Meeting Minutes 6 June 2007

Meeting Minutes 6 June 2007
Present: Randall Britten, Sarala Dissanayake, James Lawson, Tommy Yu, Dave Brooks, Peter Hunter

Andrew noted that the PCEnv manual and tutorial needs to be updated as it is very out of date. Andrew has already produced an updated tutorial for the NIH model sharing meeting, and the group decided that it would be worth adapting that to become the normal PCEnv tutorial, to replace the current one.

Dave suggested that the manual have a version at the top of it, so it is clear what version it applies to.

Peter suggested that Catherine might be able to update the manual. Andrew asked about whether we should keep the images in the tutorial, as they can be a pain to keep updated. Peter thinks that Catherine could go through the current images, and update them where they appear to be out of date.

Peter thinks that the graphs in PCEnv should be wider by default, at the expense of some of the width of the integration parameter text boxes. Andrew will look into this.

Peter also thinks that we need to make the session support in PCEnv available on the website. There is currently no way to associate other files with a model in the repository (as discussed last week), but this is something which we could work on. Andrew suggested that as a temporary measure we could just put the sessions up on the Plone site and link to them from the temporary documentation. This would of course mean that we need to update everything manually after every version change, because the model will link to the the session, which in turn links back to the model.

James thinks that it would not be that much work to use the temporary measure, as there are only about 30 models which he would like to add sessions for.

James has been looking at the CSML repository. He noted that they had taken only the first versions of CellML models, not the latest ones, and converted them into CellML. He suggested that there be some dialogue with the CSML group about the curation process.

James has also looked at the BioModels database. He thinks that it is well curated with respect to ontologies, and we might be able to make use of some of their work to help with our curation.

Tommy has finished implementing key words editing in the repository. He is currently testing it locally, but he expects for it to be on the live site some time in the next few days.

Sarala has been trying to use CellML imports. She plans to use them partly to imply biological meaning. She still hasn't got this working yet. She is also looking for an example of how to use imports. Andre has one example which she has looked at. Peter suggested that looking at Jonna's work might also be useful.

Dave has been looking into Agent Based Modelling. Andrew is not sure how CellML will support the state machines used in the models he is discussing. Using reset rules, as described in one of Andrew's BCP documents, might be one way to achieve this, although it would not be the cleanest formulation of the model.