ABI CellML meeting minutes 2009-11-25

Present: Andrew Miller, Catherine Lloyd, James Lawson, [students], Peter Hunter, Tommy Yu, Justin Marsh, Adam Reeve, Randall Britten, Dougal Cowan, Poul Nielsen

Apologies: Geoff Nunns

Last week's action items:

1) James to give Dougal a xul template for SVG sessionprs

  • Done.

2) Tommy to create an aggregated workspace commit RSS after PMR2 0.2 is deployed

This week's agenda:

1) (James) Terms of use for CellML models and associated content hosted on models.cellml.org

  • James reported that the MIRIAM standard requires terms of use/license.
  • James raised the issue of people accessing repository assets such as images through a Google™ search, and that we need a way to inform people of the need to properly acknowledge these images.
  • Tracker item 2055 is to be used to discuss this issue.
  • There was a discussion about which license to use.
  • Peter said that we should choose a license and require that models in the repository use that license.
  • Peter said that we do not want to restrict use, but we do want to ensure correct acknowledgement. Citations should cite the model in the repository, and also the original paper if applicable.
  • Randall suggested that the license/agreement/terms of use could be presented at the time of registration for access to the repository.
  • Justin said that the attribution-only Creative Commons license might be suitable.
  • Randall suggested that Tracker item 2055 be emailed to the cellml-discussion mailing list.

Action item 1) James to update Tracker Item 2055 and email a request for comment on this item to cellml-discussion.

2) PMR2 development - update

  • Tommy has created the exposure rollover feature. Changes can be committed and used to create a new exposure much more easily.
  • There was a discussion about testing of PMR2, and where the testing instance will be hosted.
  • Tommy said that a testing instance could be up on a VM by Friday.
  • Tommy performed a demo of the new features to the meeting:
      • The new expire workflow (and there was much rejoicing).
      • The new exposure listing in the workspaces.
      • Exposure rollover functionality.
  • Randall suggested a dual-selection scheme for rolling over exposures, where the user selects both an exposure and a commit from the workspace listing.
  • James asked if the workspace listing dates could be changed from "## days ago" to a real date.
  • Tommy reported that Mercurial 1.4 is now in PMR2 (will be available when PMR2 v0.2 deployed).

3) Repository contributions update

  • Geoff has been working on the Miles Rubin models together with Prasad to interface the CellML with CMISS.
  • James has been working on 3 new PKPD models, which are not yet running.
  • Catherine reported that Jeelean has finished for the year. All of her cell cycle models are finished. Alys Clark and Nic Warren will complete the curation of the Warren et al. lung model.
  • Geoff has got the Saucerman model working as exported MATLAB code from the CellML model.
  • There was a discussion about how to get the Saucerman model working in OpenCell.
  • Catherine has completed Mathieu Cloutier's second brain metabolism model, which Mathieu has kindly agreed to curate.
  • The summer students - Tessa, Ethan and Mark - have just started and they reported that have been working on a set models of pancreatic beta cells and neurons published by Richard Bertram and his colleagues. The students have picked up the fundamentals of CellML quickly and have already curated at least one model each. James and Catherine are happy with their progress.

4) CellML core specs - update

  • No update.

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

  • No update.

6) OpenCell development update

  • Justin reported that OpenCell is now working on Mac OSX 10.6.
  • Tracker item 2053 has been fixed.
  • Justin fixed a problem reported by Geoff, that FORTRAN77 output should be limited to 72 characters instead of 80.
  • Andrew has been closing off and fixing a number of tracker items.
  • Randall called a breakaway to discuss bug priorities for the 0.7 release.
  • Randall reported that FORTRAN77 code generation will not be disabled in this release.
  • Justin has removed the XML view syntax highlighting in order to make the XML view more usable.

7) CellML API - update

  • No update.

8) cellml.org update

  • Seven case studies of CellML users have been published within the Community section
  • Publication of the reorganised tools section (with the addition of a 'Visualisation and Annotation Tools' subsection and merger of 'CellML Environments' and 'Modelling Environments' sections,) is pending feedback from Sarala and Alyson Lister who are to meet in Newcastle (UK) this week.
  • The CellML Project Team pictures are too dark and are being altered by Michael Backhaus to increase contrast.
  • James is writing a tutorial explaining private interfaces and encapsulation, as this is an aspect of CellML that newcomers often find confusing.