Genome-scale metabolic model of Salmonella Typhimurium SL1344 and example scripts for the reconstrcuction and analysis performed in the manuscript: Vayena et al. "Metabolic network reconstruction as a resource for analyzing Salmonella Typhimurium SL1344 growth in the mouse intestine"
You will need to have Git LFS <https://git-lfs.github.com/>_ in order to properly download some binary files:
.. code-block:: shell
git clone https://github.com/EPFL-LCSB/iNTS_SL1344.git cd iNTS_SL1344 git lfs install git lfs pull
The scripts have been developed with MATLAB 2019b, and CPLEX 12.7.1 (freely downloadable with the IBM Academic initiative <https://developer.ibm.com/academic/>), and successfully ran on several other versions of both software. However, it is important to respect the IBM compatibility specs sheets between Matlab, CPLEX, and the computer OS - available on IBM's website <https://www.ibm.com/software/reports/compatibility/clarity/index.html>.
This module requires matTFA <https://github.com/EPFL-LCSB/mattfa>, redGEMX <https://github.com/EPFL-LCSB/redhuman>,
NICEgame <https://github.com/EPFL-LCSB/NICEgame>, and phenomapping <https://github.com/EPFL-LCSB/phenomapping>.
For the redGEMX analysis (it requires the redGEMX module):
- run the script script_prepareModel4redGEMX.m
- adjust your paths in the functions case_salmonella and get_salmonella in the additionalFunctions folder.
- run the function get_salmonella