ABI Meeting minutes 2009-01-21

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

Last week's action items:

1.) Randall to create tracker items for Steve's ideas.
  • Randall was not present.
2.) James to post about the AGM to the discussion list; propose that we hold the AGM at the Workshop, and discuss how we organize voting.
  • James has not yet posted the leadership document, and so will wait and post both when they are ready.

This week's agenda:

1) CellML AGM
  • There was a discussion about how to get the community to comment on the AGM proposal; via the mailing list or against some version-controlled baseline document?
  • Andrew raised the question of who can vote or comment, as the mailing list is public.
  • James said that his intention was originally to have the steering group appointed at the AGM.
  • Andrew said that we would need to have formalized the agenda and organization structure previous to the AGM for this to occur.
  • Justin warned that there are examples where formalizing a structure has led to an organization or project being led away from its original mission or vision.
  • Andrew suggested looking at existing public documents from organizations or projects in and form the basis of a constitution or structure from these.
  • Mike suggested that the AGM be more of a discussion session, using this to form a first cut of policies and organizational procedures for the CellML "foundation", to give us an initial framework to make decisions within.
Action item 1.) James to start a discussion on the mailing list about leadership/constitution/voting/AGM.

2) IRSES applications
  • James mentioned the need for any interested parties to talk to Catherine about applications.

3) PCEnv/COR name change
  • James asked if the intent for PCEnv/COR is to be a general modelling environment or a CellML specific application.
  • There was extensive discussion about the pros and cons of a number of names or naming criteria.
  • Mike asked if there was a list of criteria anywhere - he suggested that since some people's criteria seem to be mutually exclusive, the criteria could be given to Poul for approval before rethinking the naming.

4) CellML API - update
  • Mike asked if there have been any volunteers to test the Java wrappers - he also mentioned (?) Goskel from Newcastle has volunteered to test them.
  • Abhishek and Sarala will also test the Java wrappers.
  • Justin has been working on e-notation.
  • Andrew has written code to test for errors from CVODE - an error message is now given instead of PCEnv hanging.
  • Adam has been working on a service to return strings used by MALAES and CCGS.

5) Repository contributions - update
  • James has been looking at possible models that represent biological motifs, and how to code them up - switch behaviours, bistability etc.
  • Jeelean has been curating and translating a couple more models.
  • Jeelean said that Linda has made more diagrams.

6) PCEnv development - update
  • Justin has been working on e-notation parsing.
  • A breakaway meeting was called on e-notation.
  • James asked if there is a document about how to write the text-equations.
  • Dougal said that he has some information on this from Justin and is planning to write such documentation.
  • Andrew suggested that Dougal look at the grammar rules as these are the basis for how the text equations are written.
Action item 2.) Andrew to send Dougal information on the grammar.

7) SBML to CellML converter - update
  • Andrew reported that this is now usable; it creates valid CellML and infers units where possible.
  • It is currently very slow, and discards a lot of SBML information.