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Ralph Gauges wrote:-
>unfortunatelly I was not there at the discussion in Boston, so I have a
>question that might has probably been discussed before.
>What happens if e.g. an sboTerm states that the kineticLaw is
>"irreversible first order mass action" but the formula is
>Michaelis-Menten? Which do I take? Same thing goes for
>SpeciesReferences. Is is an error if a SpeciesReference that is in the
>listOfProducts has an sboTerm that states that it is an inhibitor? How
>should inconsistencies like this be handled?

Take the authors and hang 'em from the nearest yardarm!

Seriously, the answer to the last point is no. It is quite possible for a
product to also be an inhibitor of the same reaction. So this would not be
an inconsistency unless it was not also included in the listOfModifiers as
well.
If your program can tell that there is a difference between the maths and
the description then it should report that there is an error. You then
have to suspend processing untill the error has been resolved. SBML is an
interchange format. PERIOD. If it is being applied wrongly in the way you
describe, it is producing an invalid model, which can not be properly
simulated.
If the simulation engine wants to refuse to go further, or if it
wants to try both versions of the model, that is up to the simulation
engine writer, but he should be aware that he is trying to simulate an
invalid model and that the results may not be as envisaged by the model
writer.

Purely a personal viewpoint of course (particularly the first
sentence).


Hugh Spence
GSK Scientific Computing and Mathematical Modelling
Medicines Research Centre
Gunnels Wood Road
Stevenage
UK
SG1 2NY