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ints_sl1344

Genome-scale metabolic model of Salmonella Typhimurium SL1344.

https://github.com/epfl-lcsb/ints_sl1344

Science Score: 52.0%

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    Low similarity (6.8%) to scientific vocabulary
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Repository

Genome-scale metabolic model of Salmonella Typhimurium SL1344.

Basic Info
  • Host: GitHub
  • Owner: EPFL-LCSB
  • License: apache-2.0
  • Language: MATLAB
  • Default Branch: main
  • Size: 9.42 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created about 2 years ago · Last pushed about 1 year ago
Metadata Files
Readme License Citation

README.md

iNTS_SL1344

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"

Requirements

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/iNTSSL1344.git cd iNTSSL1344 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): 1. run the script scriptprepareModel4redGEMX.m 2. adjust your paths in the functions casesalmonella and getsalmonella in the additionalFunctions folder. 3. run the function getsalmonella

Owner

  • Name: LCSB@EPFL
  • Login: EPFL-LCSB
  • Kind: organization
  • Location: Lausanne, Switzerland

Laboratory of Computational Systems Biotechnology

Citation (CITATION.cff) 

Evangelia Vayena. (2024). EPFL-LCSB/iNTS_SL1344: v1.0 (v1.0). Zenodo.

GitHub Events

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Last Year
  • Release event: 1
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  • Push event: 4
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