NICEgame

5. Vayena, A. Chiappino-Pepe, H. MohammadiPeyhani, Y. Francioli, N. Hadadi, M. Ataman, J. Hafner, S. Pavlou, & V. Hatzimanikatis, A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions, Proc. Natl. Acad. Sci. U.S.A. 119 (46) e2211197119, https://doi.org/10.1073/pnas.2211197119 (2022).

Requirements - MATLAB

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

git clone https://github.com/EPFL-LCSB/NICEgame.git /path/to/NICEgame
cd /path/to/NICEgame
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

Requirements - python

Further the following pip-python packages are required (can be found in detail in requirements.txt)

• bokeh>=0.12.1
• cobra>0.13
• equilibrator-api
• equilibrator-cache
• ipdb
• lxml
• networkx
• openpyxl
• pymysql
• pytest
• python-libsbml==5.11.4
• scipy
• sqlalchemy
• tabulate
• tqdm
• sphinx
• sphinx-rtd-theme

Container-based install

You might want to use this program inside of a container. The docker/ subfolder has all the necessary information and source files to set it up.

cd NICEgame/python/nicegamepy/docker
./build.sh
./run.sh

Building the docker image takes approximately 5 mins.

Setup

If container-based installation is not preferred you can also install this module from source using pip: For Python 3, you might have to use pip3 instead of pip

git clone https://github.com/EPFL-LCSB/NICEgame.git /path/to/NICEgame/python
pip3 install -e /path/to/NICEgame

The installation process should not exceed a minute if the requirements are installed. If they are not, it might take longer as the installer installs them first.