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Hello Howard,

I was not explicit enough in my previous mail, what I meant is that
you are wrong in calling 'I' a modifier in SBML. To encode the reaction
in SBML you would have to write the following:

<listOfSpecies>
<species id="Metabolite_2" name="I" ... />
<species id="Metabolite_1" name="P" ... />
<species id="Metabolite_3" name="S" ... />
</listOfSpecies>
<listOfReactions>
<reaction id="Reaction_0" name="reaction" reversible="false">
<listOfReactants>
<speciesReference species="Metabolite_2" stoichiometry="2"/>
<speciesReference species="Metabolite_3"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="Metabolite_2" stoichiometry="2"/>
<speciesReference species="Metabolite_1"/>
</listOfProducts>
</reaction>
</listOfReactions>

Thanks,
Stefan

On Thu, 28 Apr 2005 07:56:40 -0400
Stefan Hoops <shoops@vbi.vt.edu> wrote:

> Hello Howard,
>
> On Thu, 28 Apr 2005 01:41:37 -0500
> Howard Salis <salis@cems.umn.edu> wrote:
>
> >
> > Well, consider the imaginary reaction:
> >
> > 2 I + S --> 2 I + P
> >
> > 'I' would be considered a modifier. It has a stoichiometry of two,
> > causing the reaction to be considered 3rd order.
> >
>
> This is exactly where you are wrong 'I' is a substrate with
> stoichiometry 2 and a product with stoichiometry 2 but not a modifier.
>
> Thanks,
> Stefan
>
> --
> Stefan Hoops, Ph.D.
> Senior Project Associate
> Virginia Bioinformatics Institute - 0477
> Virginia Tech
> Bioinformatics Facility I
> Blacksburg, Va 24061, USA
>
> Phone: (540) 231-1799
> Fax: (540) 231-2606
> Email: shoops@vbi.vt.edu


--
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Virginia Tech
Bioinformatics Facility I
Blacksburg, Va 24061, USA

Phone: (540) 231-1799
Fax: (540) 231-2606
Email: shoops@vbi.vt.edu