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On Fri, 10 Mar 2006, Herbert Sauro wrote:

> I also think there is a real problem, how would one know that a given
> rate law in an SBML model is valid for a stochastic model? As far as I
> know, and I please correct me if I am wrong, there are only a very small
> number of rate laws that have been shown to be usable for stochastic
> simulations. I can't blindly read a SBML file, Level 1 or 2 (and we use
> level 2), and just plug all the equations into a, say, Gillespie
> simulator. I think this is what the SBO idea will solve?

You can't just put the in the kinetics, but you can look at the units
associated with the kinetic constant and the units and stoichiometry of
the reactants and from that you can determine a) if the kinetics were
written for a stiochiometric reaction and b) if they weren't, how to
convert them to stiochiometric rates. I'm not familiar with all
stochastic models, but this would definitely work for Gillespie, one of
the (if not the) most common.

Getting back to the root of what I was originally requesting, I would just
like to be able to include two kinetic laws if the reaction is reversible.
All software would have to be able to do would be to reuse the general
reaction description with both sets of kinetics. I think it would fit
well in L2v2 (though I understand that it may be too late for that)
because it would require a trivial change to the specification and only
relatively small adjustments to software packages.

It would allow the reactions, for the stochastic simulators among us, to
be specified in a more logical manner, and presumably, it would allow for
elementary mode analysis to perform better when reactions are specified as
actually being reversible instead of two irreversible reactions (I
assume-- I'm not familiar with elementary mode analysis). Finally, it
would allow graphics packages to easily and correctly recognise and
display reversible reactions.

Bill

--
"I only lied because it was the easiest way to get what I wanted."
-- Bart Simpson