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.
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/
|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|
|LICENSE.txt||License file (GPL v3)|
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)
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