ABI CellML Meeting Minutes, 23rd June 2010

Present: Dougal Cowan, Andrew Miller, Randall Britten, David "Andre" Nickerson, Tommy Yu, Poul Nielsen, Justin Marsh

Apologies: Peter Hunter, Catherine Lloyd

Last week's action items:

1) Justin to e-mail Catherine to ask her to update the curation guidelines. Justin also to add a tracker item to remind us to improve error messages in OpenCell.

1a) Justin to create tracker item for Mac OS X 10.5 issue

2) Tommy to send the application note around to all authors who haven't seen it yet.

  • Done.

This week's agenda:

1) Repository contributions - update

  • Poul has been working on updating the constants co-data model, including many radical changes, such as MathML equalities instead of initial values, and the addition of uncertainties. This model will be updated as required, with a whole new model being created when new values are published.
  • Poul would like some feedback on the style of the CellML, from Catherine etc.
  • Randall said that it is worthwhile encouraging the use of this model for imports.
  • Hanne has been pushing a large number of SVG session files for cardiac models.

2) (Andre) Use of model provenance outside PMR2/Mercurial.

  • Andre said that as BioModels are importing 100+ CellML models, and all the Mercurial information will be lost, we need to think about how to maintain this provenance information.
  • Andre puts a lot of provenance/change information directly into the XML of the model file, annotating the changes as they are made. This is not lost when the models are taken out of Mercurial.
  • Andrew said that it should be up to the people who are working with models outside Mercurial to maintain the provenance information, and that we should always encourage the use of Mercurial with CellML.
  • Randall said that direct annotation of CellML elements in the XML still has its advantages.
  • There was an extensive discussion about the problems of tracking changes via Mercurial or XML annotations.

3) PMR2 development - update

  • Tommy reported that PMR2 0.3 is now live on models.cellml.org. He has since had to make a small point release to fix an issue with exposure creation.
  • Randall asked if there is any FieldML on the live site - Tommy reported that there is not.
  • There was a discussion about FieldML exposures/workspaces.
  • Randall said that the FieldML exposures should be added. There should also be a note explaining that currently field models are being represented using the cmgui exnode/exelem format rather than FieldML, since work is still in progress on FieldML and the supporting tools.
  • Tommy has been working on a metadata editor for MIRIAM flags (curation).
  • Randall asked what the goals are for 0.4. Important goals for 0.4 seem to be improving the search, curation flags, and considering revising the way exposures work.
  • Andre suggested that curation flags rely on a different exposure type, one that can reproduce the results that the curation flags report as being matched.
  • Randall said that we need to involve Catherine in any exposure/curation discussion.
  • There was a short discussion about bugs in 0.3 that have been reported by Mike Cooling.

4) CellML API - update

  • Andrew has made some fixes to code generation, and has fixed the crashing bug on Windows.
  • Andrew is working on the buildbot issues, which possibly involve another timeout problem.

5) OpenCell development

  • Justin has been working on IDA support.

6) CellML core specs - update

  • No update.

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

  • Mike has sent an email saying that he will be working on the metadata spec. It is not known if he will be working based off James Lawson's initial work, or starting from scratch.

8) (Dougal) Discussion of content for the CellML tutorial at EMBC 2010.

  • There was a discussion about who will be at the tutorial. Poul will probably not be there.
  • Randall suggested that we may need to send another member of the CellML team.
  • Andre said that it would be good to see the proposal.

Action item 1) Dougal to find out about what was contained in the proposal.

9) Time permitting: Updates or additional items from volunteering attendees

  • Justin gave a presentation of his metadata editor, which is currently usable for editing author metadata in CellML models.

metadata editor screenshot