ABI CellML meeting minutes 2010-01-20

Present: Randall Britten, Dougal Cowan, Mark Hanna, Ethan Cho, Tessa Paris, Justin Marsh, David "Andre" Nickerson, Andrew Miller, Catherine Lloyd, Tommy Yu, Poul Nielsen

This week's agenda:

1) (Catherine) Creative Commons Atrribution 3.0. Confirming (with Randall and Poul) this will go on the website directly and also into the model metadata.

  • Catherine said that we still need to decide what to do about the terms of use and license for the repository.
  • Andre said that MIRIAM compliance requires the license to be in the RDF. Catherine asked if this could be added to existing models by a script, Justin said that it could.
  • There was a discussion about where to put the license on the site.
  • Andrew said that we will probably need explicit permission from all model authors (of the CellML files) to add the license to their models.
  • Catherine said that we know who wrote most of the CellML, and we will have to contact some people.

Action item 1) Catherine to come up with a wording for the license, and to look at the Dublin Core RDF for the license.

  • Randall said that he thinks that the ABI has already agreed to the creative commons license for all its models. Other models author's need to be contacted and asked to agree. All other (i.e. non-ABI) registered users should be contacted about the license/terms of use. It was also said that that all new logins should be subject to agreement with the license terms, i.e. that content submitted to models.cellml.org will be under the creative commons license.
  • Poul said that it would be useful to get Nicolas Le Novère's comments on these licensing issues.

Action item 2) Catherine to contact the model authors of the existing repository contents and also to contact Nicolas to get his opinions on our proposed plan of action.

2) CellML specs - update

  • Randall said that he needs to catch up on progress over the last month, because he has been on leave.

3) Metadata specifications (general, citations, graphing, simulation, other)

  • Catherine asked Tommy how this was left by James.
  • Tommy said that he and James had discussed this before he left, but this will need to be looked in to.

4) OpenCell development update

  • Justin reported that there has been a round of Litmus testing, which had some failures on all platforms: Changing imports in CellML 1.1 models (fixed) and session issues.
  • Catherine reported that Tessa has been using a recent snapshot of OpenCell and has seen a number of problems with saving and opening session files.
  • There was a discussion about installation of OpenCell snapshots on summer student machines.

5) CellML API - update

  • Andrew has received the paper back from the reviewers, there was a comment that the paper does not mention libSBML.
  • There was a discussion about changes required for the paper.
  • Poul said that a paragraph about differences between the SBML and CellML APIs would be good.
  • Andrew has continued to work on IDA solver support, which is getting closer.

6) cellml.org update

  • No update.

7) Repository contributions update

  • Tessa has been working on a number of HIV models.
  • Ethan has been working on immunology models - he reported that it is common for immunology model papers to contain multiple models.
  • Catherine reported that Hanne has been working on sessions and SVG diagrams.
  • Catherine is working on Andrew McCulloch's cardiac models - she has requested copies of the original code to complete the models - they are both working with no obvious errors, but they are not giving the correct results.

8) PMR2 development - update

  • Tommy has fixed the crash issue, which was a config issue with the new Zope software stack.
  • Tommy is working on getting github style URLs working so that every user can create their own private workspaces.
  • There was a discussion about mixing of FieldML and CellML in a single PMR2 instance.
  • Dougal has been working on a basic PMR2 guide.
  • Randall said that we will need to start discussing priorities for PMR2 0.3. The 0.2 plan was reviewed.
  • Features such as PDF MathML downloads, improved search results, metadata editing, and updated code generation are possible features for 0.3.
  • Randall said that people should think about possible features for 0.3 to be discussed at next week's meeting.
  • Poul said it would be useful to have access to an image format for equations.
  • Andrew said it might be good to provide export of presentation MathML from OpenCell.

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

  • Mark has been working on OpenCell session JavaScript. He has pan, scroll, and highlighting working, but is still working on the interface for these features.
  • A breakaway was called to discuss the session JavaScript.