ABI CellML Meeting Minutes, 20th July, 2011

Present: Dougal Cowan, Caton Little, Tommy Yu, Andrew Miller, David "Andre" Nickerson, Poul Nielsen, Randall Britten (later)

This week's agenda:

1) CellML core specs - update


    1. Convert all models in the repository, and provide tools for conversion. Expect that users will need to convert.
    2. Provide a webservice where converted models can be obtained using the URL of an old model appended to a specific URL.
    3. Say nothing about the problem and let tool developers deal with it.
  • Andre: perhaps 1.2 should be 2.0, because it will break backwards compatibility.
  • There was a discussion about these various compatibility issues.
  • Further discusssion was put off until the 1.2 breakaway.

2) CellML API - update


  • Andrew: temporarily put the work on uncertain parameters on hold in order to prioritize the binary releases.
  • Andrew: CMake now supports running tests. Clean builds are now working on Linux & Mac, which required an overhaul of the buildbot configuration. Working on buildbot for Windows. Working on packaging with CMake, using CPackage.
  • Andrew: only 32bit Mac available at present. It may be possible to build 64bit Mac versions on 32bit with an updated version of XCode, but this now has to be purchased.


  • Andrew: it may be possible to build a Mac linker using the open source version from Apple, which would eliminate the need for XCode.
  • There was a discussion about how much work this would be.

3) PMR2 development - update


  • Tommy: backported the security fix to 0.3 and released it. Work on the security plugin revealed a CSRF vulnerability in Plone, which has been reported to them.
  • Tommy: cleaning up the JSON API to make it easier to extend.


  • Tommy: Peter Hunter reported issues accessing cellml.org from overseas. This may be caused by some networking issue.
  • There was an extensive discussion about problems with the hosting for cellml.org and the repository.
  • Andre: the site[s] should be hosted somewhere else and tested, to see if the issue arises from the hosting.
  • It was agreed to test the sites on US hosting services, and potentially move them if the problems are not seen.

4) Repository contributions - update


  • Poul: Hanne is back encoding liver models & sessions.
  • Andrew: do we want to make sessions? Should we be making SED-ML files instead?
  • Dougal: it should be possible to convert sessions, and this would be desirable in any case due to the very large number of sessions already existing.
  • There was a discussion of summer students working on this project.

Action item 1: Andrew - write a summer student project for the session to SED-ML converter.

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

  • Andre: discussion of the COMBINE standards is ongoing. We need to have an elected editorial board to be a part of COMBINE. We should probably adopt the SBML procedures for this. Having an editorial board is a good idea anyway, to expedite approval and publication of specifications.
  • There was an extensive discussion about editorial board election.
  • Andrew: should use STV to avoid vote splitting.
  • Andre: we need to call for nominations for the board to get the ball rolling as soon as possible.
  • Randall: Dougal will be returning officer for the voting when it occurs.