Team:RHIT
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Metabolism Model
The last modeled portion of the project used the Flux Balance Analysis tool to predict the growth rate of the E. coli cells on the sole carbon source of PET. The original matrix and parameters where downloaded from the CoBRA toolbox iJO1366 model [ ]. The model was then expanded to include this new pathway and genes and then the system was optimized for biomass growth and the objective value was proportional to the growth rate of the bacteria.
FBA uses a stochastic matrix of the all the metabolisms’ chemical reactions and optimizes these various equations to produce a unit of biomass, which is inferred as another metabolite of the system. The general form of the model is:
s.t. L≤v≤U and v≠0
The variable column V are fluxes, which are bounded by the upper and lower bounds of U and L. The S matrix is a matrix of stoichiometric coefficients for the metabolites in the reactions. A flux is best described as the number of times the reaction must run forwards or backwards for the entire system to meet the homogenous assumption that the rates of the metabolites changing are zero. The dimensions of the matrix is MxN, where M is number of metabolites and N is number of reactions in the metabolism. The maximized flux, vg, is the flux for the biomass growth equation.
For the fake chemical reaction: 2 [A] ↔ [B] + 3 [C]
The reaction is input into the matrix so that metabolite A loses 2 units, while metabolites B and C gain 1 and 3 units respectively.
The dotted column shows the biomass growth reaction with it producing 1 unit of biomass. All the reactions have some bounds on the flux values so that the system will return a real number.
Project Abstract
We can put a general project description on this first page
Obviously we can replace these with better pictures, I just thought the picture links were kinda cool too
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