Table 4.

List of software for Boolean modeling.

Software (implementation)	Application	Reference
BoolNet (R)	Reconstruction from time-series data and simulation of Boolean networks	Müssel et al., 2010
BooleanNet (Python)	Simulation of Boolean networks	Albert et al., 2008
PyBoolNet (Python)	Simulation of Boolean networks	Klarner et al., 2016
The Cell Collective (web application)	Exchange and simulation of Boolean networks	Helikar et al., 2012
CoLoMoTo Interactive Notebook (Python)	Containerized collection of Boolean modeling software	Naldi et al., 2018