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Hello all,

I think an interpretation can be found for which the example is correct. Still
the model is not done nicely:

the dimensions of all the Ks are such that the kinetics are given in amount of
substance/time (as required).
Then you have to divide by the compartment volume to get a concentration
change (as is done in the example).

However that implies (at least for the reactions that take place in one
compartment) that the k value implicitly contains the compartment volume
since usually you assume that the reaction scales with compartment volume
(i.e. if the volume doubles the amount-of-substance-rate of a first order
reaction should also double). The dimension of the Ks would be volume/time.

So far it would be (quite) ok, just not nice. We should still not encourage
people to write the models like this.
However in this case the volume of one of the compartments is variable. And
under this circumstances things are different. You can not include a changing
volume in the k-value implicitly. So the model explicitly states that there
is a first order reaction in the second compartment that does not scale with
the volume.
If that is indeed the intention of the example it should be stated in the
description.

Sven

Am Monday, 14. November 2005 20:28 schrieb Stefan Hoops:
> Hello All,
>
> I am reading section "4.9.7 KineticLaw" of the Level 2 Version 1
> specifications. It is clearly stated that the units of the result of the
> kinetic law must be in substance/time which probably all of us agree is
> correct. However when I continue reading and look at the example in
> section
> "5.6 Example of translation from a multi-compartmental model to ODEs"
> I see that the rate law is given in concentration/time and it is up to
> the software to explicitly correct by dividing by the species'
> compartment.
>
> I am either missing something or we have a serious conflict. Please help
> met out.
>
> Thanks,
> Stefan