Meeting Minutes 12 December 2007

Present: Sarala Dissanayake, James Lawson, Catherine Lloyd, Poul Nielsen, Andrew Miller, Tommy Yu

Apologies: Randall Britten

Review of last week's action items

  • James will look into the website redesign with Tommy.

    • It is ongoing, James has put some design together and gave a visual overview.

    • Will need to bring this up again next week, and to keep Poul in the loop.

  • Tommy to look into all of these suggestions for the download page for the repository.

    • Actually, James took the initiative and put a plan together for the cleaned up version of the download/solve model page of the repository.

    • Action item: Tommy will implement this new model download page

  • Poul to find and check on those old meeting minutes.

    • Poul did not do that yet.

    • Action item: Poul to look for those minutes (pre-2001)

  • James to put up/update the project page to better reflect the status of various projects and proposals.

    • James ended up not doing it, because he felt people thought it will be unimportant and they have a lack of interest in such a page. Randall also told him that it may not be a good idea to duplicate the information that is found in the tracker onto the website.

    • Catherine suggests the removal of the development page if it won't be updated.

    • Tommy suggests replacing that page with links to relevant saved searches on the tracker

      • Andrew said that can be done, just have to create the correct search links.

      • Action item: James to change the current development page to include search links to the tracker with relevant explanations.


Sarala and Ontology

  • Idea is to use SBO to annotate models.

  • Sarala will give an example on how to do that to Catherine, and Catherine will help out with her.

  • Mapping of models and elements currently have to be done manually, which is not an issue for Catherine as she codes up CellML models manually also.

  • Sarala also has her own mappings that she came up with, a sort of glue ontology but it is incomplete.

    • Poul noted that it won't need to be fully complete

    • Catherine agreed, as Sarala's ontology won't be pushed to its limits.

  • Poul noted that multiple ontologies can be used for a single model.

  • Catherine will use Sarala's ontology as part of her best practice materials.

CellML workshop/meeting 2008

  • Nothing much happened as we are still waiting on people

    • Catherine has a proposed program

    • There was a brief discussion on what the program will be like

    • Poul noted that it will be good to keep it to one day

    • James noted that keeping each session short will help people focus

    • This will be brought up again next week, and send the proposed program onto the discussion list.

CellML 1.2

  • Andrew worked on the skeleton of the specification document

  • There is a need to define terminologies, and there was a discussion on that.

    • What defines a model, what defines a file

    • Andrew wants a way to explain the difference between a complete model, a model that is to be imported, a model that imports other models (but before the imports had taken place), and the final model that has been processed to contain the imported elements.

    • Poul noted that terminologies that already exists (such as file) should not be overridden to explain the concepts that may have similarities but different in nature.

    • Action item: Andrew needs to come up with terminologies for that.

Issue from Alan Garny

  • Discussion on the future of PCEnv and COR, what will be the name, what will be the focus of the software.

    • Poul thinks the focus of PCEnv should be on CellML

    • Andrew noted that Alan has a different goal in mind, where PCEnv will eventually support various different kinds of model formats and expand beyond CellML.

    • James thinks keeping PCEnv focus as an editor for CellML while allowing exports to other file formats (such as SBML, but let the user know the caveats involved) will be a good direction to take

    • There was also a discussion on various name choices for PCEnv.

    • In the end, we need Andrew, Alan, Poul and Peter to agree on the changes and directions to take, after soliciting comments from people.

    • Action item: Andrew to send a email to solicit comments.