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 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.
Remind-me why can't you use a reversible reaction with a kineticLaw of
kon * react - koff * prod
On Thu, 9 Mar 2006, Bill Denney wrote:
> This is what I've been doing, but it doesn't really seem like the best
> solution, and I was thinking this would be a place where the standard could
> use some improvement. I didn't know why the flag was there-- it seems a bit
> specific (and it could be detected other ways).
> On Thu, 9 Mar 2006, Herbert Sauro wrote:
>> In this situtation I would simply define two reactions, one for the on
>> rate and one for the off rate. Ignore the reversibility flag, it was
>> originally intended to be used in elemetnary mode and flux balance
>> Herbert Sauro
>> -----Original Message-----
>> From: Bill Denney [mailto:firstname.lastname@example.org]
>> Sent: Thursday, March 09, 2006 10:15 AM
>> To: email@example.com
>> Subject: [sbml-discuss] Multiple kineticLaw Sections Per Reaction
>> I'm wanting to put multiple kineticlaw sections in each reaction. The
>> reason that I want to do this is because I have kinetic data on both the
>> on and off rates of the reactions that I need to model as separate
>> reactions. I thought that it made sense that if I said that the
>> reaction was reversible then I could have both the forward and reverse
>> kinetics within that reaction.
>> Something similar to this seems to have been discussed before:
>> Is there a better, more accepted way to do this?
>> Another issue that I've been thinking about is: what is the best way to
>> store multiple values for the same kinetic rate constants. The reason I
>> want to do this is that I have tables that list a set of kinetics for
>> reactions from several groups that may not agree. I would like to store
>> all these values within my sbml so that my tools can try to enumerate
>> which kinetics seem to be the most consistent. I could do this within
>> an annotation, but it seems as though it could be an issue that could
>> more generally useful to the sbml community.
>> Emily's Lullaby n. - A tranquilizer dart.
>> -- Will Miller
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