ABI Meeting minutes 2009-01-28

Present: Randall Britten, Dougal Cowan, Adam Reeve, Andrew Miller, Catherine Lloyd, Poul Nielsen, Mike Cooling, Michael Backhaus, Justin Marsh, James Lawson, Jeelean Lim, Jonna Terkildsen
Apologies: Peter Hunter, Tommy Yu

Last week's action items:

1.) James to start a discussion on the mailing list about leadership/constitution/voting/AGM.
  • James posted on the mailing list, and there have been several responses.
  • James mentioned the suggestion of a relatively informal "do-ocracy".  This could be good for day-to-day decisions but not necessarily for major decisions.
  • Andrew suggested that it is the big decisions for which the process is most needed.  He described the Debian process, a ranked voting system with an algorithm that leads to most preferred outcomes.
  • Poul suggested having some time to get feedback on the two or more suggestions made, with a subsequent vote to determine the system that is adopted.
  • Randall raised the question of how to determine who gets a vote; Andrew mentioned that the Debian system has rules in place for this: the committee chooses members, and the members control the committee.
  • Poul mentioned that in practice, very few eligible members actually vote.
  • Randall suggested that it be left up to a working group (James and Andrew) to come up with a recommendation, which is then brought to a committee (minimally, Poul) or the specification panel for approval.
  •  Andrew said that if we were to form an incorporated society, with a minimum of 15 members, these members could then choose a committee before the workshop.  New members could then join at the workshop as a first step.
  • A breakaway meeting was called to continue discussion on the decision making process.
2.) Andrew to send Dougal information on the grammar.
  • Not yet.

This week's agenda:

1) A new name for PCEnv/COR
  • Catherine asked if we have made any progress on the decision, as she has been away - have we got any better candidates than OpenCell?
  • Randall brought up the issue as to whether we want Cell or CellML in the name.
  • Poul mentioned that OpenCell is consistent with OpenCMISS.
  • Randall brought up his suggestion of a "suite" style naming scheme, possibly with Physiome Tool Kit (PTK) as an overall title, with each tool having it's own name under this umbrella term.
  • Poul said that PCEnv still gets funded largely as a reference platform for solving CellML - a reason to keep Cell/ML as part of the name.
  • Catherine said that the debate continues; we might want to wait for Peter Hunter to return before deciding.
Action item 1.) Catherine to come up with a shortlist of names to be voted on, and to send it to the mailing list.

2) CellML.org: Content update
  • FAQ has been written and awaits checking and editing by Poul.
  • Other tutorials are finished, apart from the 1.1 tutorial which will be more of an overview.  The 1.1 "tutorial" may be based on Sarala's paper.
  • Gareth is to distribute templates for selection of a style for the new site.
  • James and Dougal to begin migrating old content to the new site.

3) Workshop programme
  • Catherine has distributed a programme; she will put it up on the website as an example programme for other groups to look at.

4) IRSES Application: expressions of interest
  • Catherine is writing an application together with groups at Paris, Oxford and Cambridge (? names ?).
  • There will be a cardiac and kidney theme, as well as a general theme of markup languages and tools.
  • Catherine is writing this now.

5) Python wrapper for CellML API
  • Randall said that after we release PCEnv 0.6 we can start the process of deciding on priorities for the next release.
Action item 2.) Randall to reply to Jonathan Cooper

6) Repository contributions - update
  • James has given a lengthy teaching session on how to create PCEnv sessions with interactive diagrams.  This is an ongoing effort, and also uncovered some issues caused by recent changes to PCEnv.
  • Catherine has been away; still waiting for information on Pasek 2006 from Martin Fink.
  • Jeelean has been working on a model, and has also been reading the papers on motifs.

7) PCEnv development - update
  • Justin has been fixing bugs due to the validation of new e-notation, and fixing some Mac issues.
  • Randall asked if there is still more to do on e-notation; Justin says that there is still more to do, but that it is ready for release. There is a tracker item on an edge case that is still open.
  • James commented on the changed output of session XML files; he would like formatted XML output.
  • Catherine mentioned that she has always been reluctant to make sessions due to the fiddly nature of the process.
  • Dougal asked if any of the processes of making interactive sessions could be included in a tool.
  • Jonna would like to see a tool to make session making easier; especially to encourage more people to make sessions.
  • Jonna asked if the validator is currently considered to be correct.  She has outstanding issues that are mentioned in open tracker items. Andrew will look for the tracker items in question.
  • Andrew has fixed a number of minor bugs.

8) CellML API - update
  • Andrew has fixed a number of bugs.
  • Adam is working on a service to get language definitions.
  • Mike would like to use and test the Java wrappers; he will get in touch with Andrew about this.

9) Website redesign - update
  • Was already covered under item 2.

10) CellML specs - update
  • James has been communicating with Andre.

11) SBML to CellML converter prototype - update
  • Andrew says this is at a stage where it can be used, although it is slow.  We need to now decide where to go next with it.
  • Poul will email Sarala for her ideas.
  • Andrew said that we could now run the entire SBML repository through the tool, but that each model would require extensive manual curation - the converted model is the bare minimum required to mathematically represent the model.
  • James asked if it would be possible to also automatically run the validation service on the converted models and create text files of the errors in each model.  Andrew said this should be quite easy and that a bundle of converted models and their errors could be produced for manual curation.