BoolDog: integrated Boolean and semi-quantitative network modelling in Python

Abstract

SummaryBoolean and logic-based modeling approaches are well suited for the analysis of complex biological systems, particularly when detailed biochemical and kinetic information is unavailable. In such settings, biological pathways are represented as networks capturing system components and their interactions, providing a simplified yet informative abstraction of system behavior. While the structural topology of these networks is often well characterized, the absence of mechanistic detail limits the applicability of parameter-dependent modeling frameworks. To address this, we present BoolDog, a Python package for the construction, simulation, and analysis of Boolean and semi-quantitative Boolean networks. BoolDog supports synchronous simulation with events, attractor and steady-state identification, network visualization, and the systematic transformation of logic-based models into continuous ordinary differential equation (ODE) systems -- enabling the seamless integration of discrete and continuous modeling paradigms. Networks can be imported and exported across standard formats, and BoolDog integrates natively with established Python libraries for network analysis and visualisation, including NetworkX, igraph, and py4Cytoscape. Together, these capabilities provide a flexible, accessible, and interoperable platform for logic-based modeling of complex biological systems. Availability and implementationBoolDog is implemented in Python and available at https://github.com/NIB-SI/BoolDog/.