ABI Meeting minutes 2009-04-15

Present: Dougal Cowan, Alan Garny, Catherine Lloyd, Tommy Yu, Poul Nielsen, Andrew Miller, Mike Cooling, Jonna Terkildsen, Abhishek Tiwari
Apologies: James Lawson, Justin Marsh, Randall Britten

Last week's action items:

1) Peter will get Suman to list names of those accepted and who has funding for IUPS.
  • There was a discussion about the funding for Andrew and Jonna.
2) Tommy to enable support for multiple MIME types.
  • Tommy will make a tracker item about this, as this is future work.

This week's agenda:

1) Journal club
  • Catherine suggested that if people come across relevant, interesting articles during their reading that they post them to the CellML mailing list.  This idea was precipitated by Abhishek posting a paper about version control of XML formats which mentioned CellML and SBML.
  • Mike mentioned a paper on little-B that he will post.

2) Model annotation: support for MIRIAM etc.
  • Catherine reported that yes, we will support MIRIAM.
  • Catherine gave the example of VCell; it includes an annotation editor which has never been used - modelers don't like to annotate!
  • Catherine questioned including annotation editing as a capability of OpenCell.  She supported using Saint.
  • Alan suggested that having a single tool would make life easier, rather that swapping between tools.
  •  Catherine asked who is responsible for developing the metadata editing tool; Andrew said that it is becoming part of OpenCell development.
  • Poul said that a discussion is required to determine the interface requirements for the two use-cases that can be forseen - adding annotations to existing models in PMR, and editing metadata in new models.
Action item 1) Catherine to get in touch with Allyson Lister to ask very nicely about CellML support in Saint.

3) e-notation script for fixing models
  • Tommy reported that Justin has checked this script into SVN.  It will be run on all models as part of the export of PMR to PMR2.
Action item 2) Tommy to check if the script supports both cases of e(E).

4) Initial conditions - and their current use to define constants - has been raised before. Has there been any progress?
  • Catherine reported that it has been agreed to keep initial conditions for ODEs only. Otherwise, constants should be defined by equations which explicitly define their value over all time.
  • Poul said that the spec needs to be cleaned up, as the examples use initial conditions to set constants.
  • Poul would prefer that the models in the repository be updated, replacing initial conditions with equations.  There was a discussion around the creation of a tool to do this.

5) Journal support for CellML
  • Catherine will talk to Peter about this.

6) PMR2 Update
  • Tommy demoed PMR2 at the workshop.
  • Tommy has cleaned up the side menus.
  • Mike has some models he would like to submit; is it worth doing this now?
  • Tommy can help Mike set up TortoiseHg for pushing to PMR2. Any exposure made now will persist in the final PMR2.
  • There was a discussion on how to reference a model in PMR2; UUID, URI, alias, etc?
  • Catherine asked what will happen to the legacy models (those outside PMR)?  Tommy said that these will have to be manually migrated.

7) Website redesign - update
  • Gareth is still working on the templates.
  • Tommy has done some work on Plone skin.
  • Dougal said that we need the "live" or final site staged in order to put up the reformatted content.
  • Poul said that all of the working group should come on Tuesday with feedback for Gareth, and to have a look at where we have got to.

8) CellML Specs - update
  • Poul reported that Andre has raised the issue of who is going to push SED-ML.
  • Alan said that it would appear (from the discussion we had at the Waiheke workshop) that SBML people are going to work on it

  • Catherine said that we will need a link person.  Alan suggested Andre and Andrew.
  • Andrew said that some of the approaches of SED-ML are not clean for CellML use.
  • Alan said that the best approach may be to keep in close contact with the SED-ML people.

9) CellML API - update
  • Nothing this week.

10) OpenCell development - update
  • Alan has made a branch for working on the COR-like text perspective.
  • There was a discussion of the layout of OpenCell for editing (COR-text and XML). Alan said that the new functionality Justin has added for layout changes would make it easy to switch to a "fullscreen text" mode for example.
  • Andrew has been working on the RDF editing interface.  He has made changes that will make it easier to add more items to the tree view.

11) Repository contributions - update
  • Catherine has fixed and curated Paul Harrington's model.
  • Catherine has curated Leloup 1999 to conform with the paper.

12) Updates or additional items
  • Poul asked about the audio files from the workshop.  Catherine reported that Mike Hucka has uploaded some, but the rest will not be available until he is back at CalTech.
  • Julian has all the video files, some 30GB.  He is investigating using an Auckland University service for video editing, otherwise simple editing will be done.  Poul suggested he could do some basic editing on the files.
Action item 3) Catherine to email workshop participants for permission to publish audio/video recordings of them.