Meeting Minutes 2008-02-13

Present: Randall Britten, Sarala Dissanayake, Michael Cooling, Catherine Lloyd, James Lawson, Justin Marsh, Andrew Miller, Anil Wipat, Tommy Yu


Action items from previous meeting:

  • Randall to speak with Gareth about creating the missing FieldML page.

    • Randall has told Gareth, but no response from him yet. It will be followed on the tracker.

  • James to organize meeting with Sarala (and others) to learn about (automating the generation of Javascript hooks between SVG diagrams in PCEnv).

    • James was able to meet with Sarala and Justin yesterday and had a nice discussion

      • However, Sarala cannot help now, but it may be possible in the future

      • Justin planned to spend some time development some kind of interface that will aid the manual process of building the Javascript bindings.

        • Andrew has a concern: how would the correct SVG components be identified?

          • Events could be bubbled up to the root container element.

          • Also there needs to be a way to group a set of SVG elements together.

    • Discussion deferred to breakaway.

Agenda

Randall: Mapping between CellML 1.1 specification and a version of draft of CellML 1.2 specification

  • There was not enough time to discuss this in last week's breakaway session.

  • This is already a tracker item.

    • Need an informative annotated version of the 1.2 specification.

  • Andre wants a more accessible draft of the CellML 1.2 specification.

    • Concern is if the draft changes, the mappings may need to be corrected.

    • Alan and Andre could really use one, however.

  • It's decided that a quick and dirty mapping could be done.

Peter: Models with delays: specification and PCEnv

  • Catherine has received an email from Rui Zhu, about a Delayed Nonlinear PBPK Model being incorrect as it does not have time delay represented properly in the CellML model.

    • He noted that SBML can support this

    • However PCEnv cannot.

    • Catherine passed this issue to Andre, and he guided Rui on how to use Virtual Cell to achieve this.

    • Anil wonders if partial differential equations (PDE) can be used to express time delays.

      • Andrew points out MathML supports this, however current tools cannot solve PDEs.

    • This may need to be a priority, as we don't want to lose users and support over deficiencies in provided tools.

      • Currently Peter makes the decisions as to what to develop.

    • New programmer will interface CMISS with CellML, and will also do what Andrew and Justin is currently doing when that task is done.

    • There will be discussion in the workshop (about 30 minutes) about what priorities the CellML project should focus on.

CellML Workshop/meeting of 2008 update.

  • The plan is basically frozen.

  • Filming people is fine, as permissions has been given by speakers.

  • Mike points out that the copyright issue still stands, as presenters could put up items that they do not own the copyright to, and if we film them and broadcasts it, we will also violate copyright.

    • We could review the videos and censor questionable parts before distributing them.

  • Jonna organized the items for the Washington Synthetic Biology conference.

    • Originally she was supposed to go, but Poul decided that Andrew is a better candidate to represent the CellML team for that conference.

    • Funding is available for someone to go, and that James and Catherine believe strongly that we need to make the case for CellML at this meeting, lest we miss an important opportunity.

    • May need to clarify with Poul about this.

  • Waiheke conference

    • James is available to do a poster about curation and other related topics.

PMR2 Update

  • Tommy has got the Mercurial repository backend to pretty much the point he got with Git.

  • He will be working on the interface that exposes the model.

  • PMR – Peter wants the 'solve model box' to be improved slightly.

CellML 1.2 Specification

  • Andrew is using the tracker to handle issues that are raised.

MathML escaping variables in CellML

  • Catherine wonders why the '$' sign is added in front of certain variables.

  • Andrew points out that it must be PCEnv's escaping mechanism which ensures that variable names don't get confused with reserved names.