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.gitWithin the MATLAB shell go to the code folder and run the install script
>> cd '<code folder>'
>> installPipeline