ABI CellML meeting minutes 2009-10-21

Present: Dougal Cowan, Andrew Miller, Randall Britten, Peter Hunter, David "Andre" Nickerson, Tommy Yu, James Lawson, Catherine Lloyd, Geoff Nunns, Poul Nielsen

Apologies: Mike Cooling

Last week's action items:

1) Dougal to update the CellML Wikipedia page.

  • Dougal has made a start on the content, but has not started editing the page. He will put up the revised history blurb.

2) Tommy to estimate the time to get code downloads working using Adam Reeve's code.

  • Tommy has had a look at this, but was stopped because the 1.6 release of the API does not seem to have the CeLEDS facilities.
  • There was an extensive discussion about the API, ways to get more languages going for the code generation in PMR2, and code generation for CellML 1.1 models.
  • Peter said that 1.1 support is a higher priority than more languages.
  • Randall suggested that both be shelved for the time being in favour of other features, and until the API is checked.

This week's agenda:

1) (Peter) Musculo-skeletal models in CellML - e-mail from Serge van Sint Jan
  • Peter said that he will wait to hear from Serge on these models.
  • Catherine suggested making sure Serge is aware of what CellML is and is not capable of.
2) (Catherine)Review of the curation flags (tracker item 87)
  • Catherine and James have both done another iteration of changing the flags and applying them to the cohort of 6 models. They are sticking to the yes/no/unknown/not applicable values.
  • Another iteration will be done.
  • Catherine said that the more verbose, detailed curation information will be taken out of temp doc and put into the metadata.
  • Andrew said that it makes sense to have a machine readable (RDF) version of the flags that can be used to generate the information presented and for searching.
  • There was a discussion about detailed model information metadata.
  • Randall said that there is a need to add version information to the "This model runs in X" flag.
  • There was a discussion about JSim related flags.
3) (Catherine) James to explain the problem with session files between versions of OpenCell
  • James said that every new version of OpenCell has the potential to break some or all of the session files.
  • Peter said that we should be testing each release of OpenCell to avoid breaking sessions. We need to re-make session files if they are broken.
  • Peter said that we should assume that no biologist is going to use models that don't have a session file - it is vital not to break sessions!
  • Peter said that session files should always work with the latest release.
  • There was a discussion of how to maintain session files between OpenCell versions.
  • James said that complex sessions (more than 8 or 10 clickable objects, for example) can become very slow.
  • There was an extensive discussion about future directions for laying out and presenting session files, making them more resistant to changes in OpenCell, etc.
Action item 1) Dougal to write a guide on how to create session files with SVG diagrams.
  • Andrew said that we could embed the OpenCell version number in the session file, and show a warning when the version does not match.
  • Peter suggested getting [Abhishek's friend] to work on the SVG handling in OpenCell & session layout; zoom, pan, etc.
  • Andrew said that it is very easy to zoom with SVGs, but we need to create a user interface for this function.
4) CellML specs - update
  • No updates.
5) Metadata specifications (general, citations, graphing, simulation, other)
  • James has started writing some RDF examples.
6) OpenCell development update
  • Justin has been working on the installer.
  • Justin has worked on tracker items 1706, 345, and 2001.
  • Andrew said that the build system is now failing on each commit because of an update to buildbot.
  • Alan has been refactoring and improving error messages for parsing COR text.
  • Alan plans to work on the following issues next:
    • For some reason, the URI information of an import statement may disappear when switching from a view to the TXT view... Why? No idea!
    • When switching from the TXT view to another view, with incorrect TXT text, then OpenCell doesn't always?) remember the TXT text when we go back to the TXT view...
    • Need to keep track of all the metadata... 
    • Do a full test of the error messages generated by OpenCell. This will also allow to do an in-depth test of the TXT grammar.
    • When editing TXT format, then when switching to the XML view we can see that all of the XML text is on one line... Why?!
    • Check the TXT editing capabilities by exporting some models to say C before and after TXT editing the model, and then compare the output.
7) CellML API - update
  • Andrew has been working on the validation issue - validation is now less strict.
  • The API paper was submitted last week.
8) cellml.org update
  • James reported that the group had a meeting at which they discussed what to do with the community section. The group will be updating existing pages, and want input from other groups as to what to do with the community part of the site.
9) Repository contributions update
  • Catherine reported that Penny has done another Manchester model (Inada, prepublication).
  • Catherine and Geoff have been working on pharmacokinetics/pharmacodynamics (PKPD) models (Overgaard 2007 and Grange 2001).
  • Catherine added 3 Benson et al 2008 cardiac models, based on Hind & Rudy 2004.
  • James has been finishing off units checking for the Jafri Rice Winslow model.  Once this is complete all the cardiac models will have been updated to match the Oxford set.  James has also created a session file for the Overgaard 2007 model.
  • Geoff has been working on the Saucerman model - this is now working up until a step change, with the help of initial condition workarounds.
  • There was a discussion about how to get the Saucerman model working in OpenCell:
    • constraints.
    • provide initial conditions for each step, or start a new model at each step.
    • use ramping switches instead of step switches.
    • look at using IDA for solving.
  • There was a discussion about IDA and solvers.
10) PMR2 development - update
  • Tommy has been finishing a new class that wraps files in workspaces. Adapters will be used to present different views.
  • Randall suggested that Tommy talk to Matt about design issues.
  • Tommy estimated that PMR2 0.2 will be in beta testing within 3 weeks.