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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


No version available



  • person_outline István Albert

Publication for BooleanNet

BooleanNet citations


Regulation of dual specificity phosphatases in breast cancer during initial treatment with Herceptin: a Boolean model analysis

BMC Syst Biol
PMCID: 5907139
PMID: 29671404
DOI: 10.1186/s12918-018-0534-5

[…] Circles represent the AND function which combines several interactions. Model construction and time course simulation of MAPK signalling pathways in response to Herceptin treatment was done using the BooleanNet toolkit under Python 2.7 []. Both synchronous and asynchronous simulations were performed. In synchronous updating rules, all variables are updated at the same time, while in asynchronous s […]


Modeling signaling‐dependent pluripotency with Boolean logic to predict cell fate transitions

Mol Syst Biol
PMCID: 5787708
PMID: 29378814
DOI: 10.15252/msb.20177952

[…] tep, 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 con […]


Boolean analysis identifies CD38 as a biomarker of aggressive localized prostate cancer

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

[…] between PSA (KLK3) 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 the transcript […]


A new discrete dynamic model of ABA induced stomatal closure predicts key feedback loops

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

[…] g 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 me […]


A Network Based Data Integration Approach to Support Drug Repurposing and Multi Target Therapies in Triple Negative Breast Cancer

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

[…] tinuous 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 a novel […]


Identification of Th1/Th2 regulatory switch to promote healing response during leishmaniasis: a computational approach

EURASIP J Bioinform Syst Biol
PMCID: 4666900
PMID: 26660865
DOI: 10.1186/s13637-015-0032-7

[…] ible for the splice site recognition in each case.The model was simulated synchronously (i.e., all equations updated simultaneously) and asynchronously (i.e., random execution of the equations) using BooleanNet-1.2.4 software until the steady state is reached []. In this model, we also defined three functions, viz. “TH_1_response*”, “TH_2_response*”, and “NO_response*”, which reflect the type of T […]

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

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