ABI CellML Meeting Minutes, 10th November 2010

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

Last week's action items:

1) Mike to check out funding sources to get people to HARMONY.

  • Done:
After an search of some hundred possible scholarships and soliciting advice
from Marty, Leo, VJ and Rob, it seems that funding for travel is available
from 2 application-inspecific sources, namely:

Charles Fleming Fund (applications due 31 march 2011)

MPPT: (applications due 1st march)

AMRF: (due 4th Feb)

In all cases it would be competitive with each other and all other
applicants. The amount would only be a partial cover from any single win.

2) Dougal to put "Developing for CellML" on the home page of cellml.org somewhere.

  • Done: API added to Tools heading. More prominence of the API needs further planning.

3) Randall to revive survey planning email thread, and add statement on the current state of API resources.

  • Done.

4) Mike to create a tracker item about metadata editing features for the API.

  • Done.

This week's agenda:

1) CellML API survey (Randall)


  • Andrew: we may need to get ethics approval for the survey.
  • There was a discussion about ethics approval, anonymity of participants, etc.
  • Andre: sees no need for the second part of the survey, this information is what we should be getting from the tracker and other sources.


  • Randall: we should probably use SurveyMonkey, and put both parts 1 & 2 on the same survey.
  • There was an extensive discussion about what to do about ethics approval, and whether the survey should be anonymous.
  • Randall: Dougal could put the survey together on SurveyMonkey.

2) CellML API - update


  • Andrew: continued work on TeLICeMS, likely to be finished either this week or next.

3) Repository contributions - update


  • Catherine: contacted by a PhD student who is trying to get the Vendelin et al. model working. There appears to be insufficient data in the paper to get the model working, and the student will need to get in touch with the authors.
  • Catherine: putting together work for the summer students who will be working on creation of the 1.1 component library. There is a bit more time before best practice of how to break down 1.0 models into 1.1 components is decided.
  • Catherine: finished work on the metabolism model, which is not quite working.


  • There was a discussion about breaking down models into components, from diagrams, annotations, etc.
  • Catherine: the students start on Tuesday. At first they will be coding up 1.0 models to get a feel for CellML, and then starting on breaking them into 1.1 components.

4) PMR2 development - update


  • Tommy: finished the core of the customized view for files and workspaces, and tested it. Also worked on the shortened ID system for exposures, which is finished now.


  • There was a discussion about whether to create copies of existing exposures to give them short IDs.


  • It was decided not to migrate old exposures to short IDs, but simply to use the new IDs for all new exposures from now on.


5) CellML core specs - update


  • Andrew: ModML - still working on the Rice 2008 model. There are still numerical convergence problems, which changes to the ModML solver attempt to fix.


  • Randall: any thoughts on how people can get an early look at ModML?
  • Andrew: people can look through the data structures, and there may be a model up on github. Some models for people to run will be the next step.
  • There was a discussion about the reasons for non-convergence.

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

Metadata meeting:

  • Catherine: the meeting on Friday about metadata was good, to see a range of options of how the metadata spec might be written.
  • Poul: it would be very good to get Bernard de Bono's input on this.

Encyclopedia article on CellML language:

  • Andrew: crashes with OpenOffice have delayed the process. Will send out a revised version soon.