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On Fri, 10 Mar 2006, Nicolas Le Novere wrote:

> Ouch! The reversible flag has a very clear meaning, and is essential
> for various treatments (graphical output, treatment of fast reactions
> where one ignore kineticLaws etc).

I'm sorry if I seemed harsh in my previous message.

Part of why I wanted to have multiple kineticLaws was that I want the
graphical output to look better. You bring up a good point about fast
reactions, and I think that if multiple kineticLaws are accepted then the
fast attribute should be optional for kineticLaws as well as reactions.

> I am probably misunderstanding the issue here, but you can just define
> two reactions as Herbert says BUT set the reversible flag to
> "false". It is true by default.

I can do that, but as you said above that breaks the graphical
interpretation.

> Remind-me why can't you use a reversible reaction with a kineticLaw of
> the form
>
> kon * react - koff * prod
>
> ?

I do stochastic reactions where the probability of each reaction is
tracked. In many cases, a reversible reaction is the one where I'm most
interested in the exact number of individual species created, and if I
have a single kinetic law to specify what is essentially the net movement
of molecules from the reactant side to the product side then I miss some
of the detail of the gross movement.

A more concrete example is

A <-> B
B -> C

where perhaps the A -> B reaction is slow but the B -> A and B -> C
reactions are fast. If I just do the kinetic law as you stated above,
essentially no B will ever be created because it does not have a
high probability of being created. Because of this, no C will be created,
and if that's my species of interest my stochastic simulation will not
capture the behavior that I'm looking for.

Bill

--
"Fools ignore complexity. Pragmatists suffer it. Some can avoid it.
Geniuses remove it."
-- Alan Perlis