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mpbn: a simple tool for efficient edition and analysis of elementary properties of Boolean networks

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arxiv 2403.06255 v1 pith:O3VTEVYE submitted 2024-03-10 cs.LO math.DSq-bio.MN

Van-Giang Trinh , Belaid Benhamou , Loïc Paulevé This is my paper · ORCID
classification cs.LOmath.DSq-bio.MN
keywords mpbntoolbooleannetworkspropertiesefficientelementaryprogramming
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The tool mpbn offers a Python programming interface for an easy interactive editing of Boolean networks and the efficient computation of elementary properties of their dynamics, including fixed points, trap spaces, and reachability properties under the Most Permissive update mode. Relying on Answer-Set Programming logical framework, we show that mpbn is scalable to models with several thousands of nodes and is one of the best-performing tool for computing minimal and maximal trap spaces of Boolean networks, a key feature for understanding and controling their stable behaviors. The tool is available at https://github.com/bnediction/mpbn.

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  1. Scalable Counting of Minimal Trap Spaces and Fixed Points in Boolean Networks

    cs.LO 2025-06 conditional novelty 6.0 of 10

    Approximate answer set counting enables counting minimal trap spaces and fixed points in Boolean networks up to 5000 variables.

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