ABI Meeting minutes 2009-02-25

Present: James Lawson, Catherine Lloyd, Dougal Cowan, Andrew Miller, Michael Backhaus, Adam Reeve, Randall Britten, Justin Marsh, Peter Hunter.
Apologies: Mike Cooling, Jonna Terkildsen, Poul Nielsen.

This week's agenda:

1) CellML community administration
  • James had nothing to report on this item.

2) PCEnv/COR name
  • Catherine reported that Peter Hunter has talked to Alan Garny and Peter Kohl, and that OpenCell will be the new name.

3) Can everyone please confirm they are happy with the programme for day 1 of the workshop
  • http://www.cellml.org/workshop/workshop2009/detailed-programme
  • Catherine reported that the programmes for days 1 & 2 are up online, and that day 3 is planned.
  • James asked what input is wanted on the programme.
  • Catherine said that she will take silence as indicating no objections.

4) Who has had an abstract accepted for IUPS?
  • Abstracts have been accepted for everyone. Jonna, Catherine and Mike also have funding.
  • Peter said that ABI will cover those who did not receive funding. Also, PhD students may have money available in their Press Account for this purpose.  Registration closes 17th April.

5) Kidney model in CellML 1.2 - Consensus? Should we continue to code this up?
  • Andrew Miller sent an email to the team list that has become a discussion on the goals and principles of CellML.
  • There was a discussion on the usage and purpose of the different mailing lists.
  • Randall said that a meeting should be scheduled with Peter and Poul present to discuss the specific issues.
  • Peter thinks that we will have to support this kind of model (Markov style approaches) and suggested deferring the discussion.

6) PMR2 update
  • Tommy has mostly finished the PMR to PMR2 exporter.
  • James has looked at the exported models on the staging server.
  • Tommy reported that the exporter requires more fine tuning.
  • Catherine asked if there is going to be a web interface yet - Tommy reported that there will only be uploading via Mercurial for the time being.
  • Catherine asked how we are going to edit metadata in PMR2.
  • Tommy said that metadata editing will eventually be part of the sandbox.
  • Andrew asked if we should make metadata editing a priority for PCEnv.
Action item 1.) James to try out XML Spy as a metadata editor.

7) PCEnv development - update
  • Justin reported that PCEnv has branched for 0.6 - a first release candidate is available.
  • There was a discussion of remaining interface bugs, some of them long-standing.  Peter commented that it is common to include a known bugs section in the docs, and suggested we did this.
Action item 2.) Dougal to add a known bugs section to the documentation.
  • Andrew has been having a look at the editors; XML and COR.
  • Andrew has looked at scintilla, and can't see any advantages over mozilla.  He is creating native code for syntax highlighting, and said it may be possible to take code from somewhere else for other editor functions (search & replace, undo etc).

8) CellML API - update
  • Adam has been testing IDA with C - requires initial conditions for rates.
  • Randall has been using IDA through MATLAB for the Saucerman model.
  • Justin fixed a minor problem with the Validation service; he mentioned that it was showing up on Windows only as gcc was more lenient than MSVC with some iterator operations. Andrew mentioned that we could probably use a flag in gcc builds to disable this behaviour, so that in future we could use valgrind and gdb to diagnose this kind of problem.

9) Website redesign - update
  • Catherine reported that much of the content has now been migrated, and that Gareth is working on the template.
  • Gareth wants to speak with Justin and Andrew about the specifics of the tools and specification sections.

10) Repository contributions - update
  • Catherine reported that Jeelean finished yesterday and has completed a good number of cell cycle models.  She highlighted Jeelean's preferences of COR for editing and PCEnv for simulation.
  • Peter thought that this could be a good thing to identify for Alan to work on - COR language support in PCEnv.

11) CellML Specs - update
  • James has put the 1.0 draft metadata spec up on git - he wants to get input from original authors about whether it's OK to finalize it.
  • Randall thinks input from original authors is not required.
  • Peter said to go ahead without contacting authors.
  • James is working on 1.1; needs to create a new repository.  James has also written an "introduction to metadata" for the summer school.
  • Andrew sent out a definition of a type to represent a complex number in CellML (lambda type calculus).
  • Randall suggested Andrew send out a more succinct version of the example, possibly a rendered version of the XML.