ABI CellML Meeting Minutes, 9th February 2011

Present: Dougal Cowan, Andrew Miller, Tommy Yu, David "Andre" Nickerson, Amy You, Randall Britten, Lukas Endler, Poul Nielsen

This week's agenda:

1) ABI summer tutorials:CellML tutorial and PMR2 tutorial


  • Randall: Dougal presented the PKPD CellML tutorial on Monday. For the CellML part of the summer tutorial, we can use this PKPD tutorial as well as the electrophysiology tutorial from EMBC.


  • Randall: Dougal is working on the PMR2 tutorial. Dates need to be set for the tutorials, this will be in early March.
  • Poul: may have to book the level 5 room as this is now on the global university booking system.

2) Repository contributions - update


  • Poul: Hanne has been creating some hepatocyte models.
  • Andre: has submitted a paper about the nephron model interface. This is up on-line but not in PMR2, and it was demonstrated at the meeting.


  • Randall: who will be exposing the new hepatocyte models?
  • There was a discussion about who will be creating exposures, who will be curating models.
  • Poul: would rather have all exposure creation go through Dougal for the time being to make sure everything is checked.
  • There was a discussion about migration away from tmpdoc, and that HTML documentation is currently the preferred method.
  • Randall: Andre's nephron interface represents an example of what mixed FieldML/CellML exposures could look like.

3) PMR2 development - update


  • Tommy: spent some time getting the CellML API Python bindings working, and wrote up a document on some of the API issues.
  • There was a discussion about the C++ and Python bindings.
  • Tommy: was able to get the mathematics view working for 1.1 models. Has done some work getting the maths rendering in browsers other than Firefox, using MathJax.


  • There was a discussion about mathematics display, how useful it is, and whether it should be performed client or server side. Server side was decided as the better method as it would allow the mathematics to be interpreted in the context of the CellML model(s).
  • Randall: the aim is to provide server-side rendering with fully component labelled 1.1 compatible mathematics displayed using MathJax.

4) CellML API - update


  • Andrew: worked with Tommy to fix Python bindings issues; name clashes in IDLs and version problems with Python.
  • Andrew: working on the SProS (SED-ML processing service), the object model and reference counting that SProS needs to use has now mostly been designed.
  • Andre: managed to build a modified version of the RunCellML test code and get it working on Windows 7 64bit.


  • There was a discussion about how Andre got CellML simulator working on Win7 64bit.
  • There was a discussion about binary releases of the API, whether there should be a limited release now or to wait for the next API release.

5) CellML core specs - update


  • Andrew: features discussed at the breakaway last week on the 1.2 spec have now been put into the draft spec, available at http://www.cellml.org/Members/miller/draft-normative-spec-andrews-preferred/toplevel.xhtml . Added type attribute. Andrew also made a branch that would maintain backwards and forwards compatibility between CellML 1.1 and CellML 1.2, as long as new features aren't used; this branch has been merged into the andrews-preferred version.


  • Randall: maybe the spec drafts could be moved to github, and we could use their commenting features.
  • There was a discussion about commenting systems, the tracker, mailing lists, and other methods to get input on the draft specs.

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


  • Andre: the announcement for the CellML workshop has gone out, and the room is booked.
  • Poul: The CellML tutorial at PAGANZ 2011 went well on Monday.

Action item 1: Dougal - put the PAGANZ PKPD CellML tutorial handouts and files up on the website.

Action item 2: Randall - create tracker item about the unit prefix bug in OpenCell.


There was a breakaway to discuss initial conditions for derivatives of variables in CellML 1.2, attended by Randall Britten, Andrew Miller, David Nickerson, Poul Nielsen and Lukas Endler. The following is a photo from the whiteboard from this meeting.