ABI CellML Meeting Minutes, 11th of May, 2011

Present: Dougal Cowan, Andrew Miller, Randall Britten, David "Andre" Nickerson, Lukas Endler

Apologies: Poul Nielsen

Last week's action items:

Action item 1: Dougal - get in touch with Tommy about creating an Andre style exposure.

  • Done - awaiting a response.

This week's agenda:

1) CellML website stability issues - Randall


  • Randall: Andrew Cantell has discovered some stability issues with cellml.org which cause the site to be unresponsive about once a day for several minutes. ITS is about to go through an update of its hosting services, so we will wait and see if this fixes the issue. There are also issues around who is the person responsible for dealing with problems like this.

2) ISCB membership - Randall


  • Randall: there is one complimentary 12 month membership of ISCB available for one of the authors of the PMR2 application note. An email will be sent around about this, and then we will need to decide who should be the recipient of this.

3) PMR2 development - update


  • Andre: tried to find 0.4 features such as embedded workspace navigation and CellML simulator style exposures. Has not been able to work out how to do these things yet.

4) Repository contributions - update


  • Dougal: have found a number of broken session files with file:// URIs. Andrew is grepping the repository for instances of this problem.
  • Andre: updated the Collier et al. model with further information for Poul.


  • Randall: it would be possible to release "versions" of the database via embedded workspaces, enabling people to clone the entire repository.

5) CellML core specs - update


  • Randall: there was a discussion at the FieldML meeting which was somewhat related to the bvar tracker item, and comments regarding this have been added to the tracker item (2902).
  • There was a discussion about different bound variable implementations.
  • Randall: it seems that the original bvar solution is still preferred.

6) CellML API - update


  • Andrew: still working on the build process on all platforms. RC2 is out, but may still have bugs.
  • Andre: there is still no .jar file in RC2.
  • Andrew: working on getting MinGW builds working for Alan.


  • Randall: has IT given Andrew a Win7 box yet? Andrew: no.
  • Randall: could possibly update bioeng46 to 64bit OSX for building, otherwise use the Mac Mini.
  • There was a discussion about building the API for various platforms.
  • Randall: we could either provide what Alan has requested or encourage him to concentrate on 32bit.
  • Andre: LibSBML are moving to CMake.

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

  • Randall: On Tuesday, Peter and Randall gave a webinar for the NIH IMAG group about PMR2 for an audience interested in model sharing.

Action item 1: Dougal - make a news item about the webinar, if appropriate.