ABI Meeting minutes 2009-03-25

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

Last week's action items:

1.) Website working group to create a tools page layout template.
  • Done, sent to Gareth.
2.) Tommy to setup Mercurial wrapped in Apache for push access on staging server.
  • Done via Plone, not Apache.
3.) Peter will get Suman to list names of those accepted and who has funding for IUPS.
  • Unknown whether Peter has done this.  This item carries over. Action item 1)
4.) Justin to roll the Java binding support for Windows into the build process.
  • Justin reported that this is problematic, even on Linux.  It can eventually be built manually, but is not repeatable.
  • Randall said to defer this task.
  • Andrew created a tracker item on changing the build system (tracker item #1679) with the hope that it will make things like this easier to cope with.

  • Randall suggested a breakaway meeting on this topic.
5.) Justin to build a stable snapshot with the Java wrapper with all options for Windows.
  • Covered under AA4.
6.) Dougal to track down the PMR2 prototype document
  • This has been found; requires updating for PMR2 0.1.

This week's agenda:

1) CellML API - update
  • Andrew added the ability to set metadata using RDF to provide initial values.
Action item 2) Justin to provide Jonna with a snapshot that has this ability.
  • Jonna asked if there was any way to identify the equations that are DAEs. (?)
  • Randall said that generated code identifies variables.
  • There was a discussion of the problems around providing initial values, especially where the model is altered.
  • Justin has suspended the work on building Java bindings.

2) OpenCell development - update
  • Justin and Alan have been working on the Windows build environment. It has been decided to use the XULRunner SDK, as per MacOS (and Ubuntu 8.10).

  • Justin has committed the Greasemonkey-like system for changing the layout of OpenCell; this allows the editing and saving of layouts.
  • Andrew has been looking at how to implement a metadata editing interface, possibly a new icon in the tree view.
  • Randall suggested it may be worth backing out of the build environment effort if it is taking too long, as Alan's time here is valuable and might be better spent developing the COR-like text perspective.

3) PMR2 update
  • Tommy has got Mercurial push and pull working through Plone.
  • The owner of a workspace can grant permissions to users, groups, etc.
  • Randall suggested that James, Catherine, Mike, and Jonna could give this a try.
  • Tommy has also been working on: imports, curation interface, rendering of metadata, search, pdf rendering of MathML.
  • Randall said that it is very important to do an import of the repository for the staging site.
  • Tommy said that the import will probably be done by Friday.
  • Tommy has been working on the facility to generate exposures.

4) Website redesign - update
  • James has been working on content, awaiting a styled staging site.
  • Andrew said that the tracker is no longer the most recent stable release and should probably be updated, although this is not urgent and could be done some time in the next 12 months.

5) CellML Specs - update
  • James has been working on metadata examples.  Current examples are very verbose, and explaining the RDF language is now no longer so critical.
  • Andrew has his own git repository of the metadata spec and has been making changes, eg. refers to elements instead of triplets.
  • James has merged Andrew's changes.
  • James is currently using HTML, and will change to DocBook when it is feasible.
  • Randall suggested deferring the documentation until after the workshop.

6) Repository contributions - update
  • James has made no additions, but Jeelean has been working on curation.
  • Alan mentioned that the current version of the Hodgkin-Huxley model in the repository is wrong.  Catherine will be working on this.
  • James explained the problem with the HH model, and the variants of it.
  • Poul suggested that this model and its variants be used as an example of the strengths of PMR2 at the workshop.
  • Andrew said that "variants" such as this should probably be put in separate workspaces. (forked)
  • Alan asked if it will be possible to view simulation graphs from PMR2, Tommy said yes but not in PMR2 0.1.

7) Time permitting: Updates or additional items from volunteering attendees
  • James asked if people want to get together to practice presentations for the workshop.
  • Alan suggested going through all the programmes to see if there is any overlap, or if anything could be changed.
  • There was a discussion about workshop talk timetables and topics.