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> 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