pystablemotifs: Python library for attractor identification and control in Boolean networks

• Published in: Bioinformatics (Oxford, England) Vol. 38; no. 5; pp. 1465 - 1466
• Main Authors: Rozum, Jordan C, Deritei, Dávid, Park, Kyu Hyong, Gómez Tejeda Zañudo, Jorge, Albert, Réka
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 07.02.2022
• Subjects: Algorithms; Gene Library; Software
• ISSN: 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btab825

Abstract Summary pystablemotifs is a Python 3 library for analyzing Boolean networks. Its non-heuristic and exhaustive attractor identification algorithm was previously presented in Rozum et al. (2021). Here, we illustrate its performance improvements over similar methods and discuss how it uses outputs of the attractor identification process to drive a system to one of its attractors from any initial state. We implement six attractor control algorithms, five of which are new in this work. By design, these algorithms can return different control strategies, allowing for synergistic use. We also give a brief overview of the other tools implemented in pystablemotifs. Availability and implementation The source code is on GitHub at https://github.com/jcrozum/pystablemotifs/. Supplementary information Supplementary data are available at Bioinformatics online.