PyBEL Notebooks

This repository contains Jupyter notebooks demonstrating the PyBEL and PyBEL Tools packages.

Cookbook

This directory contains notebooks that address small problems.

Summary

This directory contains notebooks that analyze the contents of a BEL graph.

1. Graph Summary
2. Citation Summary
3. Error Analysis

Integration

This directory contains notebooks dealing with input/output and data integration.

1. Parsing JGIF
2. Resolving Protein Complexes

Algorithms

This directory contains notebooks demonstrating algorithms implemented with PyBEL and NetworkX.

1. Generation of Unbiased Candidate Mechanisms
2. Subgraph Expansion
3. Subgraph Comparison
4. Candidate Mechanism Pertubation Amplitude
5. Time Series Analysis with CMPA
6. Concordance Analysis

Root Directory

Template Notebook (source)

This notebook serves as a style guide for other notebooks in this repository.

BEL Compiler Comparison Notebook (source) (nbviewer)

The speed and usability of the PyBEL compiler is compared to the two legacy options: bel.rb and the OpenBEL Framework.

test.py (source)

This file can be run with python3 -m nose to check that notebooks run to completion.