Meeting minutes 2008-10-08

Present: Dougal Cowan, Andrew Miller, Randall Britten, Edmund Crampin, Peter Hunter, Michael Backhaus, Poul Nielsen, James Lawson, Tommy Yu, Justin Marsh, Catherine Lloyd.

Apologies: Peter Schmiedeskamp, Jonna Terkildsen, Mike Cooling, Sarala Dissanayake.


Last week's action items:

1) James to write up a plan/roadmap for the spec, including ideas of who to assign to particular tasks or areas.

  • James discussed this extensively at the meeting, summarizing discussions both from the tracker and other communications. A summary of his notes can be found under tracker item 1406.
  • There was discussion around the release schedule and targets: Sarala's ontology to probably be part of CellML 2.0 or possibly 1.2; 1.1 to be fixes and minor additions to 1.0 and not a major feature release.
  • Andrew suggested "subset" specifications for metadata - smaller specifications for specialized metadata usages rather than a single spec.
  • Poul suggested that a note on these "subset" specs be added to tracker item 1406.
  • Andrew suggested putting the "core" metadata spec into the CellML spec; probably very basic, and only specifying the use of metadata overall.
  • Randall raised the idea of extracting PMR2 curation flags into XML/RDF. Also possibly for revision history.

2) Andrew to create a tracker item and send an email to the discussion list, proposing to finalize the spec.

3) Dougal to complete the tutorial ready for 0.5 release.

  • Done.

4) Tommy to email Poul a copy of the PMR2 paper.

  • Done.

5) Everyone to think of ideas for proposals for the NIH grant.

  • Poul discussed the main ideas for this grant: These will be summarized in an email to the group.

This week's agenda:

Copyright on the site

  • James raised the issue of copyright on content on the website.
  • It was suggested that for models, a range of licence or copyright options could be provided upon submission.
  • Poul supports the idea of a single licence for all models.

Action item 1) James to create a tracker item to discuss copyright issues on the website.

Action item 2) Peter Hunter suggested that James write a relatively detailed roadmap of tasks, with a completion date of the CellML meeting next year. People assigned to tasks should be part of this roadmap.


Forum style web front-end to the mailing list

  • James started a discussion on whether people supported the idea of a forum-like front end to the mailing list to be featured on the site.
  • Randall said that this should go ahead as long as it involves only a small effort.


CellML Spec progress update

  • Not much progress since last week.


PCEnv progress update

  • Justin has built a release candidate for PCEnv 0.5.
  • All PCEnv users should use the RC during the coming week, and report any issues or bugs.


CellML API progress update

  • Andrew has finished the parser and data model.
  • Andrew is going to test the API for conformance with the W3C guidelines.
  • James suggested that other people (For example, Jonathon Cooper) could be kindly convinced to write some documentation for the API.


Update on repository contributions

  • James has made a few session files.

  • Catherine has been investigating the Saucerman 2008 model; found some typos. The model also uses a procedural "work around" to achieve its results, this needs to be implemented somehow in CellML.
  • Catherine has been curating the Teusink et al. 2000 glycolysis model.
  • Catherine requested a script be written by Andrew or Justin to replace exponentials - "e"s - to tags or values.
  • Peter Hunter and Randall Britten suggested that we will want to move towards the XML tag version to avoid the long strings involved in entering the value.
Action item 3) Randall to create a tracker item about the exponential issues/scripts.


PMR2 update

  • Tommy has got the Mercurial library to a usable state - almost finished.
  • Randall suggested that PMR2 features could be pointed out on a Mercurial mailing list; possibly recruit developers for collaboration.


Updates or additional items

  • Peter Hunter enquired on the status of the circadian rhythm models; a package for Albert Goldbeter to write a summary/history of the field around.
  • Catherine and James said that they are almost all done; they should be all finished with SVG sessions this week.