User:Daniela A. Garcia S./Notebook/Modeling 2011 UNAM GenomicsMexico/2011/04/01
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FBA BibliographySupplementary Appendix 1: FBA Primer
Metabolic Network Reconstruction
Matlab Bibliography
It was needed to install a different solver glpx, but initCobraToolbox still shows warnings. However once downloading the E.coli Model it is possible to follow the Tutorial: What is flux balance analysis?, Supplementary Tutorial Tutorial
model = changeRxnBounds(model,'EX_glc(e)',18.5,'l'); model = changeRxnBounds(model,'EX_o2(e)',1000,'l'); model = changeObjective(model,'Biomass_Ecoli_core_w_GAM'); FBAsolution = optimizeCbModel(model,'max'); .f, solution of the objetive function .x, steady state vector
Exchange reactions are written as export reactions changeObjetive Changes the objective function of a constraintbased model optimizeCbModel Solve a flux balance analysis problem Flux maps were drawn using SimPheny
FBA can predict if it is possible for the organism to grown under a specific set of constrains depending in the bounds fixed. The maximum amount of ATP that can be produced from this amount of succinate is less than the minimum bound of 8.39 mmol gDW^{1} hr1 of the ATP maintenance reaction, ATPM, there is no feasible solution...The growth rates are all much lower anaerobically (0 hr^{1} in most cases) because the electron transport chain cannot be used to fully oxidize the substrates and generate as much ATP.
model = changeRxnBounds(model,'EX_glc(e)',1,'b'); model = changeObjective(model,'ATPM'); model = changeRxnBounds(model,'ATPM',0,'l'); FBAsolution = optimizeCbModel(model,'max'); ATPM is a stoichiometrically balanced reaction that hydrolyzes ATP (atp[c])and produces ADP (adp[c]), inorganic phosphate (pi[c]), and a proton (h[c]). It works as an objective for maximizing ATP production' Other
