The RC2 item is up. Forgot to put the PMR2 staging item up.

Action item 2: Tommy - investigate building Python eggs with the binary release.

  • Created a buildout which locates the API correctly.

This week's agenda:

1) CellML website front page


  • Randall: take down editorial board nominations item.

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

2) Repository contributions - update


3) PMR2 development - update


  • Tommy: made buildout for CellML API. This also lets anyone use the API from Python. Performed more testing, found that embedded workspace links were broken, now fixed. Integration tests updated. Migrating the MathML support to Python.


  • Randall: There was an idea to use the SED-ML webservices to generate simulation results as part of exposure creation.
  • There was a discussion about using the SED-ML webservices and how this could work.

4) CellML core specs - update


  • Andrew: have put up a draft proposal for 1.2, combining comments from all tracker items. Put together a secondary spec draft.


  • Andre: is the core spec 1.2, or a combination of core and secondary? 
  • Andrew: still to be decided.
  • Andre:Wasn't it decided not to use MathML 3.0?
  • Andrew: it turns out that using 3.0 will make some things easier due to clearer semantics.
  • Andre: closing related tracker items makes the draft seem more official than it really is. Need to discuss how to handle tracker item status.
  • Andrew: still need to write an informative spec.

5) CellML API - update


  • Andrew: put out release candidate 2. Alan has reported that something is not working in Qt Creator.


  • Andre: we should be using exactly what Alan is using to ensure we get the binaries working for him.
  • There was a discussion about Alan's requirements and development environment.
  • Randall: it should be a minimum requirement to get this working for Alan.
  • Randall: there have been discussions about integration of software. Combination of APIs could be via one monolithic binary or access to various APIs via some other service(s). We need to look at what integration layers we would prefer and those users would prefer. The current push is for use of all APIs from a Python environment.
  • There was a discussion of rapid prototyping/proof of concept development.

6) Report from COMBINE - Andre


  • Someone in the Netherlands has created a SED-ML repository using Plone, which accesses C++ models stored in Google Code. He is looking at extending SED-ML to create movies (virtual leaf).
  • There is work going on between SBRML and SED-ML to get them working better together. This will probably involve a new ML to store simulation results. Andre has suggested the use of FieldML for this, but the status of FieldML is possibly not advanced enough at the moment.
  • There is a lot of work on SBML packages, for example a package for boolean network models.
  • There was talk about SBML-spatial and FieldML, we need to keep these channels open as there is some interest in using FieldML.
  • Lots of work on annotations and ontologies. SBML-Harvester is a tool that can perform biological validation of models from BioModels using the extensive annotation of these models.