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Ok I see what you're saying, it makes sense. I have to admit I've not
been following the thread too closely which explains my confusion.

Herbert


-----Original Message-----
From: Pedro Mendes [mailto:mendes@vbi.vt.edu]
Sent: Tuesday, January 24, 2006 6:27 PM
To: sbml-discuss@caltech.edu
Subject: Re: [sbml-discuss] SBML L2v2 specification vote #7: Making
'math' optional in KineticLaw

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