ABI CellML meeting minutes 2010-04-07

Present: Dougal Cowan, David "Andre" Nickerson, Justin Marsh, Geoff Nunns, Andrew Miller, Poul Nielsen, Catherine Lloyd

Apologies: Randall Britten

Last week's action items:

1) Andrew to get in touch with the Saint developers and offer them the Java shim.

  • Done. They seem happy to try the Java shim.

2) Dougal to put PDF versions of the OpenCell documentation up somewhere, linked to from the site.

  • Not done, will be done today.

This week's agenda:

1) (Catherine) e-notation: please can a script be run through the repository to correct all the broken e-notation? We are still having to fix this by hand.

  • Catherine keeps coming across models that need to have the e-notation fixed, and she really wants this to be scripted for the entire repository.
  • There was a discussion about how to implement exposure roll-over for fixed models, and how to select models to be fixed.
  • Andrew suggested that it might be worth making a library to support future systematic changes such as this.

2) PMR2 development - update

  • No update.

3) Repository contributions - update

  • Catherine has finished curating Lucian Smith's list of broken models, which are now all fixed and pushed back into the repository. One of these models contained PDEs which can't be curated.
  • There was a discussion about PDE models.
  • Poul said that models containing PDEs should just be left uncurated, and should remain in the repository.
  • Geoff has uploaded the Grandi model. This does not use embedded workspaces, although it is CellML 1.1. By user request a 1.0 version was also made.
  • Geoff has also adapted Albert 2005 from the BioModels Database. This now needs metadata to be added before it can be pushed into the repository.

4) CellML specifications - update

  • ModML: Andrew has made progress on support for reactions, although there are some problems with the way ModML does not treat time as special. There are several possible solutions to this, which were discussed.

5) Metadata specifications (general, citations, graphing, simulation, other) - update

  • No update.

6) OpenCell development - update

  • Justin has continued work on the Scala proof-of-concept.

7) CellML API - update

  • Andrew has been working on an RDF container library, which currently performs a number of container operations and has a test suite.
  • Andrew may have the Java shim ready today for the Saint developers.

8) cellml.org - update

  • Catherine wants to be removed as the recipient for the webmaster emails, as she is getting a large volume of filter-avoidant spam.