ABI Meeting Minutes 2008-05-28

Present: Catherine Lloyd, James Lawson, Tommy Yu, Justin Marsh, Mike Cooling, Geoff Nunns, Edmund Crampin, Poul Nielsen, Andrew Miller

Review of last week's action items:

James has started making notes but wasn't sure where to put them, given the content audit of the cellml.org website currently being carried out. Mike suggested that we could put a folder up on the ABI CMS

Action item 1.) James to investigate

2.)  Tommy has turned on the Plone commenting functionality for model pages in the model repository.

3.)  Item to be added to agenda of cellml.org content & design working group

Agenda for this week:

Geoff Nunns starting internship

  • Geoff Nunns is from Johns Hopkins University in Baltimore, USA
  • He is starting an internship under Catherine and will be working here until August
  • He will primarily be working on coding up new CellML models

Mike - Tutorials / primers on CellML
  • Mike has created three tutorials on how to work with CellML files for the Newcastle iGEM team
    • The first deals with using COR to create a simple one-component model with some mass-action kinetics math
    • The second deals with a two-component model and connections
    • The third deals with imports and PCEnv
  • He wondered if it would be a good idea to make these tutorials available via www.cellml.org
  • It would be good to let the Newcastle group, who don't know much about CellML, trial the tutorials first
  • Geoff could also check out these tutorials, as he is just learning how to work with CellML
  • Mike has written the tutorials in Word. The format of the tutorials on the website was discussed
    • A wiki was suggested to allow easy editing, or they could be converted into a Plone 'page,' which would also allow editing
    • Mike isn't keen to spend time translating the Word documents into another format
Action item 2.)  Mike to send copies of his tutorials to Catherine, who will put them up on the site

Randall - PCEnv 0.4 documentation
  • PCEnv 0.4 release will be coming up soon, but the documentation needs to be updated
  • This shouldn't be too much work, but screenshots need to be replaced and some new features need to be documented
  • James and Catherine worked on this for PCEnv 0.3 - Randall wanted to know if they could do it this time as well.
  • James is happy to work on this with Justin
Action item 3.)  James to meet with Justin to discuss documentation requirements and then start work on the updates

PCEnv / CellML API progress update
  • Justin has been working on the bugs marked as blocking the release of PCEnv 0.4
  • Andrew has code generation for differential algebraic equation (DAE) systems operational
    • Andrew is still looking into different minimisation / root-finding methods to be called from the generated code.
  • He was able to generate code for the Saucerman & McCulloch 2003 model - 6 pages of code were generated and 11 DAE's were found by the system
  • Poul asked if attendees of last week's seminar on DAEs received any useful feedback
    • Randall asked about the validity of using separate solvers for DAEs and ODEs as a numerical approach for solving models that contain both. Apparently separating DAEs from ODEs using separate solvers on them can reduce error handling capabilities.
  • Poul noted that the "RADAU5" solver would be worth looking into
    • Andrew said this solver was used in MozCellML
  • Edmund mentioned that the "NAG" libraries would also be worth checking out. They are closed source but should give a good sense of the current state of the art.
  • John Butcher in the University of Auckland Department of Mathematics is a world expert on numerical methods for the solution of ODEs and would definitely be a good person to talk to about our work in this field.
  • Randall suggested that if we have the analytical solution to an appropriate problem, we could compare this with our numerical solution.
  • GAMS (Guide to Available Mathematical Software) is a resource that may be relevant.
  • Randall mentioned that Andrew's current software could be used for MATLAB code generation with not too much modification.

PMR2 progress update
  • Tommy solicited comments from various people after last week's meeting
  • He has been working on cleaning up the interface to get the prototype ready for preliminary user testing
  • The VM should be ready for distribution and hosting by tomorrow.
  • He has also built and played around with Andre's 'decompose' tool.
    • The Ten Tusscher 2004 model variants do not quite have identical mathematics and variable units. This complicates using imports to create a one main model that imports different parameter sets to describe the variants.
    • James mentioned that there are some strange units such as milliamps per picoamp, which may be an artefact of unit curation but realistically be inconsequential.

CellML 1.2 specification update
  • Andrew talked with Kevin Burrage last Friday about how stochastic systems might potentially be represented in CellML 1.2
  • The audiocast of this conversation can be found at: http://www.gcast.com/u/millerak/main
  • The conversation was useful but Andrew's proposal on how to represent stochastic systems in CellML 1.2 still stands as it was.
  • Presently no further discussions with Kevin Burrage are scheduled.
  • There are a number of classes of stochastic systems we could represent. Andrew's proposed approach is to allow generic representation and then identify specific classes, such as systems described by the Gillespie algorithm.
  • Andrew noted that while we don't have to explicitly provide a representation of stochastic systems in CellML 1.2, we should be making 1.2 generic enough to allow for a secondary specification representing these systems.

Catherine - CellML 1.1 tutorials
  • The CellML 1.1 tutorial currently on the site is old. There are a number of new CellML 1.1 files that could be used to create a better tutorial, such as Randall's 'buckets' model, or Jonna's published 1.1 models of cardiac systems.
  • Catherine is keen to get a new CellML 1.1 tutorial up

Catherine - CellML in teaching?
  • Is CellML currently being used in any teaching?
  • Not in Auckland, but Poul is keen to look into it
  • He is giving a set of lectures of physiological control systems as described using ODEs and CellML may be pretty useful for this.