ABI CellML Meeting Minutes, 19th of January 2011


Present: Andrew Miller, Lukas Endler, Tommy Yu, Poul Nielsen, Amy You, Mona Zhou, Camille Nicodemus, David 'Andre' Nickerson

Last week's action items:

  • Action Item 1: Status unknown - it doesn't look like the survey went out to the SBML list.
  • Action Item 2: Discussed under 'API'.

This week's agenda

  • CellML API:
    • Progress: Andrew has fixed a number of issues with the Windows build. The code runs cleanly under valgrind on Linux, but RunCellML crashes in the CIS code on Windows. The exact reasons for this crash are being tracked down.
  • CellML 1.2:
    • Planning: A break-away meeting was held on the status of CellML 1.2. Poul noted that some of this is relevant to the requirements of the IME grant, which is run through the EBI, with Bernard de Bono and Nicholas Le Novere involved alongside Poul.
  • ModML:
    • Progress: More work has been done on the Tran et. al. model, to re-add the equations that were deleted from the Rice et. al. model so Tran et. al. is expressed as the differences from Rice et. al.
  • Repository contributions:
    • Progress: Mona and Camille have both been working on models; some of these models have yet to be pushed.
    • Planning: There was a discussion on the process for adding figures. Where figures are created anyway, it would be good to add them. Andre should also let Hanne know about changed models so she can do figures where required.
  • PMR2:
    • Progress:
      • Tommy discovered that roll-over from exposures in non-default containers was broken. He has cleaned up the code to fix the issue and improved the testsuite.
      • Tommy also cleaned up other testcases for Mercurial and PMR2 support, to remove mutual dependencies. There is still some additional cleaning up required.
      • Tommy has been working towards MathML display, but exactly how this should be done is not clear. One possibility would be to work with the API to rename variables so the mathematics makes sense as a stand-alone description of the model. However, this would require a fair amount of work for Tommy, so might not be a priority.
  • HARMONY survey - Andre noted it had not been sent to the list, because it was stuck in the moderation queue. Tommy approved it.
  • Fourth year projects - Poul noted the deadline is approaching.
  • Article on Distributed Version Control for Repositories has now been published. Action Item 1: Tommy will put out a news release for both repository related papers on the site, and also put up information on how to cite the repository.