ABI CellML meeting minutes 2009-12-09

Present: Dougal Cowan, Randall Britten, Andrew Miller, Catherine Lloyd, Tessa Paris, Mark Hanna, Justin Marsh, James Lawson, Tommy Yu, Geoff Nunns, Mike Cooling, Poul Nielsen

Apologies: Peter Hunter

Last week's action items:

1) Catherine to search for an existing tracker item [about diagrams that are too large and break the layout of exposures] and to create one if it doesn't already exist.

  • Done

This week's agenda:

1. (Catherine) Terms of use for CellML models and associated content hosted on models.cellml.org.  Tracker item 2056

  • Catherine has updated tracker item 2056, and has received email feedback, which has been appended to the TI.

Action item 1) Catherine to get in touch with John Monk at uniservices to ask about IP issues.

2. (Catherine) Potential revision of the description of groupings in the CellML 1.2 specification in response to this feedback from a user:

  • From Catherine, quoting the feedback: "in regard to encapsulation, maybe you could point out to someone that the CellML specifications could perhaps do with a little elaboration in this area. I read the groups section on a couple of different occasions -- as did a colleague of mine. Both of us got the impression that the group element allows components to be grouped together but does nothing with respect to connections between members of the group. Perhaps the specs could be revised to make this clear?"

Action item 2) Catherine and Andrew to get in touch with the users to direct them to the clearer descriptions in the 1.2 draft spec.

3. (Catherine) Should we/can we update the current CellML 1.1 tutorial: http://www.cellml.org/getting-started/tutorials/cellml-1.1-tutorial. 

  • From Catherine: At the time this was intentionally vague as we did not have a "best  practice" 1.1 format.  To my knowledge we still don't have any "best  practice" guidelines, but we probably need to address this as we now  have users who are interested in building their models in 1.1 and they  need more instruction. Currently we have Andre, Mike and Jonna frequently using 1.1. I have used it a bit, and Sarala has a method outlined in her modularisation  paper.  I believe all of us approach it slightly differently.  Are we  able to come up with a single best practice set of guidelines?
  • Mike has written a book chapter about this topic, but he can't give this out until the book is published.
  • This item was put off until Andre returns.

4. (Catherine) Idea: Should we have a CellML 1.1 model library building effort early next year (2-3 days set aside)?  We'd have to agree on a common format (template?) before hand.  We have been talking about a component library for a while now and the timing might be right as we currently have a larger-than-normal team of curators to work on this.

  • Catherine says that this requires us to first agree on best practice.
  • Mike reported that he already has a library of around 60 components, created using his methods.
  • This topic was put off until Andre returns.

5. OpenCell development update

  • Justin has added two new blockers, TI 2227 and TI 2354.
  • Justin reported that the latest snapshots of OpenCell won't run after being installed on a Windows machine that has never had OpenCell installed on it previously.
  • There was a discussion of blocker items.
  • Randall asked if anyone has tested, or is able to spend some time testing the TXT view of OpenCell. He suggested that James, Catherine, and others who have used COR get the latest TXT view enabled snapshot of OpenCell and test it.
  • There was a discussion about how to go about testing the TXT view.

6. CellML API - update

  • Geoff has shown that the LEVMAR solver is causing the problems with the Saucerman model, by reproducing the errors in MATLAB with the LEVMAR solver.
  • Geoff will now try testing Kinsol on Saucerman in MATLAB.

7. PMR2 development - update

  • Tommy has staged release candidate 1 of PMR2 0.2.
  • Randall gave a demo of the exposure rollover feature.
  • Randall said that James, Catherine, Geoff, and Andre should test the RC.
  • There was a discussion of what features to test.
  • Randall said that first we need to establish that all existing functionality still works, and then test the new 0.2 features.
  • Catherine asked whether expired exposures still appear in the exposure listing - they do. Tommy will have a look at how quick this is to fix, if it is a big job then it will be put off until 0.3.
  • There was a discussion about how and where to "tag" exposures as expired.

8. Repository contributions update

  • James has been cleaning up duplicate exposures.
  • James has been creating SVG sessions for some cardiac models. He is starting with models that have good matches between the diagram and the model.
  • Tessa has pushed a Goldbeter model that she has been working on.
  • The summer students are working quickly so Catherine has created an additional list of (immunology) models which need curating.
  • Geoff has been continuing to work with Miles.
  • Geoff has been fixing errors in some of his old models, including a large Dan Beard model.
  • Catherine has curated Lockwood 2006 and has uploaded the model.
  • James created two PKPD session files for Sarala to demo in Amsterdam (Overgaard 2007 and Tham 2008).
  • Catherine has been re-exposing models Hanne has been working on.
  • There was a discussion about models containing and how to deal with them - they are currently visible in the repository but they have been clearly marked as "containing PDEs" in the model status comment.

9. CellML core specs - update

  • no update.

10. Metadata specifications (general, citations, graphing, simulation, other)

  • Randall mentioned that Peter Hunter said that we should be looking at ideas around probability distribution variable values for grant applications.
  • Poul said that the description of probability density functions etc should probably be part of a SED-ML or other markup.

11. cellml.org update

  • James has updated the Tools section, making a new section and combining the CellML tools sections into one.
  • There was a discussion about fixing the specifications pages.

Action item 3) Dougal to update the 1.0 spec to fix the broken images.

  • There was a discussion about how to maintain old specification URLs.
  • Randall said that the website group should look at how to provide for old static HTML, as well as possible future static content.