Meeting Minutes 17th July 2006

Meeting Minutes 19th June 2006
Present: Poul Nielsen, Andrew Miller, Edmund Crampin, Sarala Dissanayake, Peter Hunter, Shane Blackett

Shane and Andrew had a meeting two weeks ago, and discussed the use of GSL.

Poul had a meeting with Alan Garny at Oxford. Alan agreed to make the COR source code available, eventually under an Open Source license. Alan was receptive to the idea of collaboration with other similar projects.

Peter attended a meeting with the NIH National Heart Lung and Blood Institute, who are working on their 10 year roadmap for computational biology. They agreed that the plan should include details on markup languages.

Sarala leaves for Japan on the 29th of July. She will work with Kitano's group, and participate in the SBGM and ICMB meetings.

Sarala has produced a new graphical notation. This graphical notation is closely modelled after the structure from BioPax. There was some discussion about whether this was a good idea, because it means that reactions and catalysts are separated. Peter and Edmund both favoured an approach which shows reactions and catalysts more closely coupled.

Shane noted that the model repository had been updated with all the models. However, he noticed that the "Validation" tab seems to provides information which is hard to interpret.

Peter noted that there were problems where the generated presentation MathML on the website do not work with all browsers. He asked whether our presentation MathML adhered to the W3C standard, and what process we could follow in the future to ensure cross-browser compatibility. The consensus was that the person taking the new position to maintain the site would test changes against all major browsers.

Andrew has made progress with the Physiome CellML Environment. It now draws data and supports box zoom. Still a number of issues to be resolved before it can be released even as an integration tool. It also doesn't yet allow any sort of editing (not even of initial conditions / parameters).

Shane asked whether the Plone product Andrew produced, which lets users upload models and download code, could be put onto all the other models in the repository. There was consensus that this should be a priority for Andrew, because it is important that people can download code. Edmund suggested that supporting MATLAB code generation would increase the use of CellML models by biologists, although this could be added later.