mpbn: a simple tool for efficient edition and analysis of elementary properties of Boolean networks
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arXiv
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| Auteurs principaux: | , , |
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| Format: | Preprint |
| Publié: |
2024
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| _version_ | 1866911792639246336 |
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| author | Trinh, Van-Giang Benhamou, Belaid Paulevé, Loïc |
| author_facet | Trinh, Van-Giang Benhamou, Belaid Paulevé, Loïc |
| contents | 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2403_06255 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | mpbn: a simple tool for efficient edition and analysis of elementary properties of Boolean networks Trinh, Van-Giang Benhamou, Belaid Paulevé, Loïc Logic in Computer Science Dynamical Systems Molecular Networks 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. |
| title | mpbn: a simple tool for efficient edition and analysis of elementary properties of Boolean networks |
| topic | Logic in Computer Science Dynamical Systems Molecular Networks |
| url | https://arxiv.org/abs/2403.06255 |