ABI CellML meeting minutes 2009-10-07

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

Last week's action items:

1) Andrew to create a a tracker item about showing warnings for unit definitions problems.

  • Done.

2) Andrew to create a tracker item about warning severity levels.

  • Done.

This week's agenda:

1) CellML Specs - update
  • No updates this week.
2) Metadata specifications (general, citations, graphing, simulation, other)
  • James brought Peter up to date on the metadata spec situation.
  • Peter asked whether we are switching to SED-ML for simulation metadata.
  • Andre said that SED-ML does not yet support everything that we need to do for simulation and graphing.
  • Andrew said that we are still trying to convince the SED-ML group to separate out graphing and simulation.
  • Andre said that you might want to change some of the graphing metadata to get different graphs from the same simulation, or vice versa.
  • Peter said that we want to encourage cooperation, and use accepted standards if they exist.
  • There was a discussion about the convergence of metadata and language standards, SBML and CellML, etc.
  • Andre said that the minimal information standard should be out soon.
3) OpenCell development update
  • Justin has been working on the windows Physiome build environment installer.
4) CellML API - update
  • Andrew has been spending time processing the manuscript for the API paper and wants to submit this as soon as possible.
  • There was a discussion about the Physiome build environment, its history and what the goals of Justin's current work is - to provide a graphical installer that can install a functional Physiome build environment on any Windows machine, without disturbing any existing build environments.
  • Most other work is waiting on this build environment work.
5) cellml.org update
  • Dougal reported that he has been made the second manager of cellml.org, to take some of the pressure off Tommy for day-to-day tasks on the website.
  • Dougal said that there have been minor changes made to the structure of the community section to make it more generic: events instead of workshops, with workshops now under events.
6) Repository contributions update
  • James reported that Catherine has been making lots of exposures.
  • Catherine's students have finished, James and Catherine helped them get their models into the repository.
  • Peter mentioned Alan Garny's reports of discrepancies in some models.
7) PMR2 development - update
  • Peter suggested that the "Download" link on exposure pages become "Download XML".
  • Tommy said that this part of exposures will be changing, and that the "Download" link will always download the top-level file that was used to create the exposure, whether this be an XML model file, a SED-ML file, etc.
  • Tommy has cleaned up the workflow to make it easier for curators.
  • Tommy has been re-factoring code to make new exposures easier and to enable expiration states.
  • Tommy is working out new ways to expose, moving away from temp doc.
  • Peter asked about whether Saint will become part of PMR2's annotation editing.
  • There was a discussion about annotation editing, support for Saint's web services, and where metadata editing is best done.

To read further discussion on these minutes, please see this thread in the cellml-discussion mailing list.