ABI CellML Meeting Minutes, 26th January 2011

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

Last week's action items:

0) Dougal to send an email asking Mike Hucka if it is appropriate to send the survey email to the SBML mailing list. Then send a reminder email to the appropriate list(s), with deadline of max 2 weeks.

  • Mike would prefer if the survey was sent to the sysbio mailing list. Dougal will send the survey out again.

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.

  • Tommy has put the information on the site, and will create a news item soon.

This week's agenda

1) PMR2 development - update


  • Tommy: more refactoring, cleaned up user authentication for the protocol level access of workspaces to make it more generic. Test cases still need to be made. More work on migration scripts for v0.4.
  • Refer to tracker item 2745 (https://tracker.physiomeproject.org/show_bug.cgi?id=2745).


  • Randall: 0.4 will most be to do with working out how to implement dynamic exposures, working with Andre. It would be useful to have an outline by next week. There will also be some futher work on FieldML support.
  • Andre: should be still be creating workspaces in the workspaces folder, or in our username folders? Should the "personal workspaces" be renamed or changed?
  • Randall: we might want to turn off the ability to create workspaces outside your username folder. Do we even need the global workspace listing?
  • There was a discussion about removal of the workspace listing from the main navigation, and other workspace listing and display issues.
  • Randall: There is a need to improve the user specific listing of workspaces.
  • Andrew: Perhaps a listing of all the workspaces that users have greater than default access to would be useful.
  • Randall: there are two separate tasks: give users a listing of workspaces that they have some non-default access to, and to enforce that workspaces are always created in the username folder.

Action item 1: Tommy - check that there is proper disaster recovery (usable backup) for PMR2.

Action item 2: Tommy - remove global workspaces list link from main navigation bar.

2) Repository contributions - update


  • Andre: Mona has workspaces where she is separating models by common mathematics, and Andre needs to have a look at these soon.

3) CellML API - update


  • Andrew: still working on trying to get the Windows build working. Has made various fixes to the test suite. Fixed an issue with a missing file for TeLICeMS. Tracker items 2813, 2798 and 2811 fixed. Working on interfaces for SED-ML processing service. Helping to get RunCellML working on Windows for Amy & Andre.
  • Randall: Alan Garny is planning a command-line mode for OpenCOR.
  • Andrew: suggested to Shoro a way that he could get his model running with CellML and imports.
  • There was a discussion about the requirements of Shoro's model.


  • Randall: is the build targetted at Windows 7 64bit?
  • Andrew: only has Windows Vista and XP 32bit VMs.
  • There was a discussion about the API and build system on Windows.
  • Randall: how broken is OpenCell without all the recent API fixes?
  • Andre: most of the models Mona is working on are underconstrained but not able to be debugged with OpenCell 0.8.
  • There was a discussion about how to debug these models.
  • A workaround will be tried: using Windows command line test tools, e.g. CellML2C.

4) CellML core specs - update


  • Poul: there was a meeting about CellML 1.2 last week. It seems that typing will need to be introduced to CellML 1.2 to handle things like breakpoints and events. A minimal set of types has been briefly discussed, but needs further discussion.
  • Randall: still planning to look at IDA's root-finding.
  • Andrew: a workaround for the problem with certain resets was found: using two versions of the same root finding condition for each condition, one for equals, one for less-than-or-equals.
  • Andrew: given up on the ModML version of Tran et al for the time being.


  • Andrew: do we want to use Andrew's PhD writing on ModML as the basis for another document? This could also probably be a paper.
  • There was discussion about how to publish Andrew's work on ModML.

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

  • Poul: Andre has put forward a part 4 project for software engineering students. There are now many projects available, so getting a project description up soon is important.
  • Randall: there will be another introductory course to CellML & CellML tools soon. We could possibly use the PKPD tutorial that Dougal is preparing.