ABI CellML Meeting Minutes, 13th of April, 2011

Present: Dougal Cowan, David "Andre" Nickerson, Tommy Yu, Poul Nielsen, Randall Britten

Apologies: Andrew Miller

Last week's action items:

Action item 1: Tommy to open tracker item to fix expired exposures that are coming up in the search.

  • Still need to find if there is an existing tracker item for this. Not done.

Action item 2: Andre to type up what he has and send it around.

  • Done.

This week's agenda:

1) New PMR2 paper


  • Randall: a more in-depth PMR2 paper is required to follow the DVCS and application note papers. There are three possible first authors - Tommy, Andre, or Dougal. Tommy is busy and does not want to be first author, Andre does not know when he will have time to do this. Dougal is happy to be first author.
  • Poul: good idea to get Dougal to be first author and coordinate this paper.
  • Randall: the author list will be similar, we need to offer people who are no longer here (such as Catherine and James) the option of being involved.


  • Randall: need to decide on an appropriate journal.
  • There was a discussion about possible journals.
  • Randall: the first task might be to pick a journal and an intended audience. The paper could tease out the non-technical design, the ideas behind PMR2 separated from the technical implementation.
  • Randall: Dougal could create an outline of the paper content, and look at journals to decide on a target journal.
  • Poul: might want to look at journals which recommend the use of databases/repositories.

2) CellML core specs - update


  • Andre: should we organise some posters for the HARMONY poster session next week? This could be something to explain the different approaches taken by CellML and SBML in terms of specifications - a broad fundamental spec with restrictive additional specs, in the case of CellML.
  • There was a discussion about HARMONY presentations.
  • Andre: on the Combine website, CellML is listed under "Related standardization efforts". It is probably worth becoming a core standard spec, and finding out what is required for this.
  • Randall: Andrew spent some time explaining ModML.

3) CellML API - update

  • No update.

4) Repository contributions - update


  • Tommy: The Li, Smith 2009 model needs fixing.


  • Andre: we need to confirm with them that the model can be made public, once fixed.
  • There was a discussion about workspace/exposure privacy issues.
  • Randall: Peter said that he would speak to PIs about curation of CellML repository sections. This is still in progress.
  • Poul: we don't have resources available for curation at this stage.


  • Randall: send an email to Steve Niederer once the model is fixed.

5) PMR2 development - update


  • Tommy: working on packaging the packages for the 0.4 release, working through version conflicts that need fixing.


  • There was a discussion about Zope/Plone version issues for PMR2.
  • Randall: the 0.4 release should probably wait for the official software stack release.
  • There was discussion about staging of the 0.4 release candidate.
  • Andre: if the official release is a long way off, then the staging should be done somewhere external for the benefit of external users.


  • Randall: stage on Amazon hosting.
  • Randall: 0.5 planning is required. Alan Garny is very keen on web services.
  • There was a discussion about PMR2 web services, and which services are part of PMR2.
  • The list of potential web services under tracker item 1909 was discussed.
  • Tommy: web services and search improvements are key 0.5 features.
  • Randall: things that can be done without the metadata spec, such as filtering on 1.0 and 1.1 models, need to be done.
  • Randall: the download link issue in tracker item 2495 needs to be addressed.
  • Randall: the interim plan for 0.5 is to work on web services and minor items from the tracker.

6) Google analytics - cellml.org and models.cellml.org


  • Andre: Catherine and James still have access to Google analytics on cellml.org.

Action item 1: Dougal - follow up with Gareth to get CL & JL removed and Randall added to Google analytics.

  • There was a discussion about what Google analytics has been telling us about the sites, and what it could be used for.

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

  • Poul: we could import all the SBML models from Biomodels into PMR2. It is important to have an illustration that the repository is for any model type.
  • There was a discussion about extending PMR2 for presentation of SBML models.
  • Randall: WebGL could be a good way to go for the future of FieldML presentation in PMR2. Demos of WebGL were viewed.