Meeting Minutes 2008-02-07
Present: Randall Britten, Michael Cooling, Edmund Crampin, Catherine Lloyd, Peter Hunter, James Lawson, Justin Marsh, Andrew Miller, Poul Nielsen, Jonna Terkildsen, Anil Wipat, Tommy Yu
Action items from previous meeting:
Justin and Randall will review the specification draft.
Randall and Justin have spent some time reviewing the specification draft.
However, Randall noted it would be good to involve more reviewers, especially reviewers who have had a longer background with CellML. Poul said he would join in the review.
- Randall also reiterated Alan Garny's suggestion for a way of cross referencing between the CellML 1.1 spec, a version of the draft of 1.2. There was some discussion about how and whether to do this.
Further discussion was deferred to breakaway session.
Agenda
FieldML URL in the CellML specification.
Mike had found a broken hyperlink to FieldML in the CellML 1.1 specification.
Andrew pointed the error out to Gareth, and wanted Gareth to create a page at the targeted URI. However, Gareth changed the URI of link on the specification instead of creating a redirection page.
This could lead to a problem where a person may have a static version of the specification, and it will not lead to the correct URI. Resolution is to have Gareth create the page at the former link also.
Action item: Randall to speak with Gareth about creating a redirect to the new FieldML page from the old URI.
Mike: Separation of initial conditions from the model in CellML
Separation of structure from data may be desired to enable overriding of initial value of a model, and changing parameters.
Andre does this already using CellML 1.1 imports; it works because he built the models with this in mind.
Mike suggests some sort of tags that would make this easier.
However the suggestion is to follow current best practices.
Poul: this would present a major change to the specification, and this is not a good enough reason to add a new tag (when current practices appear to be sufficient).
Mike: CellML specification "what's new" pages.
Mike wants a page that briefly states what has changed between different versions of the CellML specification.
There is not much between 1.0 and 1.1 as only imports are added.
As for the changes to be implemented between 1.1 and 1.2, it's still under discussion.
However such a page will be useful, and can be done later as CellML 1.2 specification becomes more solid.
Mike: Standard Unit Files online.
Poul created a CellML file that defines all the secondary derived units that are based on SI from the standard units that are part of the CellML specification.
It was pointed out that "block importing" of all these units will be desirable to save time typing all of them out.
This could be automated by software tools so no need to add the feature that allows block importing of units into CellML (plus it's a major change).
James: SBML to CellML converter
James wants to know what kind of priorities this has, how long it will take.
A suggestion was API mappings between data structures
However the implementation are in different languages (C++ vs Java).
Peter will speak with Mike Hucka regarding possible ways of jointly funding this; it similar to a previous grant.
James: CellML imports into CMISS
James proposes having the CellML repository to generate Fortran code will help this.
There are two tasks. Firstly, the repository integration with the code generation service (CCGS) needs to be upgraded to the CellML API version 1.3, which has significant changes. Secondly, a Fortran definition file (.mal file) needs to be written for the CCGS.
CellML Specification update
Discussed in breakaway session.
Peter: Automating the generation of Javascript hooks between SVG diagrams in PCEnv.
Peter wants to know if this can be automated, as components of the diagram must map to CellML components.
However, the components of the SVG diagram might not use the same identifier (name) as the cmeta:id of the components found in the CellML file, thus render automation of this process difficult or even impossible.
Sarala may have done something in this area that will still allow mapping of identical components identified with different identifiers.
Action item: James to organize meeting with Justin and Sarala (and others) to learn about this issue.