[Biothermokinetics] Re: bounds of fluxes of e.coli metabolism (JS)

[Pep Charusanti]

First off, is there any reason you're working with JR904?  I ask because 
there is a newer E. coli model, AF1260.

As for setting bounds on fluxes, you only really need to set bounds for 
uptake reactions.  In other words, if you're doing a simulation in which 
glucose is your only carbon source, then you will need to determine the 
glucose uptake rate for the experimental system you're interested in, use 
this value as the uptake rate in the model, and then set bounds 
accordingly.  The lower bound should be zero, and the upper bound is 
usually set to the uptake rate in rich medium.  Obviously, you'll want to 
use common sense too.  If glucose is you're only carbon source, set uptake 
rates for all other carbon sources to zero.

For internal fluxes, a good starting point is simply to set the lower 
bound to -1000 and the upper bound to +1000 (this approximates -infinity 
and +infinity) if the reaction is reversible.  Otherwise, the lower bound 
is 0 for irreversible.  This works well because the uptake rates you set 
will automatically constrain the internal fluxes in the system since the 
system is mass balanced.  Just be sure to check your simulation results 
for values that do not make sense.  This usually means there are internal 
loops somewhere in your simulation such that mass is not flowing 
throughout the entire system.

Hope this helps,
Pep




>
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> Today's Topics:
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>   1. bounds of fluxes of e.coli metabolism (JS)
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> Message: 1
> Date: Tue, 7 Oct 2008 12:56:30 -0700 (PDT)
> From: JS <lee.joosang from gmail.com>
> Subject: [Biothermokinetics] bounds of fluxes of e.coli metabolism
> To: bionet-metabolic-reg from moderators.isc.org
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>
> hello,
>
> I am looking for the upper and lower bounds the fluxes e. coli
> metabolic network. Does anybody happen to know of any reference which
> contains some information on the bounds of individual fluxes of e.coli
> metabolism? I am using JR904 model, but other models are also fine.
>
> best regards,
> JS
>
>
>
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