ABI CellML Meeting Minutes, 21st April 2010

Present: Dougal Cowan, Catherine Lloyd, David "Andre" Nickerson, Justin Marsh, Tommy Yu, Andrew Miller, Geoff Nunns

Apologies: Randall Britten, Peter Hunter, Poul Nielsen

Last week's action items:

1) Justin will post a comment on the tracker item asking for the fixes to the XSD to be attached to the tracker item.

  • Done, but Justin has not yet received any responses.

2) Andrew will go through all tracker components and identify ones which are missing default CCs. Once Andrew is done, Randall will look into who needs to be the default CC on any remaining items

  • Done.
  • Justin said that it would be a good idea for us to all go through and check if there are any tracker items that can be closed.
  • There was a discussion about tracker usage, especially with regards to models.

This week's agenda:

1) (Sarala) I will be back at the Institute 10th-22nd of May. Can I please request some help on getting the CellMLAPI working on my windows 64-bit laptop?

  • Catherine said that it would be good for people to reply to Sarala's email .
  • Andrew commented that 64bit might be making this harder; there was a discussion of 32bit/64bit options.
  • Justin said that it would be good to get a 64bit Windows machine for some testing before Sarala arrives.

2) (Andre) is this something we should participate in? http://bioinformatics.oxfordjournals.org/cgi/content/short/26/8/991

  • Put off until next week.

3) CellML core specs - update

  • No updates.

4) Metadata specifications (general, citations, graphing, simulation, other) - update

  • No updates.

5) OpenCell development - update

  • Justin is continuing work on the Scala prototype - this now has a functional syntax highlighting XML editor, MathML rendering, and the beginnings of graphing.
  • Justin would like to give a demo of the prototype when interested parties are available.
  • Justin commented that Scala makes it easy to write internal DSLs, even for trivial things like menu layout, which speeds up changes and leads to more readable code.
  • Justin reported that in general Eclipse dependency management is painful when using external libraries, but that this is something that only has to be done once for each library, at development time
  • Justin has found the menu/layout development much faster and easier in Scala under Eclipse than Qt/C++. He also now believes that development in general will be faster with Scala.
  • There was a discussion about the development platform testing.

6) CellML API - update

  • Andrew has been working on getting the CellML Integration Service to support IDA, so that you can run models with IDA using the test tools.
  • Andrew says that the biggest problem is using IDA's default solver for initial conditions, which is not very robust, and requires a lot of tweaking, not all of which can be done via OpenCell options.
  • Andre asked about the status of Java bindings under Windows - Andrew replied that this is not currently being worked on.
  • Andrew has had feedback from Morgan about the Java shim, and what they need added to it in order to access the RDF. The wrapper has been updated, and we are now waiting on what the Saint team do with it.

7) PMR2 development - update

  • Tommy has been cleaning up the interface to prepare for a demo release, the alpha version of PMR2 0.3, which is currently working on the Amazon hosting.
  • Catherine has written a CellML model repository essay.
  • Geoff has drafted an essay on curation.
  • Andrew has sent out an abstract of a repository paper to interested parties, and is awaiting feedback.
  • Tommy will draft a PMR2 application note.

8) Repository contributions - update

  • Geoff reported that the endocrine section has been finished.
  • Geoff has done Tabak et al. 2010.
  • Geoff and Catherine are working through the metabolic pathway section.
  • David noted that some of the SVG diagrams recently created by Hanne have issues with the fonts. The text will now be exported from Illustrator as paths to fix this issue.

9) Time permitting: Updates or additional items from volunteering attendees

  • There was a discussion about editing of the CellML meeting minutes. These minutes will only be edited by a single editor, and all suggested changes must be copied to all attendees.
  • Dougal will prepare the agendas in Catherine's absence.