Re: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
19 Jan '06 07:03
On Wed, 18 Jan 2006 21:22:55 +0000 (GMT)
Nicolas Le Novère <email@example.com> 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
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 :)
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Bioinformatics Facility I
Blacksburg, Va 24061, USA
Phone: (540) 231-1799
Fax: (540) 231-2606