ABI CellML meeting minutes 2010-02-10

Present: Randall Britten, Catherine Lloyd, David "Andre" Nickerson, Poul Nielsen, Justin Marsh, Mark Hanna, Ethan Cho, Tommy Yu, Dougal Cowan, Tessa Paris, Andrew Miller, Mike Cooling

Apologies: Peter Hunter

Last week's action items:

1) Tommy to add a "how to cite" link to the PMR2 list.

  • Not done.

2) Catherine to create a tracker item about connection creation.

This week's agenda:

1) (Dagmar) Model URL inconsistency is causing a problem when trying to cite particular models in a paper manuscript

  • Catherine reported that this URL inconsistency has been fixed. There is a call from users for a simpler URL scheme, as requested by Peter.

2) (Dougal) What information do we want in the CellML tutorial at the workshop?

  • Catherine said that we need to discuss and decide what to do for the workshop CellML tutorial. This could be a very simple OpenCell tutorial, and then a PMR2 tutorial.
  • Andrew suggested checking the list of attendees, as maybe this tutorial will not be relevant to them.
  • There was a discussion about who might attend the tutorial.
  • Andre suggested using the same tutorial as was used at IUPS in Kyoto.
  • Mike said that he is happy to do his simple tutorial.
  • There was a discussion about the workshop, time spent on tutorials, etc.
  • Andrew asked if we have any idea about working groups for the hackathon.
  • Mike asked if it is worth putting a slot in to cover issues discussed at meetings with Sarala - Poul said he could cover these in his talk.

3) CellML core specs - update

  • Andrew continues to work on the converter, from base ModML into IDA code. It is nearly at a stage where models could be written in base ModML.
  • Andrew said he will need to talk to Mike about his work.
  • Randall asked if ModML will require a new API. Andrew said that the demo will have its own API, but that does not mean we're stuck with this.
  • Mike asked if there could be a demo for the workshop. Andrew said that it will only really be possible to cover the concepts at the workshop.
  • There was a discussion about finite delays, and the possibility of getting a student to work on this as a project.

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

  • Randall again mentioned the need to look at SEDML for OpenCell 0.8.

5) cellml.org update

  • Only the workshop pages have been updated.

6) OpenCell development update

  • Justin has been working on the keyboard tree navigation, which is largely fixed with a new version of xulrunner - however this introduces other problems.
  • Justin reported that the CSV export now gives full paths for variables.
  • Andrew has been working on the Windows build environment installer. He has started work on this using NSIS instead of Ruby Shoes.
  • A breakaway was called to discuss the Windows build environment installer.

7) CellML API - update

  • Andrew reported that Alan has made some minor changes, which now need to be approved by the other authors.
  • There was a discussion about changes to the paper.

8) PMR2 development - update

  • Tommy has the cmgui demo done for Peter, which should be hosted tomorrow.
  • Tommy continues work on github (user-prefixed) style URLs.
  • Tommy has been refactoring PMR2 code.

9) Repository contributions update

      1. Models

  • Catherine has been working on endocrine models, going through the whole list.
  • Tessa is working on immunology models; she has made a T cell and a couple of cancer models.
  • Ethan has finished off a Rong model, and was working on another one that required a distribution and can't be done in CellML.
  • Randall asked what the distribution was doing in this model - it was randomly setting a variable to 1 according to a normal distribution.
  • There was a discussion about use of distributions in models.
  • Poul said that this has cropped up before, about whether CellMl can handle variables that are stochastic.
  • There was a discussion about including probability distributions in CellML, where to include these, as inputs or functions, etc.
  • Randall asked if papers the CellML repository models are based on specify uncertainty for variable values, and whether it could be useful to capture these uncertainties with distributions.
  • Poul said that it might be useful to have structured types - it would be nice to be able to specify a variable that is tied to a distribution, for example.

      2. Sessions

  • Mark, Hanne and Dougal have created a number of SVG sessions for electrophysiology models.
  • Randall asked about progress on including Mark's JavaScript template in OpenCell. There has been no further progress on this.

Action item 1) Dougal to talk to Justin about how to include Mark's JavaScript template in the OpenCell installer.