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View printFuxVector_iJO1366.m
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
laurentheirendt / exampleFVAR2017a.m
Created Nov 25, 2017
Example for FVA in R2017a
View exampleFVAR2017a.m
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
laurentheirendt / createCbModel.jl
Last active Sep 27, 2017
create a COBRA model in Julia
View createCbModel.jl
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
laurentheirendt / gource.sh
Last active Feb 11, 2019 — forked from qiaoxueshi/gource.sh
Generate a MP4 Video for your Git project commits using Gource!
View gource.sh
# 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
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