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