ABI CellML Meeting Minutes 2009-07-22

ABI CellML Meeting minutes 2009-07-22



Present: Andrew Miller, Amir Shirkhani, David "Andre" Nickerson, Tommy Yu, Justin Marsh, Catherine Lloyd, James Lawson, Mike Cooling

Apologies: Peter Hunter, Poul Nielsen, Randall Britten

Last week's action items:


1) James to freeze the metadata spec.

  • This will be done today.

This week's agenda:


1) IUPS breakaway

  • Action Item 1). James to replace the CellML workshop blurb with the IUPS conference information.

2) Model Annotation

  • There has been some communication between Sarala and Morgan Taschuk.
  • Issues are being raised in the Tracker.

2) PMR2 Update

  • Tommy fixed a bug with empty manifests.

3) Repository Contributions

  • James helped Jonna with the Guyton model.
  • Penny sent Catherine a cardiac model.

4) Website Redesign

  • The new cellml.org site is up.
  • The link check has been done
  • Gareth noted that there was inconsistency in the about page.
  • cellml.org is currently going through the bioeng server, but will fall back to site.cellml.org if there is an outage or crash.
  • Andrew Cantell is going to flip the switch, as Tommy will be en route to IUPS.

4) OpenCell

  • Alan has finished the CellML to COR language conversion, and is making progress on the COR language to CellML conversion.
  • Andrew has the Linux and Mac OS versions of OpenCell building under the build bot system, but the MSVC version still does not, as the CellML DOM API does not yet build under MSVC.
  • Justin worked on bugfixes for James.

5) CellML API

  • Andrew has the Linux and Mac OS versions of the CellML DOM API building under the build bot system, but the MSVC version still does not finish building, due to static initialisers which do not get run under MSVC.
  • Amir is going through the interface generators, and has written some code for the Python binding generators.

6) CellML Specifications

  • Nothing to report.

7) CellML Metadata Specifications

  • The old specification is getting frozen.
  • There has been a large amount of development in SedML
  • Dagmar has emailed about annotations; more metadata is needed than what we currently include in models in PMR2.
  • The use of bioentity or Dublin Core was discussed.
  • One issue is with biomodels qualifiers.
  • James mentioned that keywords are a hack, and are not extensible for general use.
  • Annotation through Saint is promising, but a question is what do we want the structure of the annotation to be?
  • There was a discussion of the Java bindings to the CellML API.
  • Mike Cooling noted that the Synthetic Biology group in Newcastle have developed a single method of annotation that works for both CellML and SBML.