ABI CellML Meeting Minutes, 18th August 2010

Currently a draft


Randall Britten, Andrew Miller, David "Andre" Nickerson, Tommy Yu, Justin Marsh.

Apologies: Peter Hunter, Dougal Cowen

Last week's action items

  • Last week's action item 1 - Dougal to get in touch with Catherine about [licensing of models with imports]. Dougal has e-mailed Catherine Lloyd.
  • Last week's action item 2 - Justin: Write script to identify all models that require e-notation or xml:base fixes, and then run the script on the entire repository. Tommy is now working on the script as Justin doesn't have time.
  • Last week's action item 3 - Tommy and Andrew: Send out final versions of papers for approval for submission - this has been done, and Tommy will be sending out another version today
  • Last week's action item 4 - Justin: E-mail Mike a link to James' work on the metadata spec: not discussed

This week's agenda

  • Core specifications & ModML - no update this week.
  • Metadata


    Andre reports that Mike is setting up a Biological Ontologies & Annotation Group.


    There was a discussion about how we could share technologies being used in geology in terms of ontologies and annotation for PMR2

  • CellML API


    Andrew has been working on the Python binding code. It is likely that the implementation will be completed today, although testing and bug fixes will likely be needed after that.


    Andre asked about whether we should start making releases of the CellML API independently of OpenCell now that development of OpenCell is being moved to Oxford. Consensus was that we probably should.

  • OpenCell


    Andrew suggested that we leave the development of OpenCell with COR-like text support with Alan Garny, as there may be a significant cost to turning it on. It would then be up to Alan to decide whether to implement support on top of the current code-base, or wait until the code is reimplmeneted. Action Item 1: Randall to ask Peter whether we should make OpenCell 0.9 with COR support in Auckland, or leave that to Alan.


    Justin noted that he had been talking to Catherine, Mike, and Dougal about doing the Litmus tests for the OpenCell release on Windows, Mac, and Linux.

    Justin also noted that Dougal found a problem where filenames with spaces in them do not work on some cases when OpenCell is launched from the browser in Windows, depending on the current working directory.

  • Repository contributions


    Randall noted that he had been testing OpenCell with the Saucerman-McCulloch model. Justin has shown that results closer to MATLAB are achieved with pacing off with IDA compared to with CVODE. With Randall's implementation of a piecewise based pacing function, using IDA, pacing behaviour is observed, but it is different to what is seen from MATLAB. This could be an issue with the model, however.

    Randall said that Dougal said that Catherine had not given him any update this week.

  • PMR2 Update


    Tommy has finished porting the code to Plone 4 - which is needed as he wants to use Plone 4 classes to implement curation flags.