ABI Meeting minutes 2009-02-18

Present: Randall Britten, Dougal Cowan, Adam Reeve, Andrew Miller, Catherine Lloyd, Poul Nielsen, Justin Marsh, James Lawson, Jeelean Lim, Jonna Terkildsen, Tommy Yu, Mike Cooling

This week's agenda:

0) Lambda calculus typing system
  • Poul and Andrew are calling for some movement in this area; Andrew is to get some concrete examples created.
  • If anyone is interested, Poul and Andrew will be pushing this during the next few weeks - take a look at the tracker item. (?)

1) CellML community administration
  • James wants to keep the ball rolling on this - he asked if anyone had read Andrew's document.
  • James likes the voting system.  He is not convinced we need to become a legal entity yet. He will raise this issue again next week.
  • James is leaning towards having a discussion on the administration (rather than having a system in place) at the workshop.

2) Status of PDE support
  • Mike pointed out the tracker item about PDE support - he wants to be able to do PDE modelling. He asked what the plans for PDE modelling are.
  • Some models in the repository have PDEs, even though we can't run them. Catherine said that this is because these were written before any CellML tools were created.
  • Andrew said that the next CellML spec should support boundary conditions.
  • Poul said that from his point of view, the boundary for CellML is lumped parameter models, and that PDEs are more suited to FieldML.
  • Mike asked if PDEs are ever going to be supported by CellML, or if he should go with FieldML.
  • Andrew said that it would be possible to write PDEs into a secondary CellML spec.
  • Randall reported that Richard Christie says PDEs are outside the initial scope for FieldML.
  • Poul said that PDE support is intended for FieldML despite being outside initial scope.
  • Randall said that different PDEs require different solvers.
  • James asked if CMISS supports PDEs; Poul said that CMISS PDEs are hard-coded.
  • Poul said it would be interesting if somebody wanted to provide a secondary CellML spec for PDEs.
  • Randall reported that Andre is working on a link between CMISS and CellML; whereby CellML parameters can be varied spatially across a CMISS field, although only at discrete points.

3) Repository contributions - update
  • Jeelean has been making sessions and finding more cell cycle models to translate.  She has put up all of her models and sessions so far.
  • Catherine has looked at the SBML to CellML translated model from Andrew's tool - the CellML model is currently over-constrained.  However she will abandon this model for now at least because the Manchester group have indicated that they are still working on it and it isn't worth converting it into CellML until they are finished.
  • Catherine suggested that the Teusink model be tried as a test for the SBML to CellML translater tool.
  • Andrew has talked to Nicolas Rodriguez, who has been looking at Andrew's code. Nicolas' priority now is to write the other direction.
  • Catherine has been working on the Moss et. al. 2009 kidney model; she is writing it in CellML 1.2.  The journal has requested the code pre-publication.
  • Andrew said that although it is possible to come up with a declarative representation of this procedural model, it is not necessarily a good fit with CellML.
  • Poul supports adding it to the repository even though it is outside the spec, as long as there are caveats.
  • There was an extensive discussion about unsupported models and procedural vs. declarative boundaries.

4) PCEnv development - update
  • Justin has been fixing bugs from the Litmus testing; it seems all bugs are now caught.
  • James asked if it is worth doing mid-term testing to speed up the development process.
  • Justin said that the main goal is to get all three platforms in use, and bug reports filed.

5) CellML API - update
  • Adam has been testing the IDA from Sundial on the Saucerman model.
  • Jonna raised the topic of the KINSOL solver. Randall said that the work on this depends on the upcoming planning for CellML-API 1.7 and PCEnv 0.7.

6) CellML Specs - update
  • James has been working on the metadata spec, and has looked at using git version control.
  • Andre is interested in cross-referencing within the spec; has Andrew got any ideas on how to do this?
  • Andrew didn't remember any discussion with Andre, and will have to find out exactly what Andre is after.

7) Website redesign - update
  • James has been migrating and creating content.
  • Catherine announced that there will be a meeting next week.
  • James thinks the content will be all done by the workshop.

8) PMR2 update
  • Tommy has finished the MathML rendering, but not to PDF.
  • Tommy has started the metadata work.
  • Tommy is now working on migration of models from PMR to PMR2, this is a priority.

9) Updates or additional items
  • Catherine has the workshop timetable tentatively fixed now for days 1 and 2 and this has been posted on the Workshop website.
  • Both Alan Garny and Jonathan Cooper have agreed to learn how to use Martin Fink's Matlab to CellML converter and will relay the tutorial to Catherine (and any others who may be interested in learning how to use it) when they are in Auckland in April.