PyBoolNet: a python package for the generation, analysis and visualization of boolean networks

• Published in: Bioinformatics (Oxford, England) Vol. 33; no. 5; pp. 770 - 772
• Main Authors: Klarner, Hannes, Streck, Adam, Siebert, Heike
• Format: Journal Article
• Language: English
• Published: England 01.03.2017
• Subjects: Algorithms; Computational Biology - methods; Gene Regulatory Networks; Models, Biological; Signal Transduction; Software
• ISSN: 1367-4803; 1367-4811; 1367-4811
• DOI: 10.1093/bioinformatics/btw682

The goal of this project is to provide a simple interface to working with Boolean networks. Emphasis is put on easy access to a large number of common tasks including the generation and manipulation of networks, attractor and basin computation, model checking and trap space computation, execution of established graph algorithms as well as graph drawing and layouts. P y B ool N et is a Python package for working with Boolean networks that supports simple access to model checking via N u SMV, standard graph algorithms via N etwork X and visualization via dot . In addition, state of the art attractor computation exploiting P otassco ASP is implemented. The package is function-based and uses only native Python and N etwork X data types. https://github.com/hklarner/PyBoolNet. hannes.klarner@fu-berlin.de.