Networkx Tutorial

Author : Nathaniel Evans (evansna@ohsu.edu)

This tutorial is intended for use in Oregon Health & Science University (OHSU) BMI 567/667: Network Science and Biology – Principles, Programming, Analysis and Visualization.

I recommend setting up a local environment to run this tutorial; however, if you run into issues it can be run using mybinder.org. It may take 5-10 minutes to set up the docker image so double check that it works before class. Also, keep in mind that some of the more computationally expensive operations in the tutorial may take longer to run on mybinder.

Setup

It's recommended to have access to bash for this installation, if you are on windows this can be done using git bash or WSL2.

Step 1: Clone the github repository

$ git clone https://github.com/nathanieljevans/networkx_tutorial.git 
$ cd networkx_tutorial

Step 1.5 (optional): To use the `Graphviz` layouts, install `graphviz`

Follow these instructions. Or, if you're using ubuntu:

$ sudo apt-get install graphviz graphviz-dev

Step 2: Install the conda environment

First, make sure you have the conda package manager installed.

If you're new to conda, this is a helpful command cheat sheet.

# create the conda env 
$ conda env create --file environment.yml

Step 3: Activate environment

$ conda activate nx_env

Step 4: Start a Jupyter session

$ jupyter notebook

Note, if you're in WSL, the window won't automatically open. You will need to copy the provided url (see output from command) into a browser.

nathanieljevans/networkx_tutorial