ABI CellML meeting minutes 2009-09-23

Present: Dougal Cowan, Andrew Miller, Catherine Lloyd, James Lawson, David "Andre" Nickerson, Justin Marsh, Tommy Yu, Randall Britten

Apologies: Mike Cooling, Poul Nielsen, Peter Hunter

This week's agenda:

1) CellML Specs - update

  • Nothing to report.

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

  • James is going to be making the metadata spec his main focus. Work will begin in earnest on the spec, and hopefully there will be something Tommy can base the PMR2 metadata editor on soon.

3) OpenCell development update

  • Randall reported that Alan has been working on getting COR text to CellML in memory.
  • Alan noted that his implementation works by completely regenerating the COR text view, or the CellML, when changes are made. Andrew noted that this was the expected approach, and what is done for the existing XML view.
  • There was a discussion of new OpenCell features, such as drag and drop.
  • Randall suggested that automated units correction could be a possible feature to add to OpenCell in the future. James expressed concern that this would lead to 'fudge factors' in models. Randall clarified that he meant that OpenCell could suggest corrections, and not that they be automatically applied.

4) CellML API - update

  • Andrew has been getting feedback from Randall and Jonathan about the API paper.
  • Andrew has also been working on top-level piecewise equations.
  • Justin has been getting some static builds of the API going to Chris Bradley, and working with Sarala on the Java bindings.

5) cellml.org update

  • Catherine reported that there was no meeting this week.
  • Heading capitalization was fixed by Tommy during the meeting.

Action item 1) Dougal to get the IUPS notes with photos up on the website.

6) Repository contributions update

  • Catherine reported on the problem that James is the only one who knows how to make exposures, creating a bottleneck.
  • James has been working with students, has added some exposures and continues to update metadata.
  • Catherine reported 7 new models from students. Jeelean has completed an aging model and a MAP kinase model.
  • Catherine said that she and James will set up projects for the three summer students and Geoff Nunns.
  • Randall said that he thinks the Saucerman model is very close to completion and could be done by one of the students.
  • Catherine reported that Peter has requested Vilar et al. 2006 from the Biomodels database to be converted to CellML.  Andrew has run the model though the SBML to CellML converter and Catherine will manually check the and edit the CellML output.
  • Penny Noble has sent us an atrial cell model for upload.
  • A group in France have been working on the Karagiannis and Popel model and James will create a new exposure.
  • A group in Russia have been working on the Katsnelson et al 2004 and James will create a new exposure.
  • Catherine has completed an astrocyte/glial model (prepublication) and has almost finished a brain metabolism model.

7) PMR2 development - update

  • Tommy has got the archive working for embedded workspaces.
  • Andre said that 3 features would be very useful to make live in PMR2; private workspaces, embedded workspaces, and archives.
  • Randall said that the features most useful to curators would be a metadata editor, and a way to quickly update existing exposures.
  • There was a discussion of features for PMR2 0.2.
  • Tommy said that Mike and Andre would greatly benefit from the release of recently implemented workspace features.
  • Randall suggested adding some kind of "roll-over" rapid exposure update functionality, and then releasing 0.2.
  • There was a discussion around the deprecation, re-creation and form of exposures.

  • Andre emphasised that deprecating exposures is an incorrect approach, since that means the URL is no longer valid, which is a problem if the URL was published elsewhere (e.g. a paper). In reply, Randall explained that the exposure rollover would be making a clone of an existing exposure, essentially copying all aspects of the source exposure, and not changing anything about the source exposure except for the visibility of the source exposure in the main listings of exposures. That way the source exposure URL remains valid, but is not listed in the main listing. Instead, the new cloned exposure is listed.

Action item 2) Tommy will look into how a rapid exposure rollover can be done.

  • Creation of new exposures will be a focus for PMR2 0.3; this requires the metadata spec. It was suggested that the metadata spec be worked with (tested?) in a staging environment.

Action item 3) Catherine to create a tracker item about the authors (curators and paper authors) for exposure pages.