Forums

>> 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.

Why is that? You would have

R1
--
+---+ ---/ \---> +---+
| A | | B |
+---+ <---\ /--- +---+
--
R2


Is-it a problem?

> 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.

Ah. Alright. You need three reactions here. Right. But the following is fine, isn't it?

R1
--
+---+ ---/ \---> +---+ R3 +---+
| A | | B | ----------> | C |
+---+ <---\ /--- +---+ +---+
--
R2

--
Nicolas LE NOVERE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223 494 521, Fax: +44(0)1223 494 468, Mob: +33(0)689218676
http://www.ebi.ac.uk/~lenov AIM screen name: nlenovere