BioLogical: a universal analysis framework for biosystem logical dynamics

Complex biosystems exhibit ordered, functional, self-organized features, yet a universal framework for exploring their logical paradigms and dynamic behaviors remains lacking. Here we present BioLogical, a user-friendly R package designed to analyze logical properties of gene regulatory systems. Through a standard workflow and multiple cases, we demonstrate its versatile capabilities in deciphering logical paradigms, computing static and dynamic biosystem indicators, simulating system evolution, and evaluating logical satisfiability. All concepts and algorithms are extended to multi-valued scenarios, and hierarchical interfaces are provided to meet diverse requirements. The open-source software is available at https://github.com/YuxiangYao/BioLogical.