Flavors of Boolean network reprogramming in the CoLoMoTo Notebook Environment

This repository gathers notebooks demonstrating different software tools for the prediction of perturbations controlling the attractors of Boolean networks.

The notebooks can be visualized and downloaded at https://nbviewer.jupyter.org/github/algorecell/flavours-of-reprogramming/tree/main.

They can be executed interactively within the CoLoMoTo Docker version 2020-07-01:

• online, using myBinder service at https://mybinder.org/v2/gh/algorecell/flavours-of-reprogramming/main
• or on your computer, provided you have Docker and Python 3 installed:
  1. download the notebooks from https://github.com/algorecell/flavors-of-reprogramming/archive/main.zip and extract the zip file
  2. execute the following commands, where flavors-of-reprogramming 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 2020-07-01 --bind flavors-of-reprogramming
  

The following tools are demonstrated:

• ActoNet
• CABEAN, with its Python interface cabean
• Caspo, with its Python interface caspo-control
• StableMotifs, with its Python interface stablemotifs