ABI CellML Meeting minutes 2009-06-03

Present: Randall Britten, Dougal Cowan, Tommy Yu, Andrew Miller, James Lawson, David "Andre" Nickerson, Catherine Lloyd, Julian Eden, Mike Cooling, Poul Nielsen.
Apologies: Peter Hunter, Justin Marsh.

Last week's action items:

1) James to test this [code generation blocker] use case again.
  • Done.  This is now fixed.
2) Poul to email the website working group with his comments on the site so far.
  • Done, Poul's comments are now being incorporated into the visual style.

This week's agenda:

1) Annotation; like SBML or Sarala's ontology.
  • Catherine said that her interpretation of the discussion between Matt and Sarala was that Sarala plans for the long term solution to include her ontology. Matt thinks that in the short term we should go ahead with something more simple, embedding the MIRIAM IDs in the RDF metadata.
  • James said that if we want to use Sarala's scheme, it would be a lot of work including a large amount of involvement from Sarala.
  • Andre said that we should put the MIRIAM IDs into the bioentity tag.
Action item 1) Catherine will contact the Newcastle group and will request input from Sarala and Matt.

2) Bangalor workshop, 19-21 November - update
  • Randall reported that a few people were interested in going, but that only one place is available.
  • Randall said that we should wait until Peter gets back before making any decisions about this.

3) IUPS preparation
  • James wondered whether there were any updates on what is happening for the workshop preparation.
  • Poul said that we need a clear plan of what we are going to cover, and asked who is participating.
  • Randall said that it is a very short time-slot - he suggested making it quite hands on, with perhaps a 15 minute intro.
  • James said that a wrap-up at the end might be worthwhile.
  • Andre asked what we are trying to show/highlight with the workshop.
  • Poul said that we should explain what CellML is and how it works. He also raised the idea of having attendees bringing their own models or problems.
  • Andre suggested the workshop could consist of the attendees downloading the Hodgkin-Huxley model and changing the sodium channel, for example. This would demonstrate re-use, model editing, etc.
  • James said it is important to also show the repository. It would be sufficient to download the model used in the workshop from PMR2.
  • Andrew said it is important to show the exchangeable/sharing aspect of CellML.
  • Randall said that the sharing of CellML could be covered in the initial 15 minute presentation.
  • Randall suggested that we might want to show how to build a simple ODE model as part of the initial presentation.
  • Andre said that the workshop needs to be promoted on the website etc, as well as emailing everyone we know who is going to IUPS.
Action item 2) James to promote IUPS workshop - email attendees, organizers, mailing list, and create a workshop web page.

4) E-notation
  • James raised the issue of the email sent by Alan stating that all e-notation would be fixed by the end of May. James would like to see this fix scripted as part of the PMR2 migration.
  • Poul said that perhaps the e-notation should be converted to long-hand (maintaining compatibility) as well as adding a comment on the new e-notation format as part of the script.
  • Tommy said it doesn't matter whether the script runs at or after migration. It will create a new set of exposures.
  • Randall said that we can probably wait until after PMR2 deployment to fix the e-notation via a script.

5) Repository contributions - update
  • James has been curating the models, fixing some and updating the curation status.
  • Randall asked if there are any high-priority models that could be done first.
  • Catherine said that herself, Jeelean and Linda can help James if time gets tight.
  • Catherine has a lot of requested models to code up.
  • James said that the current incorrect units warnings in OpenCell are a problem.
  • James said that he is confident of finishing the curation update before IUPS.

6) CellML Specs - update
  • Randall reported that Andrew's proposal was thought to be powerful and promising, but there was discussion of whether time should be spent on CellML 1.2 or other CellML issues. Randall called another breakaway on this topic.

7) CellML API - update
  • Andrew has been working on getting the build system working with Mercurial. Hopes to make it possible to have automated Java builds on commit.
  • Andrew said that the Java API issue will require an update of the API (?).
  • Randall said that Sarala is to work on Java, update the documentation and make the whole thing more user-friendly.
  • Andrew has started writing a short paper (?) on the API.

8) OpenCell development - update
  • Randall said that Alan is making progress towards COR-like text in OpenCell. This is being worked on in two parts; CellML -> CORtext, and CORtext -> CellML.

9) PMR2 update
  • Randall reported that PMR2 is awaiting hosting from ITS. It is ready to deploy, possibly later today.

10) Website redesign - update
  • Catherine said that Poul's comments on the skin are now being incorporated.
  • James said that the website is ready to go, pending final approval of the skin.
  • Randall has emailed ABI IT, and is awaiting a response about hosting of cellml.org.
  • There was a discussion of various visual tweaks to the website skin.

11) Additional items
  • Poul raised the issue of CellML and Wolfram Alpha, as initially brought up by Abhishek.
  • There was a discussion of how to get CellML into Wolfram Alpha, and what the usefulness of doing so might be.
  • James brought up the email to the list about CellML for simple neuronal models. Various people have responded with information to the initial enquiry.