ABI Meeting minutes 2008-11-26

Present: Randall Britten, Tommy Yu, Justin Marsh, Dougal Cowan, James Lawson, Andrew Miller, Catherine Lloyd, Michael Backhaus, Poul Nielsen
Apologies: Mike Cooling, Peter Hunter

Last week's action items:

1.) James to email the decision making process document to the mailing list for comments.
  • James received comments from Alan, suggesting a more "senatorial" system; representatives from working groups on the steering group.
  • The process described by the document is ready to be applied to the metadata and CellML 1.2 decisions.

2.) Randall and Tommy to deploy weekly builds of PMR2 for modelers to try.

1) Repository contributions - update
  • Catherine has added two Noble models that Alan is about to use in a paper.
  • Catherine is still working on the Pasek models.
  • There was a discussion about best practice for encapsulating nested imports.  This was related to a Richard Faville model Catherine is working on which imports parameters for 7 generic pacemaker units from another pacemaker unit.

2) PMR2 development - update
  • Tommy is finishing the file browser.
  • Tommy is working on creating an exposure from a workspace.

3) PCEnv development - update
  • There was much rejoicing as Justin announced that PCEnv is working (substantially, but not completely) on Mac OS X.
  • PCEnv on Mac can load, edit, save etc but does not integrate/simulate.

4) CellML API - update
  • Andrew has almost finished the code to call from Java to the CellML API, including the code to convert JNI types to PCM types, but still needs to write up the PCM to Java calling. Both directions are needed for the callback. However, as the conversion is the bulk of the work, it should not take as long to do the code to call in the other direction.
  • There was a discussion of the issue covered by tracker item 1497. This is where certain DAEs can give different results each time they are integrated.
  • Andrew suggested that extra constraints are added.
  • Randall mentioned that the model may not even be coded correctly.
  • Randall suggested checking if the original (Matlab) code has multiple solutions.
  • There was a discussion about initial values.
  • Randall suggested the approach of specifying constants with an equation:
      • States explicitly what the value is
      • Current functionality only really for differential equations, and is being misused.
  • SBML has a "constant" attribute.
  • Poul raised the issue that with imports it is difficult to determine whether a variable could change or not; this approach ("constant" attribute) was rejected.
  • Catherine asked whether it is possible to have a script to fix bad initial condition models.
  • Andrew mentioned that in CellML 1.1, initial values can be variables.
  • Randall said that PCEnv encourages the wrong practice for initial values.
  • Catherine wanted to know if there was any progress on a script to fix scientific notation in CellML models; Randall and Justin said this has been scoped.

5) Website redesign - update
  • Catherine reported that there was no meeting this week.
  • James has a Plone 3 instance on his machine for development and population of the website with content.
  • James asked about a way to back-up the content from the development site.
Action item 1.) Tommy to help James set up a way to back up the development site content.

6) CellML specs - update
  • Randall raised the possibility of using metadata for initial values.

7) SBML to CellML converter prototype - update
  • Andrew has not worked on this this week.

8) Updates or additional items
  • Peter Hunter wants modules created for summer school/new students, on software training.
  • Summer school students will be using the current repository, so James and Catherine can create the relevant modules for the repository.
  • Pulasthi and Linda are doing an excellent job on the SVG diagrams.
  • Abstracts are due for Kyoto by the 10th of December.  Registration is in April.  Peter wants as many as possible to attend.