BooLEVARD: Boolean Logical Evaluation of Activation and Repression in Directed pathways

Abstract

Boolean models are widely used for studying dynamic processes of biological systems. However, their inherent discrete nature limits their ability to capture continuous aspects of signal transduction, such as signal strength or protein activation levels. Although existing tools provide some path exploration capabilities that can be used to explore signal transduction circuits, the computational workload often requires simplifying assumptions that compromise the accuracy of the analysis. Here, we introduce BooLEVARD, a Python package designed to efficiently quantify the number of paths leading either to node activation or repression in Boolean models, which offers a more detailed and quantitative perspective on how molecular signals propagate through signaling networks. By focusing on the collection of non-redundant paths directly influencing Boolean outcomes, BooLEVARD enhances the precision of signal strength representation. We showcase the application of BooLEVARD in studying cell-fate decisions using a Boolean model of cancer metastasis, demonstrating its ability to identify critical signaling events. Furthermore, BooLEVARD provides a refined understanding of signaling dynamics, which can increase our understanding of disease development and drug responses. BooLEVARD is freely available at https://github.com/farinasm/boolevard.