Forums

Robert Phair wrote:

> But I think the ListOfModifiers much more. I think it is a vital
> communication link between the SBML community and the experimental
> biology community.

I won't convince you, but I entirely disagree. SBML is not supposed to be seen by anyone. Not modelers, and of course even less "experimentalists". The communication link between theoreticians and wet biologists is the scientific publishing at large: book, articles, webpages etc.

NB: "SBML community" and "experimental community" are not disjoint or complementary. "SBML community" does not mean "modeling community" or "theoretical biology community"

> If, however, we have a larger goal for SBML, one in which it serves
> as an interface between qualitative diagrams and quantitative models,
> then I think the ListOfModifiers is every bit as important as the
> ListOfReactants and the ListOfProducts.

If the purpose is to encode "pathways", SBML is not the way to go. There is another effort, with much higher semantics, that suits your needs. It is called BioPAX (http://www.biopax.org)

But formal models (logical networks, petri-net etc.) is the topic of an extension for L3. An initial spec will be presented at the next SBML forum.

> To me there is an important reason that the SBML specification says
> the kinetic law is OPTIONAL and the ListOfModifiers is REQUIRED.

No, it does not. See figure 21 page 64. ListOfReactants, ListOfProducts, and ListOfModifiers, are all optional.

--
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nlenovere@hotmail.com
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/
____________________________________________________________
To manage your sbml-discuss list subscription, visit
https://utils.its.caltech.edu/mailman/listinfo/sbml-discuss

For a web interface to the sbml-discuss mailing list, visit
http://sbml.org/Forums/

For questions or feedback about the sbml-discuss list,
contact sbml-team@caltech.edu