ntekasi / redgem

redGEM, redGEMX and lumpGEM

Reduction of human genome-scale models. Papers: * redGEM: Ataman, M., et al., "redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models". Plos Computational Biology, 2017. 13(7). * redGEMX: Maria Masid, Meriç Ataman and Vassily Hatzimanikatis. "redHUMAN: analyzing human metabolism and growth media through systematic reductions of thermodynamically curated genome-scale models" * lumpGEM: Meric Ataman and Vassily Hatzimanikatis."lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites". Plos Computational Biology, 2017. 13(7).

Requirements

You will need to have Git LFS in order to properly download some binary files:

git clone https://github.com/EPFL-LCSB/redhuman.git /path/to/redhuman
cd /path/to/redhuman
git lfs install
git lfs pull

The scripts have been developed with Matlab 2017b, and CPLEX 12.7 (freely downloadable with the IBM Academic initiative), and successfully ran on several other versions of both softwares. However, it is important to respect the IBM compatibility specs sheets between Matlab, CPLEX, and the computer OS - available on IBM's website.

This module requires matTFA

Generating reduced models

1. Place the thermodynamic data for the corresponding orgnanism into the matTFA thermoDatabases folder.
2. Place the corresponding curated GEM into the GEMs folder.
3. Place the get file into the runFileExample folder.
4. Run the get file

License

The software in this repository is put under an APACHE licensing scheme - please see the LICENSE file for more details.