[SOSlib-devel] implement variable compartments

[Rainer M. <ra...@tb...>]

Hi Everyone,

A related problem to the one from the previous email (species in 
substance units):

Currently SOSlib can not handle variable compartments (just as e.g. 
copasi and MathSBML).

For this case ALL ODEs need to be formulated in substance rather than 
substance/volume units, and species in concentration units will need 
additional assignment rules to map their values from the ODE variables, 
and this will probably involve significant changes to the code.


To have ODEs in substance units we only need to leave out the division 
by the compartment, as the kinetic laws in SBML are already in 
substance/time units.

Instead of (current) ODEs:

1) for X in substance units:
dX/dt = stoichiometry * kineticLaw(X)

2) for X in substance/volume:
dX/dt = stoichiometry * kineticLaw(X) / volume

we will have:

1) for X in substance units, as above:
dX/dt = stoichiometry * kineticLaw(X)

2) for X in substance/volume:
dX_amount /dt = stoichiometry * kineticLaw(X)
X = X_amount / volume

where X_amount is an internal variable we need to define and X is 
defined by a new internal assignment rule.

Does anyone see any problems with above approach?

Rainer