ABI Meeting minutes 2008-10-29

Present: Dougal Cowan, Randall Britten, Tommy Yu, Catherine Lloyd, Andrew Miller, James Lawson, Justin Marsh,
Apologies: Poul Nielsen, Mike Cooling, Peter Hunter

Last week's action items:

1) James will distribute the metadata spec roadmap
  • Done.  James has received quite a bit of good feedback.

This week's agenda:

1) Metadata 1.0 spec decision process compared to main spec decision process
  • James and Andre have discussed the need for a decision making process.
  • Andre is keen to see a document created detailing the decision making process: there is an email from Poul, which has been made into a tracker item.
Action item 1.) James to draft a document detailing the decision making process, based on the tracker and the discussions.

2) CellML Specs - update
  • James has been doing a lot of work on tracker items; there has been a lot of interest and input.
  • James suggested that the cmeta:sex and cmeta:species elements be removed and replaced with a more extensible element that can incorporate other descriptive terms.
  • Andrew said that a limited vocabulary would need to be established first.
  • James wondered whether curation tags should be taken out of metadata.
  • James said that the tags should probably be used and tested in PMR2 before being serialized into the metadata spec.
  • Andrew suggested making a draft of curation tag metadata before starting to use the tags.
  • Randall suggested that we do not need to serialize the curation tags into metadata at this stage, but that it can be done easily when it becomes necessary.
  • James suggested that the metadata spec could refer to the curation spec documents.
  • Randall stressed the importance of getting PCEnv to implement the latest drafts of the graphing and simulation metadata.

3) PCEnv development - update
  • Andrew has been working on getting PCEnv to call the CellML RDF API.  This is not ready yet, there are issues with the simulation metadata.
  • Justin has been working on a column to show initial computed values; this is required to support the final computed values column which has also been requested.
  • Catherine again raised the issue of slow Javascript in session files.  This issue needs to be fixed before the circadian rhythm models paper is published, so that these sessions do not appear broken.
  • Justin and Andrew need to discuss Mac OS X issues to do with XULRunner.

4) CellML API - update
  • Andrew has made a number of bug fixes.
  • Andrew has started on getting PCEnv to call the CellML RDF API.
  • Andrew is working on a prototype of an SBML to CellML translation tool.
  • Catherine suggested that Andrew get in touch with Nicolas Rodriguez about collaborating on the translator.

5) Website redesign - update
  • Gareth sent out the wireframes, and so far has had responses from Andrew and Randall.
  • Not enough material for a meeting this week, there will be another next week.

6) Repository contributions - update
  • Catherine is working on the Pasek 2006 model.
  • Catherine had a paper published this week, stemming from work begun at the Amsterdam conference; the model from this paper can now be made public.
  • All of the circadian rhythm models and sessions are complete.

7) PMR2 development - update
  • Tommy has been working on Plone workflows for PMR2
  • Tommy has continued to work on building the foundation for the code to sit on.
  • Tommy built a clean Plone 3 buildout to be deployed as a development site.

8) Updates or additional items
  • James has had confirmation for the Singapore conference - he has a 15 minute oral presentation.
  • Tommy has had a 90 minute poster presentation confirmed for Singapore.
  • Catherine is going to send an email with more information about the workshop; people don't have to swim to Waiheke with their luggage.  ;)