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The intepertation of the reversible flag maybe now be what you suggest
but originally it was not the case. I know this because I was the one
who introduced it, its very purpose was to support elementary mode
analysis. However, I think what you suggest makes it more useful, the
only thing one has to watch is that the flag and the reaction rate law
are consistent.

I would reinterate what Niolas says, it is quite natural to specify a
reversible reaction in the manner he indicated. Check out any kinetics
textbook and you'll see that it is quite frequently used.

Herbert

-----Original Message-----
From: Nicolas Le Novere [mailto:lenov@ebi.ac.uk]
Sent: Friday, March 10, 2006 1:02 AM
To: SBML Discussion List
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
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