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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.

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.
H

-----Original Message-----
From: Pedro Mendes [mailto:mendes@vbi.vt.edu]
Sent: Tuesday, January 24, 2006 6:00 AM
To: sbml-discuss@caltech.edu
Subject: Re: [sbml-discuss] SBML L2v2 specification vote #7: Making
'math' optional in KineticLaw

FBA also uses rate laws, these are of the type
v(i)=j(i) , for reaction i, and where where j(i) is a constant. Can be
written in MathML, no problems. In fact the whole FBA exercise is just a
parameter estimation problem where the j(i) have to be determined given
a set of linear constraints. No problem with this. What are the other
reactions without a rate law?

Pedro

On Monday 23 January 2006 18:35, Herbert Sauro wrote:
> There are a whole range of models which do not depend on rate laws,
> probably the most ell know begin flux balance analysis, but others
> exist to. However, SBML databasea such as biomodels.net do not
> consider these to be valuable models and will not accept them into the

> database. So perhaps rate law free models in SBML should not be
> permitted althohgh I think otherwise.
>
> Herbert Sauro
>
> -----Original Message-----
> From: Darren Wilkinson [mailto:darrenjwilkinson@btinternet.com]
> Sent: Thursday, January 19, 2006 1:28 PM
> To: SBML Discussion List
> Subject: Re: [sbml-discuss] SBML L2v2 specification vote #7: Making
> 'math' optional in KineticLaw
>
> --- Stefan Hoops <shoops@vbi.vt.edu> wrote:
> > Nicolas Le Novere <lenov@ebi.ac.uk> wrote:
> > > On Tue, 17 Jan 2006, Stefan Hoops wrote:
> > > > Any kind of local parameter is associated with a
> >
> > mathematical
> >
> > > > expression, be it for 'traditional ODE' modelling,
> >
> > stochastic
> >
> > > > modelling, or flux balance analysis.
> > >
> > > I'm not sure for logical modelling or petri net. Also, you
> >
> > can
> >
> > I am not sure either but not being sure is bad reason either way :).
>
> Clearly you both need to read my book! ;-)
>
> I'm certainly not aware of any modelling framework where a rate
> parameter makes sense completely independently of any rate law.
> There are frameworks where rates and rate laws are not used at all,
> but then kinetic laws are not required, so we are all happy. There are

> also frameworks where there is a _default_assumption_ about the nature

> of the rate law (such as for stochastic petri nets and discrete
> stochastic modelling more
> generally) - namely that unless otherwise stated, irreversible
> mass-action stochastic kinetics is assumed. But in this case it is
> clear what the rate law is, so there is no problem for tools to
> include it when they write the SBML, and there is nothing to stop
> tools from ignoring it when they read it. So I must admit that I am a
> bit puzzled as to why it is such a big deal to make the math optional.

> What is the harm in including it for completeness?
>
> Yours,
>
>
> --
> Darren Wilkinson
> email: darrenjwilkinson@btinternet.com home www:
> http://www.darrenjwilkinson.btinternet.co.uk/
> work www: http://www.staff.ncl.ac.uk/d.j.wilkinson/

--
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