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But that is not the case. It is not invalidated, it is perfectly valid. The
current proposal (vote 7) is not about that, it is about having a kinetic
law without the math component. As several others have expressed, there is
no reason for that as it is already possible to have a reaction without a
rate law (which is what you were arguing). What does not make sense to me
is a rate law without the math (the expression of the rate law). No one is
arguing against reactions without rate laws...

P

On Tuesday 24 January 2006 20:28, Herbert Sauro wrote:
> 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

--
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