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Protocols

BoolNet specifications

Information


Unique identifier OMICS_06963
Name BoolNet
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 2.1.4
Stability Stable
Requirements
XML, igraph(≥0.6)
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Hans A. Kestler

Publication for BoolNet

BoolNet citations

 (54)
library_books

Automatic Screening for Perturbations in Boolean Networks

2018
Front Physiol
PMCID: 5928136
PMID: 29740342
DOI: 10.3389/fphys.2018.00431

[…] ustness analysis for synchronous, asynchronous, and probabilistic Boolean networks (Müssel et al., ). Additionally, it allows for visualization of dependencies in the network and attractors. However, BoolNet requires programming skills and a basic understanding of the programming language R.GUI-based software like GinSim (Gonzalez et al., ) incorporates different simulation methods for logical mod […]

call_split

A Boolean network of the crosstalk between IGF and Wnt signaling in aging satellite cells

2018
PLoS One
PMCID: 5875862
PMID: 29596489
DOI: 10.1371/journal.pone.0195126
call_split See protocol

[…] rom collecting literature data. Modeling of the network functions was performed using ViSiBooL []. The exhaustive attractor search simulation to analyze the network was carried out with the R-package BoolNet [].To further analyze the effects of IGF/Wnt crosstalk in our network model, we divided the model in its IGF and Wnt sub-networks. Therefore, we removed the crosstalk elements from the Boolean […]

library_books

A systems pharmacology model for inflammatory bowel disease

2018
PLoS One
PMCID: 5841748
PMID: 29513758
DOI: 10.1371/journal.pone.0192949

[…] There are already several tools for Boolean modeling of regulatory networks in which it is possible to define direct activation-inhibition relationships between the components of the network, such as BoolNet R [] or GINsim []. More recently, the R package SPIDDOR (Systems Pharmacology for effIcient Drug Development On R) among others, has implemented new types of regulatory interactions and pertur […]

library_books

ATLANTIS Attractor Landscape Analysis Toolbox for Cell Fate Discovery and Reprogramming

2018
Sci Rep
PMCID: 5824948
PMID: 29476134
DOI: 10.1038/s41598-018-22031-3

[…] ipeline. Previously, several tools have been developed for construction,, visualization, and analyses, of logical networks. From amongst them, the leading tools for computing attractor states include BoolNet, The Cell Collective and CellNetAnalyzer. However, these tools fail to associate biologically relevant network states with emergent cell fates. It is the lack of this functionality which furth […]

library_books

Transcription Factor Target Gene Network governs the Logical Abstraction Analysis of the Synthetic Circuit in Leishmaniasis

2018
Sci Rep
PMCID: 5823942
PMID: 29472639
DOI: 10.1038/s41598-018-21840-w

[…] ymadonna.com) and simulated using the Runge Kutta 4 (RK4) method. Time series data for 100 s was generated and analysed by Gene Regulatory Network Inference using Time Series (GRENITS) (v 1.24.0) and BoolNet (v 2.1.3) packages in Bioconductor’s R console. Circuit’s convergence, possible attractor states, the probability of Boolean network transitions and network wiring were created. Nullclines for […]

library_books

Therapeutic target discovery using Boolean network attractors: improvements of kali

2018
R Soc Open Sci
PMCID: 5830779
PMID: 29515890
DOI: 10.1098/rsos.171852

[…] To incorporate asynchronous updating, the corresponding algorithms coming from BoolNet were implemented into kali. BoolNet is an R [] package for generation, reconstruction and analysis of Boolean networks []. Asynchronous updating is implemented so that one randomly selected va […]

Citations

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BoolNet institution(s)
Institute of Neural Information Processing, University of Ulm and Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany

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