ITM Probe network information flow tool

Introduction

ITM Probe is a tool for calculating information flow in biological networks. It is part of the qmbpmn-tools package from the NCBI.

This repository provides a small wrapper script (infflow.py) and a virtual environment to get up and running with ITM Probe quickly. The wrapper inputs and outputs to the widely used GML format.

Virtual environment with Docker

ITM Probe has many software dependencies which are difficult and time consuming to install manually. Docker is a virtual environment which allows you to get up and running quickly with ITM Probe. It's like a virtual machine but with less overhead.

First, you'll need to install Docker. See its documentation for help with that.

Then you can install the ITM Probe virtual environment using the Dockerfile supplied here:

sudo docker build -t itmprobe .

Once installed, you can run the virtual environment like so:

sudo docker run -it itmprobe /bin/bash

Then you can proceed within the virtual environment in the same way as if you'd installed everything locally.

The ITM Probe wrapper

For help and list of command line options:

python infflow.py --help

Example using supplied gml file:

python infflow.py example.gml