ABI Meeting Minutes 2008-05-07

Present: Randall Britten, Sarala Dissanayake, Michael Cooling, Catherine Lloyd, Justin Marsh, Andrew Miller, Poul Nielsen, Tommy Yu

Apologies: Peter Hunter, James Lawson

Action items from previous meeting:

  • Item 1: Justin sent the email regarding the RDF parser

  • Item 2: Justin built the new PCEnv snapshot on Windows, now has prettier content MathML renderings.

  • Item 3: Java bindings have been deferred as the effort required will be significant. This item created a lengthy discussion:

    • The bindings have been deferred as the priorities were for PCEnv, namely a systems of algebraic equation solver that the Japanese group have added that Justin is looking into, and having some features that were in COR that will be added to PCEnv by Alan Garny.

    • Also the need to put the plan together for YAPE. A discussion between Alan, Andrew, Justin and Randall was proposed for some time over this coming week to discuss the future for COR/PCEnv/YAPE, and so there will be something from there to bring to the table for next meeting.

    • Peter's input will be required on this (Java bindings, and other things) to learn whether the grants received has allocation for this kind of work.

    • Need to decide how to tackle this Java issue, as many groups elsewhere (such as the Newcastle groups) use Java rather extensively.

    • Sarala pointed out that there is a Java API that she uses, and it handles CellML fine but is not as complete as the current API, e.g. does not simulate models.

    • Poul pointed out that Nimrod (software that solves optimization problems) developers are interested to have support for CellML, it is open source but likely not GPL.

    • Randall sugested that we apply for a grant for the development and maintenance of the Java CellML API as there may be a number of interested parties with ties to possible funding sources for this.

  • Item 4: Tracker items for having symbols and sub and super scripts in the MathML display have been added.

Agenda for this week:

Catherine went to the conference in Amsterdam and gave a keynote on CellML. It was well received and many questions were asked. It appears to be much interests generated. Catherine has this list of items to discuss.

Request for PCEnv release

  • Catherine has curated models against the latest PCEnv snapshots, and she used that to give some models in the repository two stars.

  • However, this means that some models may not actually work in the current release of PCEnv, as there are some bugs that were fixed in the snapshot that may have made those models work.

Extension of CellML files downloaded from Repository

  • The extension should be .cellml, but in Opera this somehow doesn't work.

Site rendering problems in Opera and MSIE

  • The curation box do not show up in Opera, and it looks funny in MSIE.

  • Randall pointed out that Opera's user base is not as major as the other browsers, and given the resources we have, we may not be able to test this on all browsers.

Best practice guidelines would be nice for model annotation

  • There is a need to define how to best annotate models, including usage of any ontologies.

  • Sarala noted that James is adding to the ontology framework she created to aid in annotation.

  • We will have to define some of our own identifiers to define some of the things in order to avoid ambiguities, as certain components have different identifiers by different groups.

  • Catherine has notes from Martin Fink regarding this and will pass them onto us.

  • Andre has a model decomposition tool, it will separate CellML files into different components, despite the caveats that are present, it does it job. This can help us in splitting out the parts that need annotation, and can help us in converting our current repository of 1.0 models into 1.1 and store them into PMR2 when it's ready.

FAQ needs update

  • As progress has been made, new information could be put up there.

  • Alan Garny has some things to add, but he was unable to as he didn't have permission.

    • Action item 1: Tommy will give Alan the permission to edit that page.

  • Catherine, Gareth, James and Tommy will be having a meeting about the content, design and layout of the CellML website next Monday and they will be discussing this.

That was all from Catherine, we now have Andrew.

Summary of CellML related discussions at the standards & specifications in synthetic biology workshop

  • Andrew's talk was somewhat rushed and there was not enough time for examples and discussions.

  • Most people have been using SBML, and would like to keep using it until its limitations are hit, then they might use CellML

  • He had a discussion with Mike Hucka and Eric Butterworth.

  • There was discussion about how Matlab integration would be helpful. The easiest initial start on this would be to add code generation for Matlab, similar to COR. Tracker item already exists.  Regarding reversing Matlab code into CellML, some Matlab expressions could be pasted into the equation editing text box, but having to place units on number literals makes this harder.  Some users currently work this way with COR.

Now the standard agenda items

PCEnv/CellML API Progress Update

  • See Action Item 2 from previous meeting.

PMR 2 Update

  • Tommy finished up getting RDFLib to work on getting metadata from CellML files to populate the Zope schema for searching. Basic searching works, and he will be working on generating a search result page similar to what we have on PMR1.

  • Tommy also building a VMWare image that will run PMR1, for demos and for staging.