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.j...@gmail.com>
> Subject: [Biothermokinetics] bounds of fluxes of e.coli metabolism
> To: bionet-met...@moderators.isc.org
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> <314c2044-e1de-4ac2...@a3g2000prm.googlegroups.com>
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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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