Meeting Minutes 18th September 2006

Meeting Minutes 18th September 2006
Present: Matt Halstead, Poul Nielsen, Tommy Yu, Shane Blackett, Andrew Miller

Poul: Peter asked about making a PDF file containing the mathematics. Tommy will work on this.
Poul and Matt haven't had time to interview the person who applied for the model curator position yet.

Poul received an e-mail from Vincent Rouilly at the Imperial College, who has been creating CellML models for gene transcription. Andrew has replied to help him to create a valid model.

Tommy: Has been working on getting Erik Butterworth's models in to the repository. This is his last week at the institute before he goes to Canada. He has sorted out the job offer for the position from the University, but still needs to arrange his work visa. He hopes he will be able to be back by December.

Shane: Has been working on getting ITK support in cmgui to work. He is planning on targetting Linux and AIX. He has been working with Andrew to get a working mozCmgui build on Linux and Win32, although some more work is needed to get it to be portable to all distributions.

Andrew: Has got PCEnv to compile on all platforms, however, there are still problems getting it to run on OS X and Win32.

Andrew has received some patches from David Nickerson (Andre) to give better diagnostics when invalid models are put into the CellML Code Generation Service. These have been committed into our repository.

Andrew has been working on moving the RDF retrieval functions from the elements to the models, allowing all the RDF in a model to be fetched, and queries on them to be made. There was unanimous agreement that this is a positive step. There was also unanimous agreement that there should be high-level support for schemas such as cmeta and the simulation / graphing specifications. However, Andrew believed that there should also be a generic API which allows basic RDF operations to be performed. Matt and Shane disagreed, as they would like to force people to stick to the specification, discuss any changes on the list, and get them put into the CellML API implementations, rather than implement additional specifications in a more modular and decentralised way. Matt suggested that some insight as to what is required could be gained from reading the archives of the SBML discussion on this. Andrew suggested that we at least support all the schemas that people have found useful for SBML models.

Matt: Has been working on the ontologies.
Sarala has been making progress. She still needs to resolve issues with the levels of detail for dimers. Has also been trying to work out what is required for entity relations (Kitano has provided some examples of this).

Matt has moved to Zope 3 technologies, which has allowed him to develop View classes for the ontologies. Shane and Poul are keen for a human interface for access to the ontologies to be set up, as there is currently only programmatic interfaces.