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BooleanNet specifications


Unique identifier OMICS_06964
Name BooleanNet
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline István Albert <>

Publication for BooleanNet

BooleanNet in publications

PMCID: 5787708
PMID: 29378814
DOI: 10.15252/msb.20177952

[…] and (ii) the state‐space is generated with all the transition history of a sufficient number of consecutive steps from a sufficient number of random initial states. r‐abs was performed using the booleannet ver.1.2.6 python package (, with 700 consecutive update steps from each of 700 random initial states per condition. five independent simulations per […]

PMCID: 5814231
PMID: 29464091
DOI: 10.18632/oncotarget.23973

[…] and other genes: “klk3 low => x low” and its counterpart “x high => klk3 high” (figure ). the resulting gene list included 57 transcripts (using s > 10, p < 0.01 threshold for the booleannet analysis). to filter this list, we assembled three independent publicly available prostate cancer datasets that were annotated for recurrence-free survival and tested whether […]

PMCID: 5627951
PMID: 28937978
DOI: 10.1371/journal.pbio.2003451

[…] signal transduction pathways [], particularly when, as in the present case, relative timescales of internal processes are largely unknown. we implemented the model using the python software library booleannet []. we used the stochastic asynchronous update algorithm, in which the nodes are updated in a randomly selected order in each time step. due to the stochasticity introduced by the update […]

PMCID: 5025072
PMID: 27632168
DOI: 10.1371/journal.pone.0162407

[…] time description, thus providing more understandable information about general pathway dynamics under different conditions. to support these studies, publicly available software tools such as booleannet [], pathologic-s [] and odefy [] have been developed; they offer a scalable boolean framework for modeling cellular signaling., following these considerations, in this work we present […]

PMCID: 4596957
PMID: 26423606
DOI: 10.1186/1471-2105-16-S13-S3

[…] is not unique and can be unstable in relation to small interaction alterations. there are also software tools that can be used to run such simulations, including cellnetanalyzer [], cellnopt [], booleannet [], and cpn tools []., furthermore, all the existing approaches, differential equations, boolean, or petri net, require a complete and exact knowledge of the network, including […]

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BooleanNet institution(s)
Huck Institutes for the Life Sciences, Pennsylvania State University, University Park, PA, USA

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