Min-Cost Flow Code

The script minCostFlow.py attempts to connect sources to targets in a graph using a minimum-cost flow algorithm.

More details of the algorithm can be found in:
Automating parameter selection to avoid implausible biological pathway models. Chris S Magnano, Anthony Gitter. npj Systems Biology and Applications, 7:12, 2021.

Dependencies

Google's OR-Tools library is required to run this script.

OR-Tools version: 9.4.1874

Python 3 is required to run this script

verison 3.10.4 or 3.10.7 work best

Usage

minCostFlow.py [-h] --edges_file EDGES_FILE --sources_file SOURCES_FILE --targets_file TARGETS_FILE [--flow FLOW] --output OUTPUT [--capacity CAPACITY]

-h, --help: Show this help message and exit.

--edges_file: Network file. File should be in SIF file format.

--sources_file: File which denotes source nodes, with one node per line.

--targets_file: File whiuch denotes target nodes, with one node per line.

--flow The amount of flow pushed through the network.

--output Prefix for all output files.

--capacity The amount of flow which can pass through a single edge.