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Hello Nicholas,

On Wed, 18 Jan 2006 21:22:55 +0000 (GMT)
Nicolas Le Novère <lenov@ebi.ac.uk> wrote:

>
> >
> > 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?

I get your point :)

>
> > 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.

You are exactly right, this is exactly why I suggest subclassing of
the kinetic law to be able to describe other mechanisms than ODE in an
earlier message in the is thread :)

Thanks,
Stefan


--
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Virginia Tech
Bioinformatics Facility I
Blacksburg, Va 24061, USA

Phone: (540) 231-1799
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