ABI CellML Meeting Minutes, 7th July 2010

Present: Dougal Cowan, Andrew Miller, David "Andre" Nickerson, Tommy Yu, Justin Marsh

Apologies: Peter Hunter, Randall Britten


Last week's action items:

1) Randall to e-mail Poul and Peter for input on [new exposure types, such as CellML simulator, for PMR2].

  • Unknown.

2) Andrew will send out a new draft [of the PMR2 paper] incorporating Andre's comments.

  • Done. More comments have been provided, and there are probably more comments to come, from Andre and Alan.

3) Catherine to send more info [on the units checking bug] to Justin.

  • Justin received emails from Catherine about this..

4) Catherine to contact Geoff Nunns about helping with the Saucerman model again.

  • Catherine has emailed Geoff, but has not yet had a response.

This week's agenda:

1) Catherine) Best practice guidelines for naming a model - or an ability in OpenCell to warn the user about case inconsistencies.


  • Justin: There is already a tracker item (2483) about this issue.
  • Best practice of using all lower-case and spaces replaced with underscores was suggested.
  • Andre: There are already 3 different views on best practice for naming. The tools need to provide warnings or hints.


  • Justin: After the platform change, it is planned to add these warnings. The platform change needs to be undertaken before a proper implementation is made. A "hacky" version of these warnings might be added to the current OpenCell if it takes less than a day.

2) (Catherine) Automatic conversion of e-notation.  According to tracker item 17) this was to be done as part of the 0.3 release.  Since the tracker item is still open I am guessing it has not been done.  Can I ask please what is the time frame for this?


  • Andre: When will this be done - can it be done now?
  • The conversion script may alter the formatting of the XML. This may make work difficult for curators.
  • Tracker item 1703 was discussed.
  • Andrew: A mini XML parser could be created that could recognise what needs changing, and maintain formatting.
  • Justin: There are DOM parsers that maintain formatting.


  • Action item 1: Dougal - ask Catherine whether it is worth bulk-converting the e-notation if the XML formatting is changed significantly.
  • Action item 2: Justin - test the script on an example model, send to Catherine to show formatting of output.

3) (Andre) Discussion of the style and format of meeting minutes - old vs. new styles.


  • Andre: are the minutes becoming something other than minutes?
  • There was a discussion about the minutes as a record of the meeting.
  • Andrew: Could people writing progress reports use the tracker as a summary of progress?
  • There were no strong objections to the new style as long as it accurately records the meetings.

4) (Alan, via Andre) Units checking in CellML API - which algorithm is used? Why are there so many problems?


  • Andrew: Are we sure that there are problems? If so, what are they?
  • Justin: There have been emails on the subject.


  • Andre: We need to find more examples and information. Compare what OpenCell, COR and JSim say are right or wrong. We want to be able to justify that something [use of units] is incorrect and why.
  • Action item 3: Justin: make a tracker item about Catherine's email, re: units checking.

5) (Sarala, via Andre) What are our plans regarding webservices? Sarala's specific requirement is for querying the model repository.


  • Andre: Sarala wants to be able to query the repository for RDF, for example - "give me all the rat cardiac electrophysiology models".
  • There was a discussion of RDF and versioning.
  • Sarala only wants the RDF from exposures.
  • There was a discussion about expiring exposures.
  • Tommy: Sarala seems to want an RDF graph per file. A global RDF store would be nice but is difficult and probably slow, and would require more hardware.

6) Repository contributions - update

  • No update.

7) PMR2 development - update


  • Tommy: Fixed a bug with failed exposure creation. Continued work on the foundation of the new curation flag system.
  • Andrew: Sent a new version of the PMR2 manuscript this morning.

8) CellML API - update


  • Andrew has reviewed a number of tracker items to identify ones that are out of date, and updated or closed a number of them to reflect changes made to the API in the interim.

9) OpenCell development


  • Justin: Fixed the "current error" issue in the validation pane, tracker item 2508. Has investigated a Mac version that will work on OSX 10.5 and 10.6, but this requires a XULRunner version 1.9.3.x or comm-central, which we want to avoid. The change should be back-ported to the 1.9.2 series some time soon.

10) CellML core specs - update

  • No update.

11) Metadata specifications (general, citations, graphing, simulation, other) - update

  • No update.

12) Time permitting: Updates or additional items from volunteering attendees

  • Justin: Has looked at Simple Build Tool for Scala. This seems much nicer than Maven or Ivy, and is compatible with both. It will work with buildbot.
  • Andrew: It is likely that we will have a Maven repository, and use Simple Build Tool.