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

被引:22
|
作者
Rozum, Jordan C. [1 ]
Deritei, David [2 ,3 ]
Park, Kyu Hyong [1 ]
Zanudo, Jorge Gomez Tejeda [4 ,5 ]
Albert, Reka [1 ,6 ]
机构
[1] Penn State Univ, Dept Phys, University Pk, PA 16802 USA
[2] Semmelweis Univ, Dept Mol Biol, H-1085 Budapest, Hungary
[3] Harvard Med Sch, Brigham & Womens Hosp, Channing Div Network Med, Boston, MA 02115 USA
[4] Eli & Edythe L Broad Inst MIT & Harvard, Cambridge, MA 02142 USA
[5] Harvard Med Sch, Dana Farber Canc Inst, Dept Med Oncol, Boston, MA 02115 USA
[6] Penn State Univ, Dept Biol, University Pk, PA 16802 USA
关键词
D O I
10.1093/bioinformatics/btab825
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:1465 / 1466
页数:2
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