BoolForge: Controlled Generation and Analysis of Boolean Functions and Networks

arXiv:2509.02496v2 Announce Type: replace
Abstract: Boolean networks are a widely used modeling framework in systems biology for studying gene regulation, signal transduction, and cellular decision-making. Empirical studies indicate that biological Boolean networks exhibit a high degree of canalization, a structural property of Boolean update rules that stabilizes dynamics and constrains state transitions. Despite its central role, existing software packages provide limited support for the systematic generation of Boolean functions and networks with prescribed canalization properties. We present BoolForge, a Python toolbox for the random generation and analysis of Boolean functions and networks, with a particular focus on canalization. BoolForge enables users to (i) generate random Boolean functions with specified canalizing depth, layer structure, and related constraints; (ii) construct Boolean networks with tunable topological and functional properties; and (iii) analyze structural and dynamical features including canalization measures, robustness, modularity, and attractor structure. By enabling controlled generation alongside analysis, BoolForge facilitates ensemble-based investigations of structure-dynamics relationships, benchmarking of theoretical predictions, and construction of biologically informed null models for Boolean network studies. Availability and Implementation: BoolForge is implemented in Python ($geq$3.10) and can be installed via textttpip install boolforge. Source code and documentation are available at https://github.com/ckadelka/BoolForge. A PDF tutorial compendium is provided as Supplementary Material.