Supplementary material to the chapter 6 "Boolean networks and their dynamics: the impact of updates" by Loïc Paulevé and Sylvain Sené of the book "Systems Biology Modelling and Analysis: Formal Bioinformatics Methods and Tools" (First Edition), edited by Elisabetta De Maria (Wiley, 2023).

These notebooks demonstate how to use the Python module colomoto.minibn for computing dynamics of Boolean networks with various updating modes.

They can be visualized online at https://nbviewer.jupyter.org/github/pauleve/updating-modes-notebooks/

They can be executed and modified online at https://mybinder.org/v2/gh/pauleve/updating-modes-notebooks/main

Local installation

The module can be installed with a recent Python (≥3.7) distribution, using pip or conda.

Using pip (Python)

In a terminal/powershell

pip install -U colomoto-jupyter

Using conda

conda install -c conda-forge -c colomoto colomoto-jupyter

Using the CoLoMoTo Docker image

These notebooks can be executed within the CoLoMoTo Docker distribution version 2022-07-01:

1. download the notebooks from https://github.com/pauleve/updating-modes-notebooks/archive/main.zip and extract the zip file
2. execute the following commands, where notebooks is the folder in which you extracted the notebooks

sudo pip install -U colomoto-docker # you may have to use pip3 instead of pip
colomoto-docker -V 2022-07-01 --bind notebooks

Related documentation

Other tutorials regarding the minibn module can be found at https://nbviewer.jupyter.org/github/colomoto/colomoto-docker/tree/master/tutorials/minibn/ as well as other tools related to boolean networks at https://nbviewer.jupyter.org/github/colomoto/colomoto-docker/tree/master/tutorials/

See http://colomoto.org/notebook for more information.