BioLogical: a universal analysis framework for biosystem logical dynamic

2025 · doi:10.1101/2025.05.30.656947
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Abstract

Complex biosystems exhibit ordered, functional, self-organized features. How-ever, a universal framework for exploring their logical paradigms and dynamic characteristics remains lacking. Here we describe BioLogical, a user-friendly R package, designed for analyzing properties of biosystems. We demonstrate its versatile capacities of deciphering multi-valued logical paradigms, calculating order parameters, and simulating system dynamic, even multi-valued Quine-McCluskey and logical satisfiability analysis. The open-source software is available at https://github.com/YuxiangYao/BioLogical .
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Abstract Complex biosystems exhibit ordered, functional, self-organized features. How-ever, a universal framework for exploring their logical paradigms and dynamic characteristics remains lacking. Here we describe BioLogical, a user-friendly R package, designed for analyzing properties of biosystems. We demonstrate its versatile capacities of deciphering multi-valued logical paradigms, calculating order parameters, and simulating system dynamic, even multi-valued Quine-McCluskey and logical satisfiability analysis. The open-source software is available at https://github.com/YuxiangYao/BioLogical. Competing Interest Statement The authors have declared no competing interest. Footnotes Funder Information Declared Key Research and Development Program of Zhejiang, 2024SSYS0031 “Pioneer” and “Leading Goose” R&D Program of Zhejiang, 2025C01115 Zhejiang Provincial Natural Science Foundation of China, LZ25C060003 Yangtze River Delta Sci-Tech Innovation Community Joint Research Project, 2022CSJGG1000 Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.

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