Re: [SOSlib-devel] Request for help with a multicompartment problem

[Andrew F. <af...@ca...>]

Folks

Assuming the issue is just how to create an encoding in SBML for
multicomparment models
and not how to map from SBML to ODEs...

I'd just like to point out one obvious point...

an equation like 

d[C]/dt = k * [A] * [B]

describes a phenomena that only really works in a single compartment.
i.e. when two species are in the same compartment and therefore can freely
react with each
other the rate of reaction is proportional to the concentrations of the
species.

if A B and C are not in the same compartment the equation doesn't make any
physical sense to describe the interactions

in that case any chemical equation A + B -> C
has be decomposed into its constituent transport and conversation components
before you can move forward,

As far as SBML is concerned there 2 ways to go either you formulate a
complex rate equation which enables you to fold in the transport and
conversion components together or
you decompose the SBML reaction into simpler ones

Must go to work now

Bye

Andrew