[sbml-discuss] Multiple kineticLaw Sections Per Reaction
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.
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.
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.
> -----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
>> 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--
>> 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 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
>>> 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
>>> 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:
> http://www.ebi.ac.uk/~lenov AIM screen name:
"You do ill if you praise, worse if you censure, what you do not rightly
-- Leonardo Da Vinci
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