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I'm guessing it's because he has data for each of the two terms separately,
and that it would be nice to have reactions go with the measurements. Right?


----- Original Message -----
From: "Nicolas Le Novere" <lenov@ebi.ac.uk>
To: "SBML Discussion List" <sbml-discuss@caltech.edu>
Sent: Friday, March 10, 2006 4:01 AM
Subject: RE: [sbml-discuss] Multiple kineticLaw Sections Per Reaction


> 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
> the form
>
> 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).
>>
>> Bill
>>
>> 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
>>> analysis.
>>>
>>> Herbert Sauro
>>>
>>> -----Original Message-----
>>> From: Bill Denney [mailto:denney@seas.upenn.edu]
>>> Sent: Thursday, March 09, 2006 10:15 AM
>>> To: sbml-discuss@caltech.edu
>>> 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:
>>> http://www.sbml.org/forums/index.php?t=tree&goto=2996&rid=0
>>>
>>> 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.
>>>
>>> Bill
>>>
>>> --
>>> 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
>