ABI CellML Meeting Minutes, 23rd of March, 2011

Present: Andrew Miller, Dougal Cowan, David "Andre" Nickerson, Tommy Yu, Lukas Endler, Poul Nielsen, Randall Britten

Last week's action items:

Action item 1: Andre to contact Eric to explain our thoughts about this. [CGS units in JSim]

  • Done. A brief reply was received from Jim Bassingthwaighte.

Action item 2: Andrew to summarise the results of the survey for next week's meeting.

  • Done, will be presented today.

Action item 3: Dougal - update the team page on cellml.org.

  • Done.

This week's agenda:


1) PMR2 exposure discussion (Andre)

  • Item was moved to a breakaway meeting.

2) CellML API survey results - discussion


  • Andrew: displayed summary sheet of results from the API survey. Noted that people were requesting some features that already existed, but they were unaware of.
  • Lukas: is there an online validator, web-based, which works on 1.1 models?
  • Andrew: not yet, but could be done. 
  • Andrew: there were lots of requests for documentation, and a lot of enthusiasm for binary releases of the API.

3) Metadata draft spec - discussion

  • Item skipped.

4) CellML core specs - update


  • Andrew: finished API for accessing SED-ML object model, the next step is general xpath support which will be used for SED-ML but can be used for various things. Looked at xpath support in LibXML2, and other options for implementing xpath support.


  • Andre: why not use existing standard XML libraries that support xpath?
  • There was a discussion about the problems with available libraries.
  • There was a discussion about the DOM-like binding, and having to write an xpath parser because of earlier decisions made in the API development.
  • Poul: do we need to re-think our approach? Development of tools is a major cost, does it make sense to enable use of existing standards/libraries?
  • There was a discussion about complying with W3C specs vs. using existing tools for xpath, for example.
  • There was an extensive discussion about the XML implementation and documentation of the API.
  • A breakaway was called to continue discussion on the API.

    5) CellML API - update

    • No update.

    6) PMR2 development - update


    • Tommy: Closed the rendering of arbitrary HTML within workspaces. Integrated Andre's CellMLSimulator viewer as a module for PMR2 such that it will remain functional after the closing of the HTML rendering security hole.
    • There was a discussion about security issues in PMR2.
    • Tommy: created a renderer for HTML so users can preview their documentation.


    • There was a discussion about binary releases of the API to support PMR2 features, and the lack of build infrastructure for the CellML API.
    • Andrew: binary releases can be done manually, but it requires that binaries are selected and packaged.
    • Randall: it is worth doing a manual binary release now.
    • There was a discussion about how to handle the initial manually built binary release, and how to version it.

      7) Repository contributions - update


      • Andre: created a new cardiac cell model exposure for Cortassa et al. 2006, which contains a cardiac cell model with electromechanics and energetics.