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These are good points but I don't think a model should be invalidated
because there is no kinetic law.

H

-----Original Message-----
From: Pedro Mendes [mailto:mendes@vbi.vt.edu]
Sent: Tuesday, January 24, 2006 1:14 PM
To: sbml-discuss@caltech.edu
Subject: Re: [sbml-discuss] SBML L2v2 specification vote #7: Making
'math' optional in KineticLaw

On Tuesday 24 January 2006 15:34, Herbert Sauro wrote:
> I was thinking of things like elementary modes, conservation analysis,

> investigating the global structure of networks (using clustering,
> power law analysis etc) including modularity, and so on.

Sure, I agree that these are all extremely important things to do; but
they are already possible with SBML by simply representing the reaction
network without rate laws, as pointed out by several others here.

> With respect to FBA one doesn't need an explict rate law (as you
> mention), true one has boundary constraints, maybe technically one
> could call them rate laws.

They are rate laws because they are functions that describe the rate of
reaction. The rate laws themselves do not have constraints as long as
they have already been determined (their parameters).

The parameter estimation procedure is where the constraints operate, but
currently there is no way to specify parameter estimation because that
is not a model itself but rather a task operating on top of one, and
SBML currently only represents the models. (Though I believe there is a
proposal around that was discussed in Heidelberg last year, which would
cover these
things) .

--
Pedro Mendes
Research Associate Professor
Virginia Bioinformatics Institute,
Virginia Tech, Washington St.,
Blacksburg, VA 24061-0477, USA
http://mendes.vbi.vt.edu fax:+1-540-231-2606