[SOSlib-discuss] accounting for species in substance units

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

Hi Everyone,

SOSlib code starts to live again a bit.

We have just recently found out that we didn't account for species that 
are defined with HasOnlySubstanceUnits == true, or which live in a 
compartment with SpatialDimension == 0.

In both cases, the units of the species in all equations of the model 
are in substance instead of concentration (substance/volume) units.

ODEs for such species change from:
dX/dt = stoichiometry * kineticLaw(X) / volume
to:
dX/dt = stoichiometry * kineticLaw(X)

While I have never seen such a model, it is possible in SBML. It should 
work now with SOSlib but I couldn't test it, because I don't know any 
model which has such species. If anyone knows about such models (doesn't 
have to be in SBML), please send me a link or reference, so I can test it.

We still solve 100 out of 113 semantic test suite models correctly, so 
nothing should have changed for usual models. The new code is at 
sourceforge CVS now.

Rainer