laurentheirendt

initCobraToolbox
model = readCbModel('iJO1366.mat');
changeCobraSolver('gurobi'); % this example uses Gurobi, but you may use any other solver
FBAsolution = optimizeCbModel(model,'max',0,0);
printFluxVector(model,FBAsolution.x, true, true);

laurentheirendt

initCobraToolbox

% Input the E.coli core model
model = readCbModel('ecoli_core_model.mat');
model = changeRxnBounds(model,'EX_glc(e)',0,'l');
model = changeRxnBounds(model,'EX_succ(e)',-20,'l');

% Set objective function
model = changeObjective(model,'EX_etoh(e)');
% model = changeObjective(model,'Biomass_Ecoli_core_N(w/GAM)_Nmet2');

laurentheirendt

using COBRA

# define the stoichiometric matrix
S = [
    1     0     0     0     0     0     0
    1    -1     0     0     0     0     0
    0    -1     0    -1     0     0     0
    0     1     0     1     0     0     0
    0     1     0     1     0     0     0
    0     1    -1     0     0     0     0

laurentheirendt

# https://github.com/acaudwell/Gource
# 1.install gource using HomeBrew
$ brew install gource

# 2.install avconv
git clone git://git.libav.org/libav.git
cd libav
# it will take 3-5 minutes to complie, be patient.
./configure --disable-yasm
make && make install