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BioNetGen specifications

Information


Unique identifier OMICS_13309
Name BioNetGen
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output format BNGL,SBML,MEX
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Perl, Python
Computer skills Advanced
Version 2.3.0
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline James R. Faeder

Additional information


http://bionetgen.org/index.php/Main_Page

Publications for BioNetGen

BioNetGen citations

 (87)
library_books

Stoichiometric balance of protein copy numbers is measurable and functionally significant in a protein protein interaction network for yeast endocytosis

2018
PLoS Comput Biol
PMCID: 5860782
PMID: 29518071
DOI: 10.1371/journal.pcbi.1006022

[…] The kinetic model was simulated using the stochastic simulation method (the Gillespie algorithm). Binding interactions were encoded via the rule-based language BioNetGen and simulated via the Network Free Simulation (NFSim) software []. Trimer cooperativity was modeled by increasing the rate of the third reaction if three members of a correct trimer were hel […]

library_books

A stochastic and dynamical view of pluripotency in mouse embryonic stem cells

2018
PLoS Comput Biol
PMCID: 5833290
PMID: 29451874
DOI: 10.1371/journal.pcbi.1006000

[…] on efficiency. The simulators are provided in the Supporting information. To facilitate the use of our computational work and ensure full reproducibility, the IB model is translated into standardized BioNetGen language [, ] and provided in Supporting Information, along with the standard SBML format of the model exported by BNGL. […]

library_books

A mathematical model of multisite phosphorylation of tau protein

2018
PLoS One
PMCID: 5800643
PMID: 29408874
DOI: 10.1371/journal.pone.0192519

[…] losion makes the traditional modeling paradigm (based on systems of differential equations) impractical [, ]. In contrast, agent-based or concurrent languages, such as kappa [] or the closely related BioNetGen language [] allow researchers to describe biological interactions in terms of some rules. Nonetheless, these methods are purely computer modeling and involve the development of specific soft […]

library_books

Molecular mechanisms of detection and discrimination of dynamic signals

2018
Sci Rep
PMCID: 5802782
PMID: 29410522
DOI: 10.1038/s41598-018-20842-y

[…] We implemented the computational models using BioNetGen, a rule-based software for modelling signaling networks and pathways. All simulations were solved deterministically.To define the parameters of the model, we used KDs (0.01 µmol.L−1, 0.1 µmo […]

library_books

Biophysical attributes that affect CaMKII activation deduced with a novel spatial stochastic simulation approach

2018
PLoS Comput Biol
PMCID: 5814094
PMID: 29401454
DOI: 10.1371/journal.pcbi.1005946

[…] tes for a holoenzyme becomes extremely large. This is a common problem in systems biology since large proteins usually consist of multiple subunits. Software that adopts a rule-based approach such as BioNetGen [] can be used to expand the network based on a set of given reaction rules. Nevertheless, for a CaMKII holoenzyme, using BioNetGen to generate the network is still computationally intensive […]

library_books

Cell fate in antiviral response arises in the crosstalk of IRF, NF κB and JAK/STAT pathways

2018
Nat Commun
PMCID: 5799375
PMID: 29402958
DOI: 10.1038/s41467-017-02640-8

[…] Model implementations in BioNetGen language (BNGL), Matlab, and SBML are provided in a ZIP archive (Supplementary Data ). […]


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BioNetGen institution(s)
Department of Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
BioNetGen funding source(s)
Supported by the US National Institutes of Health Grants P41GM103712, R01GM115805, R01AI107825, and P01HL114453 and the US National Science Foundation Expeditions in Computing award 0926181.

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