From lee.joosang from gmail.com Tue Oct 7 14:56:30 2008 From: lee.joosang from gmail.com (JS) Date: Tue Oct 7 16:33:56 2008 Subject: [Biothermokinetics] bounds of fluxes of e.coli metabolism Message-ID: <314c2044-e1de-4ac2-8512-e68fe0811ef6@a3g2000prm.googlegroups.com> 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 From pcharusa from bioeng.ucsd.edu Thu Oct 9 11:33:15 2008 From: pcharusa from bioeng.ucsd.edu (Pep Charusanti) Date: Thu Oct 9 13:16:35 2008 Subject: [Biothermokinetics] Re: bounds of fluxes of e.coli metabolism (JS) In-Reply-To: <200810081704.m98H4wV26747@net.bio.net> References: <200810081704.m98H4wV26747@net.bio.net> Message-ID: 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 > > > Today's Topics: > > 1. bounds of fluxes of e.coli metabolism (JS) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 7 Oct 2008 12:56:30 -0700 (PDT) > From: JS > Subject: [Biothermokinetics] bounds of fluxes of e.coli metabolism > To: bionet-metabolic-reg@moderators.isc.org > Message-ID: > <314c2044-e1de-4ac2-8512-e68fe0811ef6@a3g2000prm.googlegroups.com> > Content-Type: text/plain; charset=ISO-8859-1 > > 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 > > > > ------------------------------ > > _______________________________________________ > Btk-mca mailing list > Btk-mca@net.bio.net > http://www.bio.net/biomail/listinfo/btk-mca > > End of Btk-mca Digest, Vol 8, Issue 1 > ************************************* >