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Nicolas

> If the namespaces of
> parameters and compartments are separated in the modeling environment,
> which is the case in *every* software I'm aware of, the
> problem occur not
> in the model, but in the SBML encoding of the model.

Please give examples of these software packages.

yours
Andrew Finney

> -----Original Message-----
> From: sbml-discuss-bounces@caltech.edu
> [mailto:sbml-discuss-bounces@caltech.edu] On Behalf Of
> Nicolas Le Novère
> Sent: 30 April 2005 15:26
> To: SBML Discussion List
> Subject: Re: [sbml-discuss] parameters and namespaces
>
> > Also note that the units of
> > 0.01 and 0.1 are unspecified.
>
> There are default units. If all the id are correctly mapped.
> There is no
> ambiguity on the unit, since the result should always be
> substance/time.
>
>
> > d[A] (0.01 * [A] * 0.1) - (0.1 * [B] * 0.01)
> > ---- = - ---------------------------------------
> > dt volume_of_compartment_cyt
> >
> > What is 'volume_of_compartment_cyt'? It is given in the
> > definition of compartment 'cyt' as 5e-15. Hence,
> >
> > d[A] (0.01 * [A] * 0.1) - (0.1 * [B] * 0.01)
> > ---- = - ---------------------------------------
> > dt 5e-15
> >
> > Similarly for the rate of change of the concentration of B:
> >
> > d[B] (0.01 * [A] * 0.1) - (0.1 * [B] * 0.01)
> > ---- = ---------------------------------------
> > dt volume_of_compartment_nuc
> >
> >
> > (0.01 * [A] * 0.1) - (0.1 * [B] * 0.01)
> > ---------------------------------------
> > 1e-15
>
> We agree on that. But this is not the correct result. The
> results intended
> by the author was:
>
> > d[A] (0.01 * [A] * 5e-15) - (0.1 * [B] * 1e-15)
> > ---- = - ---------------------------------------
> > dt 5e-15
> >
> > d[B] (0.01 * [A] * 5e-15) - (0.1 * [B] * 1e-15)
> > ---- = ---------------------------------------
> > dt 1e-15
> >
>
> > The given example in my mind is
> > a problem that falls squarely in the lap of the model
> > author: they created a bad model.
>
> Yes if we consider here the model "author" as the sum of the model
> creators and the developers of the SBML export. If the namespaces of
> parameters and compartments are separated in the modeling environment,
> which is the case in *every* software I'm aware of, the
> problem occur not
> in the model, but in the SBML encoding of the model.
>
>
> --
> 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
>
>
>