Hi, I am trying to understand how to turn the following equations into matlab code that works within the CVX.

within this formulation j= set of reactions and i = set of metabolites

load ‘Ecoli_core_model.mat’

c=model.c;

S=model.S;

lb=model.lb;

ub=model.ub;

nrxns=length(model.rxns);

% FBA

cvx_begin

variables v(nrxns)

minimize (c’*v)
subject to
S*v == 0

lb <= v <= ub

cvx_end

The following above is the Flux balance analysis part which would be corresponding to equation 10.

But here is about where my understanding of this stops.

And eventually we will have to try to formulate this whole thing. Which is beyond me.

This is from the journal paper “Constraint-based strain design using continuous

modifications (CosMos) of flux bounds finds new

strategies for metabolic engineering” by Cameron Cotten and Jennifer L. Reed (2013)

I’ve tried to do this but i don’t seem to be able, since I just started to learn using Matlab this February and my background is in Biochemistry, but my prof. wants me to study this but this is something I am unable to figure out on my own.

Can someone show me how to formulate this? Been reading a lot of material but I lack the understanding of some key concepts.

Best regards.

Arnar Sigurdsson