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Hello Nicolas,

Of course you are right I have overlooked that one :)

However, we have still a problem here. The way a kinetic law is meant to
be interpreted is stated as:
Rate expressions in SBML are expressed in terms of
substance/time,

Here we have two problems at once :(

1) "Rate expression" vs. "reaction propensities"
2) "substance per time" vs. "events per time"


I know that it is often possible to convert between them. Especially,
for mass action kinetics we probably can agree on the rules guiding the
conversion. But in general these are fundamental different things and as
long as we try to put them into the same object, we will run into
difficulties.


Thanks,
Stefan


On Sat, 11 Mar 2006 00:21:23 +0000 (GMT)
Nicolas Le Novère <lenov@ebi.ac.uk> wrote:

>
> > I am not sure about that. Actually I think it is impossible if we
> > interpret what is said in the kinetic law section strictly :( The
> > kinetic law section states in paragraph 3:
> >
> > The expression in math may refer to species identifiers; in that
> > case, as discussed in Section 3.6.3, the units of each species
> > reference are those of concentration.
> >
> > However section 3.6.3 somewhat contradicts that and says that it may
> > also be substance units depending on the species definition.
> >
> > The minimum we need to do is to correct the paragraph 3 in 4.9.7 and
> > add this to the errata.
>
> Stefan,
>
> This has been documented as an erratum for years. That points out how
> important will be the new system of revision, with periodical
> corrections.
>
> see http://sbml.org/wiki/SBML_Level_2_Version_1_Errata
> errata 16
>
> --
> Nicolas LE NOVÈRE, Computational Neurobiology,
> EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD,
> UK Tel: +44(0)1223 494 521, Fax: +44(0)1223 494 468, Mob:
> +33(0)689218676 http://www.ebi.ac.uk/~lenov
>
>


--
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