[SOSlib-devel] implementing variable compartments

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

Stefan, thanks for the clarification in your last email.

i think i got it now :)

you wrote:

> the ode for conc can be derived by differentiating x=X/V:
> dx/dt = (dX/dt)/V - x*(dV/dt)/V
> where dX/dt is given by the kinetic law above.


dX/dt is just the sum of the +/- (stoichiometry*kineticLaw) expressions 
for all reactions where X is a product/reactant, i.e. it is a function of 
concentrations x, y, z ...

Right? (If not forget, the rest ...)


So actually, the first part of this equation (dX/dt)/V is the current form 
of ODEs in SOSlib!


Could the implementation of variable compartments in SOSlib would be as 
easy as:

1) add the expression " - x*(dV/dt)/V "
to the concentration ODEs for species in a variable compartment?


2a) if the compartment is defined by a rate rule, this rate rule could be 
appended to all ODEs directly, i.e.

newODE = currentODE - (x/V) * rateRule


2b) if the compartment is defined by an assignment rule, we would have
differentiate it towards time? For this we need to convert the assignment 
rule to a form, where differentiateAST recognizes time dependent variables 
that are in the assignment rule, e.g. x(t), which appears only as ASTNode 
"x". Is this possible/easy?

2c) if the compartment is changed by events, we don't need to append 
anything but just recalculate concentrations and re-initialize the solver, 
just as we do now for events.


If above is right - but i guess it might just not be that easy - 
we would have extracted two alternatives:

A) use ODEs in substance/time, write assignment rules for
x.amount = x / volume and replace all x by x.amount in ODEs, as Andrew 
suggested

or

B) use above approach.

Is that it?

Rainer