Dear All, This email is aimed at anyone who has comments, but we particularly want to draw Matt's attention.
In the CellML meeting yesterday I brought up the issue of replacement of reaction components with straight math. At present PCEnv isn't handling reaction components well - models which use reaction components aren't integrating, for one. There are also issues with math elements not being picked up if they are under role elements. Andrew has written a script to pull these math elements up a level so that they're a direct child of the component, not the role element. The script also defines delta variables as rate * stoichiometry. Running this script on the models which contain reaction components has cleared up most of the errors with undefined delta variables, so now many of the models with reaction components can now be loaded in PCEnv. The problem is that *none of them* will integrate properly. I am making the assumption that this effect is due to the reaction component, not the models, since it is so widespread among many very different models. I'm going to start rebuilding models without reaction components. However, one of the primary issues around this is that the information represented by the attributes defined in the reaction components is, while not essential for computation of the model, definitely something that we want to keep. For example, what species are reactants, products, catalysts, activators, inhibitors (and what kind of inhibitor,) etc. Ideally, these attributes would be recorded as metadata. We don't as yet have this facility, however. So the questions are: 1.) what to do with this data meanwhile 2.) how to redesign reaction descriptions using a combination of math and metadata. One of the reasons we're seeking your input Matt, is that ontologies such as BioPAX could be really useful in providing a framework for how we assign metadata to reactions, in a biological sense. Also, Sarala mentioned in the meeting yesterday that she was using BioPAX to describe reactions in her work. Regarding the first question, some of the ideas that were suggested were: a.) use commenting to describe the attributes of each reaction b.) keep the files (well, we already do anyway,) that describe the models in terms of reaction components and refer back to them later when we have the facilities to enter metadata on reactions to the models which have been rebuilt without the reaction components. So if anyone has any comments on this, they'd be much appreciated. James _______________________________________________ cellml-discussion mailing list [email protected] http://www.cellml.org/mailman/listinfo/cellml-discussion
