EPFL-LCSB / nicepath

NICEpath - find pathways in a biochemical network

NICEpath is a pathway search tool for biochemical networks. To install the dependencies, go to the nicepath directory and run:

$ cd /path/to/nicepath
$ make

To run NICEpath, go to the ./nicepath/ folder and run:

$ cd nicepath
$ python main.py INPUT-NAME

To search for pathways, you can

1. use the available reaction networks (KEGG, available Retrobiosynthesis networks) --> set INPUT-NAME to KEGG or Retrobio

2. add your own biochemical network, including weighted reactant-product pairs, and set the parameters according to your search criteria in ./input/INPUT-NAME

Input:

1. Reaction network, in the format of a BNICE.ch systemFile.txt (in ROOT/PROJECT/COMPOUND/)
2. Starting compounds for pathway search : source_compounds.txt
3. Parameter settings: parameters.txt

Output: in ./data/

Structure: ROOT/PROJECT/COMPOUND

ROOT: location of your project (default: ./data), PROJECT: name of your project (default: Retrobio), COMPOUND: name of your target compound (default: 3HP, test case)