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>> describe an equilibrium with a Kd, without developping into a
>> reversible mass-action law. If you know the Kd, you can use a rapid
>> equilibrium in StochSim. You do not need the kon and koff. But if you
>> need to represent the reaction velocities, you need to.
>
> In StochSim you have an underlying set of assumption and rules, i.e.,
> mathematical expressions or functions. For anyone to understand how your
> tool interprets the model you need to phrase that in the Math element.
> It is probably not a rate law instead it is an algebraic expression
> something like SE = kd * E.

You are right with that example.

> You should not do that via sboTerms as this
> removes the contents from SBML.

I'm bewildered. How comes SBO sneaked in here again. What is the relevance?

> In anyway, "Mathematics" is considered a
> rich universal language and that is why we agreed to use it in SBML to
> begin with.

But the math element of kineticLaw is not any mathematical expression. It
is a mathematical expression describing the velocity of a reaction in
substance/tiem units.


--
Nicolas LE NOVÈRE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223 494 521, Fax: +44(0)1223 494 468, Mob: +33(0)689218676
http://www.ebi.ac.uk/~lenov