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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/