BoolNet

MaRDI QIDQ19397swMATHCRANFDO

Authors Hans A. Kestler, Dao Zhou, Christoph Müssel, Martin Hopfensitz

Last update 2 October 2023

Copyright license Artistic License 2.0

Software version identifier 2.1.8, 1.3, 1.4, 1.41, 1.42, 1.43, 1.44, 1.45, 1.46, 1.50, 1.51, 1.60, 1.61, 1.62, 1.63, 2.0.1, 2.0.2, 2.0, 2.1.0, 2.1.1, 2.1.3, 2.1.4, 2.1.5, 2.1.7, 2.1.9

Official website http://cran.r-project.org/web/packages/BoolNet/index.html

Source code repository https://github.com/cran/BoolNet

Description

Functions to reconstruct, generate, and simulate synchronous, asynchronous, probabilistic, and temporal Boolean networks. Provides also functions to analyze and visualize attractors in Boolean networks <doi:10.1093/bioinformatics/btq124>.

Cites work

• BoolNet—an R package for generation, reconstruction and analysis of Boolean networks

Cited in

(45)

• diffeRenTES
• TotemBioNet
• ATLANTIS
• caspo
• CoLoMoTo
• SNOOPY
• On the number of driver nodes for controlling a Boolean network when the targets are restricted to attractors
• Computational cell biology. Methods and protocols
• JBool
• Computing maximal and minimal trap spaces of Boolean networks
• Ginsim
• Minimal trap spaces of logical models are maximal siphons of their Petri net encoding
• An extension of ERODE to reduce Boolean networks by backward Boolean equivalence
• Bilevel integer programming on a Boolean network for discovering critical genetic alterations in cancer development and therapy
• Bogdanov-Takens and Hopf bifurcations analysis of a genetic regulatory network
• Aeon 2021: bifurcation decision trees in Boolean networks
• Attractors in Boolean networks: a tutorial
• Inferring Boolean functions via higher-order correlations
• Exact tests for singular network data
• Boolean network analysis through the joint use of linear algebra and algebraic geometry
• Attractor stability in finite asynchronous biological system models
• ddepn
• Boolean function metrics can assist modelers to check and choose logical rules
• Boolean models of the transport, synthesis, and metabolism of tryptophan in \textit{Escherichia coli}
• Cellnoptr
• MIDER
• BooleSim
• ADAM
• BoolFilter
• BioModelAnalyzer
• CANA
• TURING
• GDSCalc
• AlzPathway
• Robust stabilization and H_ controllers design for stochastic genetic regulatory networks with time-varying delays and structured uncertainties
• ASSA-PBN
• MaBoSS
• The Regulation of Gene Expression by Operons and the Local Modeling Framework
• PyBoolNet
• BioLQM
• Pint
• REVEAL
• ConGRI
• Aeon
• Computational methods for asynchronous basins

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