Work

BioLogical: a universal analysis framework for biosystem logical dynamics

Year: 2025

Type: article

Abstract: 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.

Source: Computational and Structural Biotechnology Journal

DOI: 10.1016/j.csbj.2025.11.049

Authors: Yuxiang Yao, Dong Liu, Zheting Zhang, Chengchen Zhao, Duanqing Pei

Institution: Westlake University

Language: English

Topic: Gene Regulatory Network Analysis

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $3,230

Funders: National Natural Science Foundation of China, National Key Research and Development Program of China, Natural Science Foundation of Zhejiang Province