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Yes, that is what I'm trying to say.

Bill

On Fri, 10 Mar 2006, Tomas Radivoyevitch wrote:

> 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
>>
>

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