[sbml-discuss] Multiple kineticLaw Sections Per Reaction

Herbert Sauro Herbert_Sauro at kgi.edu
Fri Mar 10 13:00:50 PST 2006


True, if you're interested in doing stochastic models then as you say
the reaction should be separated into two reactions.
Herbert 

-----Original Message-----
From: Bill Denney [mailto:denney at seas.upenn.edu] 
Sent: Friday, March 10, 2006 10:37 AM
To: SBML Discussion List
Subject: RE: [sbml-discuss] Multiple kineticLaw Sections Per Reaction

I know it's natural to do with the k_on - k_off method, and for
continuous ode-type modeling as done in most text books, it would be
just fine.  I'm just not sure that it will work for stochastics (if B is
only occasionally formed and I'm using a Gillespie solver, would I ever
see any C)?

I didn't mean to say that the reversible flag was bad in any way; I just
thought that if I could add multiple kineticLaws to a single reaction,
then that would expand its usefulness.

Bill

On Fri, 10 Mar 2006, Herbert Sauro wrote:

> 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 at 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 at seas.upenn.edu]
>>> Sent: Thursday, March 09, 2006 10:15 AM
>>> To: sbml-discuss at 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
>

--
"You do ill if you praise, worse if you censure, what you do not rightly
understand."
   -- Leonardo Da Vinci


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