ABI CellML meeting minutes 2009-10-28

Present: Dougal Cowan, Randall Britten, Geoff Nunns, Tommy Yu, David "Andre" Nickerson, Justin Marsh, Catherine Lloyd, Andrew Miller, James Lawson, Poul Nielsen, Peter Hunter
Apologies: Mike Cooling

Last week's action items:

1) Dougal to write a guide on how to create session files with SVG diagrams.

  • Dougal is awaiting the chance to sit in on a session with James on how to create sessions.

This week's agenda:

1) (Catherine) Review of the curation flags ( tracker item 87 )

  • Catherine reported that she is now going through the curation test models using the MIRIAM flags. Catherine, after discussing it with various people, decided to use the MIRIAM flags as they are an existing standard which seems to cover many of the requirements for our curation flags. We will probably need additional flags of our own.
  • There was a discussion about the additional flags required, and what in the latest MIRIAM standard counts as a flag.
  • There was a discussion about what the differences are between the original MIRIAM paper and the current standard as shown on the website.
  • Peter supported the use of MIRIAM and said that we should get involved in the future development of the standard.
  • Andrew said that if there have been changes to the MIRIAM standard, that there should at least be a version number that can be referred to when using it.

2) CellML specs - update

  • No update.

3) Metadata specifications (general, citations, graphing,   simulation, other)

  • No update.

4) OpenCell development update

  • Justin has been working on fixes for various tracker items.
  • Andrew has been working on getting OpenCell working on Windows.
  • Alan has been working on solving issues when switching between views (TXT view to other views)
  • There was a discussion about the name of the TXT view.

5) CellML API - update

  • Randall reported bugs in the MATLAB code generation service that have been revealed by the Saucerman model. These should be trivial to fix.

6) cellml.org update

  • Catherine reported that work continues on the community section. The related efforts page has been updated by James, and the CellML users section is going to be changed to a small collection of case studies, instead of an out of date, non-ordered list of links. Workshop pages have been created, and await the creation of a registration form.
  • Andrew said that we should still try to get groups to contribute content to the site, and offer to provide hosting for their projects.
  • Andre commented that we have offered this in the past but have had no response.
  • There was a discussion about comparison with the Haskell site, which hosts related projects.
  • Peter said that it is worth having an announcement and information on the site that offers hosting for CellML related projects.
Action item 1) James to add the offer of hosting to the site.

7) Repository contributions update

  • Catherine reported that units curation is complete for the Oxford models.
  • Catherine has been teaching Nick Holford about CellML and how to use OpenCell.
  • James asked if it would be good to add some keywords, such as brain or neuronal.
  • Peter said that we should add a keyword for these, and a keyword for PKPD models.
  • Peter asked if it is worth training Hannah to make sessions - it was agreed that this would be good.
  • Geoff has been working on Saucerman, and had thought that it was working in OpenCell - however some initial condition hints seem to be ignored, and the model gives non-physiological results. A breakaway was called to discuss the Saucerman model.

8) PMR2 development - update

  • Tommy continues to work on the foundation for the new exposure style, and is making progress.
  • Randall suggested again that Tommy get in touch with Matt about design issues.

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

  • Randall started a discussion on a possible MATLAB code generation paper, which Adam Reeve has already written a good portion of.
  • Andre will write some of the paper.
  • This paper will need to reference the API paper.
  • There was a discussion about making the complete model structure tree view the default view in OpenCell. It was agreed that this should be done.
  • Peter said that we need to base interface decisions on feedback from new users.