ABI Meeting minutes 2008-11-19

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

Last week's action items:

1.) James to draft a document on the decision making process
  • This document is now fairly complete.
  • There was discussion on the scope of the steering group's decisions, and the make-up of the group.
Action item 1.) James to email this document to the mailing list for comments.


1) Repository contributions - update
  • Catherine has continued to work on the Pasek models.
  • Randall has done some more work on the Saucerman 2003 model.
  • David has fixed the Ben-Tal 2006 model.  This is one of the most highly accessed models in the repository, and having it working is fantastic.
  • Peter put forward the idea of having some kind of display for popularity of models on the website.
  • Jonna has been creating session files.
  • James has got Abhishek up to speed on making sessions, which he is now doing.

2) PMR2 development - update
  • Tommy has got basic workspaces, log histories, and a file browser/viewer working.
  • Tommy reported a Plone bug which was found during PMR2 development on the plone.org tracker.
  • Randall suggested setting up a weekly build of PMR2 on some external hosting for testing and to enable people to see progress.
Action item 2.) Randall and Tommy to deploy weekly builds of PMR2 for modelers to try.


3) PCEnv development - update
  • Justin has been working on XPCOM registering in Mac OS
  • Jonna asked if there were plans to avoid scrolling in large SVG diagrams; either through pop-out windows or zoom & pan.  This is discussed in tracker items 1308 and 1100.
  • There was a discussion about zoom & pan, and whether this will work with the mixed XUL and SVG content. Discussion was continued in a break-away meeting after main meeting.
  • Randall mentioned that Alan has got PCEnv to build with the latest XULRunner builds on the latest Ubuntu.
  • There was a discussion on switching to nightly builds of XULRunner for PCEnv.

4) CellML API - update
  • Andrew has been working on Java bindings - currently generating Java code to construct wrapper.
  • Justin has made a few bug fixes.

5) Website redesign - update
  • James reported the plan to put a development site up on his computer, on to which we can place content as it is written.
  • James has written the FAQ.

6) CellML specs - update
  • James reported that most of the metadata spec is ready to implement or discuss.
  • The roadmap is now up on the site.

  • The use of the initial_value attribute on algebraic state variables was raised, and discussed further in a break-away meeting after the main meeting.


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

8) Updates or additional items
  • Randall mentioned Andre's work on CellML in OpenCMISS.
  • Catherine mentioned the new photographs for the site, which will be taken next Wednesday.
  • Peter Hunter reported that Mike Hucka has secured NIH funding for USA participants to travel to the workshop.
  • There was a discussion on a new name for PCEnv/COR.  Encore was suggested (Peter Kohl) and is a preferred option, pending a search for software that already uses this name.