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
-
use the available reaction networks (KEGG, available Retrobiosynthesis networks) --> set INPUT-NAME to KEGG or Retrobio
-
add your own biochemical network, including weighted reactant-product pairs, and set the parameters according to your search criteria in ./input/INPUT-NAME
Input:
- Reaction network, in the format of a BNICE.ch systemFile.txt (in ROOT/PROJECT/COMPOUND/)
- Starting compounds for pathway search : source_compounds.txt
- 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)