ABI CellML meeting minutes 2009-12-02

Present: Andrew Miller, Catherine Lloyd, Geoff Nunns, [students], Peter Hunter, Tommy Yu, Justin Marsh, Randall Britten, Dougal Cowan, Poul Nielsen, David "Andre" Nickerson,

Apologies: James Lawson

Last week's action items:

1) James to update Tracker Item 2055 and email a request for comment on this item to cellml-discussion.

  • Not done.
  • Catherine offered to update 2056 (Andre pointed out 2055 was a duplicate and is closed) and email cellml-discussion.

This week's agenda:

1) Andre's report from the INCF Workshop

  • Andre reported back from the INCF Workshop in Bangalore.
  • The first version of NeuroML is not very usable, but a couple of tools already support it.
  • There has been a lot of work by the SBML and Virtual Cell groups on spatial models.
  • A taskforce is being set up to develop standards.
  • Peter asked how NeuroML differs from SBML or CellML.
  • Andre said that NeuroML allows you to describe axons, dendrites, etc; a connectivity spatial modelling. SBML packages are used for the geometrical spatial modelling.
  • Randall asked if we should be taking a look at the SBML geometry modelling package.

2) PMR2 development - update

  • Tommy has created the "two radio button" UI for migrating (rolling over) exposures. He gave a demonstration.
  • Catherine asked whether we need a tracker item about the big diagrams on exposure pages.

Action item 1) Catherine to search for an existing tracker item and to create one if it doesn't already exist

  • There was a discussion about image sizes on the exposure pages, and possible solutions within Plone.
  • Andre said that we should not be putting the PNGs into the repository, only the orginial source SVGs.
  • Tommy said that eventually we should be able to use the SVGs and transform them on the fly to PNG for the exposures.
  • Randall suggested we address the image size problem for PMR2 0.3.

3) Repository contributions update

  • Geoff uploaded a heart model, and is still working with Miles Rubin.
  • Catherine finished a Cloutier brain metabolism model, and has uploaded it.
  • Tessa has been working on a Bertram ATP model and is currently balancing the units.
  • Ethan has been working on several Dupont models, and is adding RDF tags now.
  • Mark has four calcium dynamics models (Goldbeter 1990) to push into the repository.
  • Catherine and Geoff are curating James' Lockwood PKPD model.
  • Peter asked about progress on a guide to creating SVG session files.
  • Dougal reported that technical issues have prevented the guide being completed.
  • There was a discussion about the javascript for the SVG session files; where the best template is and that we should probably have it under version control.
  • Peter emphasised the importance of SVG session files.
  • Catherine asked whether we should expose the Saucermann et al (2003) model.
  • Randall said that this should probably be exposed as the latest version is better than the currently exposed version.
  • There was a discussion of how to get this model working in OpenCell.

4) CellML core specs - update

  • A breakaway was called.

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

  • A breakaway was called to discuss probability distributions of parameter values.

6) OpenCell development update

  • Justin reported that more blockers have been identified.
  • (Tracker items fixed?)
  • Andrew explained the problems described in tracker item 1716 - it was generally agreed to change this item to a feature, and remove it as a blocker.
  • Randall called a breakaway to discuss outstanding bugs.

7) CellML API - update

  • Catherine asked whether Andrew McCulloch asked about Continuity.
  • Andrew said that we may need to help out with this later, but probably not right now.
  • There was a discussion about the current state of the Java wrapper. Randall reported that there have been some small test cases written and it does work, but only on Linux.
  • There was a discussion about wrappers and SWIG.
  • Andre reported that libSBML is now almost completely re-written for Java.

8) cellml.org update

  • Michael Backhaus has re-levelled all the team pictures, and the team page has been updated.
  • James has merged some of the standfirsts on the tools page.
  • Content is being created by Morgan and Sarala for the annotation and visualisation page.