a Pipeline for Optimizing Metabolic Engineering Targets, based on a consensus approach
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README.md

OptPipe - a Pipeline for Optimizing Metabolic Engineering Targets


This software contains up-to date standardized methods for the optimization of metabolic engineering targets in genome-scale metabolic networks. This software was developed in the frame of the BaCHBerry project (European Union FP7- 613793)

The code was written by Ana Vila Santa and András Hartmann under the supervision of Susana Vinga.

License


© 2015 - 2017 Susana Vinga, András Hartmann and Ana Vila Santa

OptPipe is a free software: you can redistribute it and/or modify it under the terms of the GNU Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This code is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Public License for more details.

You should have received a copy of the GNU Public License along with this code. If not, see http://www.gnu.org/licenses/

Contents


Folder Description
common_functions Folder for the common function shared by the methods
examples Folder for working examples including models
external Folder containing external libraries and toolboxes
methods Folder containing the methods
installPipeline.m Install script
LICENSE.txt License file (GPL v3)
README.md This file

Install


Prerequisites

You will need:

  • MATLAB software for scientific computing
    • Tested on version 2015a and 2016b
    • Compatibility issues might arise between gurobi and MATLAB 2017a
    • Parallel toolbox (optional, but highly recommended in order to shorten running time)
  • COBRA toolbox from the openCOBRA project (release 2.0)
  • SBML toolbox
  • gurobi optimization software installed for MATLAB (free for academic users)

Installation

Place the content of the package in a separate folder, start MATLAB. You can use git to download the current version from the repository

$ git clone --recursive https://github.com/AndrasHartmann/OptPipe.git

Within the MATLAB shell go to the code folder and run the install script

>> cd '<code folder>'
>> installPipeline