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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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Documentation


Maintainer


  • person_outline Hans A. Kestler

Publication for BoolNet

BoolNet citations

 (43)
library_books

Automatic Screening for Perturbations in Boolean Networks

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

[…] that cause a desired effect on the long-term behavior of the system., there are various tools and frameworks to model, simulate or visualize different types of boolean networks. the r-package boolnet comprises a number of simulation algorithms, for instance, attractor search, network perturbation or robustness analysis for synchronous, asynchronous, and probabilistic boolean networks […]

library_books

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

[…] 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 […]

library_books

A systems pharmacology model for inflammatory bowel disease

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

[…] 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 […]

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

[…] 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 […]

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

[…] the oscillations generated due to impulse of iptg at 24 hour time point at a concentration of 1 mm (fig. ).figure 3, the time series data generated in berkeley madonna was further analyzed in r boolnet package, which shows that the system has two attractor states, i.e. either on or off state. attractor states suggest the stable gene expression pattern of the boolean network. this system […]

library_books

A logic based dynamic modeling approach to explicate the evolution of the central dogma of molecular biology

2017
PLoS One
PMCID: 5739447
PMID: 29267315
DOI: 10.1371/journal.pone.0189922

[…] generates eight different versions of present-day cd (). for more details about boolean models reconstruction, see ., to identify the synchronous and asynchronous attractors, we used the r package “boolnet”[] which conducts an exhaustive search in identifying attractors. the difference between these attractors is based on the updating procedure of components in each time step of the simulation. […]


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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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