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
2) IRSES applications
3) PCEnv/COR name change
4) CellML API - update
5) Repository contributions - update
6) PCEnv development - update
7) SBML to CellML converter - update
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.
- 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.
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.
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.