ABI CellML Meeting Minutes, 25th August 2010


Present: Dougal Cowan, Andrew Miller, David "Andre" Nickerson, Catherine Lloyd, Mike Cooling, Randall Britten, Tommy Yu, Justin Marsh

Last week's action items:

1) Randall: ask Peter whether we should make OpenCell 0.9 with COR support in Auckland, or leave that to Alan.

  • Email has been sent, still waiting on a reply.

This week's agenda:

1) (Catherine) Tracker item 1703: e-notation and xml:base issues: Now we know how many models require fixing (quite a few - please see the attached PDF!), how are we going to approach this?  i.e. can this be an automated fix or are "we" (Hanne and I) going to have to go through these models by hand and fix them in a text editor?


  • Tommy is now working on this instead of Justin.
  • Catherine: Can the fixing of these issues be automated now?
  • Andre: has a script that will fix e-notation.
  • Tommy: Justin has a script that will fix everything.
  • Randall: Does Catherine want the fixed models to be automatically re-exposed?
  • Catherine: Automatic re-exposure not important as long as tip revision is correct.

2) Repository contributions - update

  • No update.

3) PMR2 development - update


  • Tommy: no changes came back from latest draft of the application note. Should be ready to submit.
  • Randall: PMR2 design meeting was held, URL shortening scheme for exposures was decided.
  • Tommy: has been refactoring workspaces and workspace listing.


  • Catherine: Application note should be submitted.
  • Andrew: is there funding for open access for the application note? This is not known.

Action item 1: Catherine: ask Peter and Poul if there is any funding for open access for the application note.

Action item 2: Tommy: get confirmation from everyone that draft is OK, and get all the requirements for submission organised.

  • There was a discussion about new exposure types and curation flags.
  • Andre: a "reproduces model" flag requires specific simulations and usually multiple models, which current exposures don't have. Different parameters mean different CellML models.
  • Andre: new exposure type should show all the tasks done to reproduce a paper. This can be defined by one RDF file, a description of all tasks performed in a hierarchy. We could use multiple SED-ML files, with a linking document.
  • Andrew: curation flags could apply to current exposures, provided an english text description is written about what the flags apply to.
  • Andre: we want to make sure any curation flag system we implement will apply to FieldML.
  • Catherine: when might 0.4 be released?
  • Tommy: PMR2 0.4 could be released around Christmas.
  • Randall: smaller changes might be possible sooner than this. Other directions to look at might be providing better web-services, or improving the search.

4) CellML core specs - update


  • Andrew: has been working on ModML reaction processing.

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


  • Mike: has spent a lot of time examining and summarising tracker item discussions and other information about past work in this area. Will present these ideas at the meeting in 2 weeks.

6) CellML API - update


  • Andrew: working on Python support, most code generation is working. Also working on the build system.
  • Justin: put together basic numerical regression test suite.

7) OpenCell development


  • Justin: branched for 0.8 release last week. Windows and half of Linux tests done.
  • Catherine: needs VPN or tunnel access to Litmus in order to do the Mac testing.

Action item 3: Andre: send Catherine a link on how to tunnel in to Litmus.


  • There was a discussion about problems with the Litmus testing scripts.

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

  • Catherine: Thanks to Mike, who has volunteered to help Hanne out with starting work on building the 1.1 component library, as she has finished diagramming the repository.