ABI CellML meeting minutes 2010-01-13

Present: Dougal Cowan, Andrew Miller, Catherine Lloyd, Mike Cooling, Justin Marsh, Tommy Yu, James Lawson, David Nickerson, Peter Hunter, Tessa Paris, Mark Hanna, Ethan Cho

Last week's action items:

1) The umbrella spec to be moved to the top of the spec page.

  • Done.

2) Andrew to work out where to put the drafts and how to link to them. Also to write up some possible definitions of draft vs proposal, endorsed draft, etc.

  • Done

3) Dougal to create (a) tracker item(s) about these bugs.

  • Tracker items were created and the bugs were fixed by Andrew.

This week's agenda:

1. (Andrew) Possible collaboration with other groups - for example, the group from Carnegie-Mellon University working on the ASCEND modelling software (similar to OpenCell in terms of the types of mathematical models it aims to support, but with a primary user base of chemists).

  • Andrew reported on a package called ASCEND which is an ODE modelling package for non-biological chemistry, which has additional modelling capabilities compared to OpenCell.
  • Andrew has contacted the ASCEND group and they have some interest in collaboration, particularly conversion to and from CellML from their internal format.
  • Peter asked Andrew to forward him the correspondence and URL.

2. (Catherine) Terms of use for CellML models and associated content hosted on models.cellml.org.  Tracker item 2056.  Confirmation that we will use Creative Commons Atrribution 3.0 http://creativecommons.org/licenses/by/3.0/ together with a specific statement about attribution. The wording of this statement, and where is should be displayed, has to be decided.

  • Catherine again re-iterated that we have decided to go with the Creative Commons attribution license, but that we need to specify the wording.
  • The bigger problem is the decision of how and where to display the license, and where to include it in the model.
  • Peter suggested waiting for Poul and Randall before making decisions.
  • David said that to be MIRIAM compliant, the license must be included in the model, whether in RDF, as a separate text file or some other way.
  • Andrew said that discussions about inclusion of the license in the model should not delay putting the license up on the site.

3. PMR2 development - update

  • Tommy has played with PMR2 0.2 with Mike, and subsequently added some missing presentational features. This has been released as 0.2.1.
  • Catherine asked whether Tommy has got to the bottom of the crashes issue yet.
  • Tommy said that he is still looking into this, although he believes it is something to do with TCP/IP sockets.

4. Repository contributions update

  • Tessa has pushed 3 Wodarz immunology models, 2 of which have been exposed.
  • Ethan has been working on immunology models. He reported that the summer students are now using the latest OpenCell snapshots instead of PCEnv 0.6.
  • Mark has been working on java script for the OpenCell sessions with embedded SVG images.
  • Hanne has been creating OpenCell sessions for curated pancreatic beta cell models and immunology models.
  • Peter asked how the documentation is progressing for SVG sessions. Dougal said that a basic checklist is complete which requires additional details.
  • There was a discussion about session files.

5. CellML core specs - update

  • Andrew has been working on ModML, a Haskell based successor to CellML. The basic language has been laid down.
  • Mike asked if anyone can try writing a model in this language. Andrew said that there are no tools yet, but he could discuss with Mike how to implement his work in ModML.

6. Metadata specifications (general, citations, graphing, simulation, other)

  • James is passing on this work to whoever wants to continue it.
  • James has been making sure that everything is in the tracker.

7. OpenCell development update

  • Justin has been working on documentation; he has written the steps to build the API on OSX, and is working on the OpenCell build procedure.
  • Peter asked if there are any plans to improve the graph drawing in OpenCell, which has delays between integrating and drawing graphs, often with glitchy looking results.
  • There was a discussion about graph display, and a breakaway was called to discuss this issue further.
  • Andrew fixed various bugs reported by Dougal.
  • There was a discussion about testing the COR-like view. This will probably be done immediately following the release of 0.7.

8. CellML API - update

  • Mike asked about the status of Java wrappers on Windows.
  • There was an extensive discussion of Java wrappers on Windows.
  • Mike will talk to Randall and possibly Sarala about the status of these wrappers.
  • Andrew has been working on generating code for use with DAE solvers like IDA. While there is some common code between the IDA-style code generator, and the generator that works with GSL and CVODE, the core of the code generation involves a completely separate code path. This work is being done on a branch so it will not interfere with the planned upcoming release.

9. cellml.org update

  • Catherine noted the decision from last week that weekly meetings about cellml.org are not required, as the site is mostly stable now, and any further work can be discussed at the weekly CellML meeting.
  • The site has been relatively static recently, although Catherine continues to update the workshop pages.

10. Time permitting: Updates or additional items from volunteering attendees

  • Peter asked about the meeting to discuss building a 1.1 component library.
  • Peter reported on the forming of a computational biology journal, in which they want to only accept papers for reproducible models that are MIRIAM and open standard compliant. This could be a way for people to get academic credit for the extra work that goes into producing these models.
  • There was a discussion about the publication of models and the ramifications of publications of this type.
  • James announced that this was to be his last CellML meeting.