12. Using the COBRA toolbox with cobrapy¶
This example demonstrates using COBRA toolbox commands in MATLAB from python through pymatbridge.
In [1]:
%load_ext pymatbridge
Starting MATLAB on ZMQ socket ipc:///tmp/pymatbridge-57ff5429-02d9-4e1a-8ed0-44e391fb0df7
Send 'exit' command to kill the server
....MATLAB started and connected!
In [2]:
import cobra.test
m = cobra.test.create_test_model("textbook")
The model_to_pymatbridge function will send the model to the workspace with the given variable name.
In [3]:
from cobra.io.mat import model_to_pymatbridge
model_to_pymatbridge(m, variable_name="model")
Now in the MATLAB workspace, the variable name ‘model’ holds a COBRA toolbox struct encoding the model.
In [4]:
%%matlab
model
model =
rev: [95x1 double]
metNames: {72x1 cell}
b: [72x1 double]
metCharge: [72x1 double]
c: [95x1 double]
csense: [72x1 char]
genes: {137x1 cell}
metFormulas: {72x1 cell}
rxns: {95x1 cell}
grRules: {95x1 cell}
rxnNames: {95x1 cell}
description: [11x1 char]
S: [72x95 double]
ub: [95x1 double]
lb: [95x1 double]
mets: {72x1 cell}
subSystems: {95x1 cell}
First, we have to initialize the COBRA toolbox in MATLAB.
In [5]:
%%matlab --silent
warning('off'); % this works around a pymatbridge bug
addpath(genpath('~/cobratoolbox/'));
initCobraToolbox();
Commands from the COBRA toolbox can now be run on the model
In [6]:
%%matlab
optimizeCbModel(model)
ans =
x: [95x1 double]
f: 0.8739
y: [71x1 double]
w: [95x1 double]
stat: 1
origStat: 5
solver: 'glpk'
time: 3.2911
FBA in the COBRA toolbox should give the same result as cobrapy (but maybe just a little bit slower :))
In [7]:
%time
m.optimize().f
CPU times: user 0 ns, sys: 0 ns, total: 0 ns
Wall time: 5.48 µs
Out[7]:
0.8739215069684909