ABI CellML Meeting Minutes, 27th July, 2011

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

Last week's action items:

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

  • Done.

This week's agenda:

1) PMR2 development - update


  • Tommy: continued development of webservices. Can now extract values from any of the views. Working on how to integrate the security features of the security plugin.


  • Andre: any news on the Plone 4.1 release date?
  • Tommy: the release candidate has been out for a while, no idea on a final date.
  • There was a discussion about Plone 4.1 and the release of PMR2 0.4
  • Andre: we probably need a meeting to discuss features for PMR2 0.5. Is there any plan to add more features to 0.4? What is the schedule for the next release?
  • Poul: has there been any further discussion of features with Duane or Thor? It would be good for Tommy to keep abreast of their thoughts.
  • There was a discussion about other groups and their requirements for PMR2.
  • Randall: an obvious need is support for storing large binary data, not necessarily version controlled.
  • There was a discussion about storage of large files, possibly in separate locations, and issues with referencing these files in exposures.
  • Poul: a good test case for this would be the CAP project.
  • There was a discussion about the CAP project requirements and current status.
  • Poul: would like to see more interaction with other groups who have requirements that seem to match PMR2.
  • Andre: this is probably not the right meeting to be discussing PMR2. A separate meeting might be required.
  • Andrew: perhaps try to find groups outside the ABI who have requirements that more closely match what PMR2 provides already.
  • Randall: the process of integrating other groups has begun, with Thor & Dougal's requirements analysis for workflows.
  • Poul: has anyone responded to the discussion list email about uploading models?

Action item 1: Dougal - email Sanjay Kharche with information about how to create and upload to a workspace, and get him to upload code & data.

2) Repository contributions - update


  • Dougal: Hanne has been working on models and has been having a problem with some session files.
  • Andrew: do we want to have SED-ML files for all new models?
  • Andre: Andre: Frank's tools (libsedml) now support CellML models. CellML 1.0 models generally work better in these tools.
  • There was a discussion about how to get Hanne up and running with SED-ML.

3) CellML API - update


  • Andrew: working on build system. Everything except packaging now working on Mac 32bit. Linux 32bit working. Windows has problems with cppunit, fixed now by including cppunit in source. Windows also has a problem with libxml2 binaries not covered by MSVC2010.


  • Andrew: could consider replacing cppunit with something that is better maintained.
  • Randall: do we know if libsbml uses cppunit?
  • There was a discussion about build slave machines for Mac (the two Mac Minis)
  • There was discussion about the recent removal of the autoconf based build system while the cmake build system is still incomplete (in-tree builds work, but out of tree builds do not work yet).


  • Randall: could Caton take a look at the CMake build system, to make it build out of source?

Action item 2: Caton - put some time into trying to get the CMake to build out of source.

  • Andre: TeLICeMS is broken: bracket precedence and confusion over subtraction and negative numbers.
  • Randall: Andrew could put a small amount of time into checking new tracker items and seeing if any need to be prioritized over the build system and binary releases. The TeLICeMS problems probably do need to be prioritized.

4) CellML core specs - update

  • No update.