Meeting Minutes 2008-01-23

Present: Michael Cooling, James Lawson, Catherine Lloyd, Andrew Miller, Poul Nielsen, Anil Wipat, Tommy Yu

Apologies: Randall Britten, Peter Hunter, Justin Marsh


MathML 3

  • Poul noted that the development for the MathML 3 specification has been started, and gave a general overview of what that may mean for CellML.

    • It deviates from MathML 2 for the content dictionary, where domain specific units can be imported, similar to how it's done in CellML.

    • It will be more inline with the OpenMath efforts.

    • More updates to follow as the specification progresses.

CellML 1.2 Specification Update

  • Andrew is nearly completed the translation of the current CellML 1.1 specification into a normative document.

    • This was raised in response to Anil's question on what kind of validation exists for CellML currently.

    • Without a solid, unambiguous normative specification it is difficult to validate a document as the interpretation of an informative specification is open.

    • There are no mentioning on the status of reaction elements, with some mentioning of directionality.

    • Method of development was mentioned again here, it is in a Git repository where everyone can pull into their own branch and develop from there, and those people can expose their changes for other people to pull also.

    • Andrew noted that if comments are needed, quote the lines and add comments for the messages that need to be sent.

Catherine: CellML Workshop 2008 Update

  • A nearly completed draft of the schedule was printed and shown. It's split into four sessions in total. The full schedule will be sorted out soon.

  • There will be 40-50 attending.

  • Since there will be many people presenting every event and presentation will be compacted.

BioBricks Conference

  • Michael gave a brief overview on what BioBricks is.

  • He also pointed out that their repository of models do support CellML, but currently it's quite sparse. He noted that Barry Canton, Vincent Rouilly, James and himself are working on translating BioBricks models into CellML.

  • He also planned to go to the upcoming BioSysBio conference in London that will be about synthetic and system biology.

  • There is a related conference in Washington that clashes with the London conference, and Michael suggests perhaps Jonna could go to that instead, as she is submitting a paper on modular CellML model construction and she might be able to contribute there. James mentioned that notification of this conference was sent to cellml-discussions, and would find the email and forward it to Poul.

  • On that note, Catherine pointed out she was also invited to a different conference in Amsterdam towards end of this coming April.

PMR update

  • Tommy is still working on expose model views.

  • He also helped out Catherine with removing the models with reaction elements from the current repository. Also he wrote a script that replace the broken links for the documentation of the current site with the list of corrected links that James put together.

  • James is keen to use Tommy's Mercurial-based PMR2 prototype as a prototype repository for the planned "Registry of Standard Biological Models."