ABI CellML meeting minutes 2009-11-18

Present: James Lawson, Geoff Nunns, Justin Marsh, Randall Britten, Andrew Miller, Tommy Yu

Apologies: Catherine Lloyd, Dougal Cowan, Poul Nielsen, Peter Hunter, David "Andre" Nickerson

Last week's action items:

1) Dougal to make John Davidson's case study the default item for the case studies section.



This week's agenda:

1) CellML core specs - update

Reset rules and prototype in API:

  • Randall has been testing the reset rule handling (Tracker Item 1543) code recently committed to the CellML API by Andrew.
  • Randall tried Andrew's test model (a simple model where d(x)/d(t) = 1, except when x = 10, at which point x is reset to 0). The reset functionality does not appear to be working correctly at this point, however. Andrew will take a look at this.

2) Metadata specifications

  • No updates this week.

3) OpenCell development update

  • Justin noted that recent versions of xulrunner do not work on OS X 10.6 Snow Leopard, because Snow Leopard and xulrunner try to use two incompatible sqlite versions. The workaround is to compile xulrunner with a non-standard patch on OS X
  • Justin has also removed the faulty syntax highlighting from the TXT (COR-like language) view (Tracker Item 2089)
  • Copy/paste functionality appears to work in the TXT editor although find/replace is still missing
  • OpenCell users are encouraged to test the TXT editor
  • It was noted that the syntax is slightly different from the COR language
  • Justin anticipates that the first release candidate of OpenCell 0.7 will be ready for testing by next Tuesday (2009-11-24) morning.

4) CellML API development update

  • Andrew has been running through the tracker addressing items that need to be resolved before the release of CellML API 1.7
  • There are 3 remaining bugs (as opposed to feature requests) in the tracker for the CellML API ( Tracker Items 2085, 1598, 1497); there are more for OpenCell, however.

5) cellml.org update

  • Dougal has put up a page with CellML logos in various sizees and formats for publication purposes
  • James is reorganising the tools section - specifically, he is currently combining the CellML Environments and Modelling Environments sections into one to allow space for a Visualisation and Annotation section
  • It was noted that some information in the Plone software centres needs to be migrated to the tools page

6) Repository contributions

  • James needs some initial conditions to finish the Lockwood 2006 model
  • James has ironed out glitches in SVG session creation and is now creating a session for Phillips et al. 2008
  • He will give Dougal a xul template for sessions

Action item 1) James to give Dougal a xul template for SVG sessions

  • James has done some curation work on the Elowitz 2000 model
  • Geoff has done work on the Decker 2009 model so that it now runs but does not produce the correct results
  • Geoff has been working on constitutive law models with Miles Rubin. This
    is being done initially using CellML, and then generated FORTRAN is modified
    by hand to be used with CMISS.

7) PMR2 development update

  • Catherine sent to the meeting her request for an aggregated RSS that covers all commits to all workspaces

Action item 2) Tommy to create an aggregated workspace commit RSS after PMR2 0.2 is deployed

  • Tommy has added the metadata note view (Tracker Item 2002) including the CellML model author information display that Catherine requested
  • He is primarily working on the exposure rollover feature (Tracker Item 1589) at the moment
  • He has also looked at how CellML 1.1 code generation might be catered for but it was decided that this should be deferred until PMR2 0.3
  • The projected release date for PMR2 0.3 is mid-late December.