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README.md

BioNetGen

Rule-based modeling framework Build Status Build status

Overview

BioNetGen is software for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks. The BioNetGen language has recently been extended to include explicit representation of compartments. A recent review of methods for rule-based modeling is available in L. A. Chylek et al. (2013) Wiley Interdiscip. Rev. Syst. Biol. Med., 6, 13–36.

BioNetGen is presently a mixture of Perl, C++, and Python. Network generation is currently implemented in Perl, the network simulator is C++, and a new SBML-to-BNGL translator is implemented in Python. In addition, a new language parser is currently being developed in ANTLR.

Installation of Distribution

Please note that this is the command line interface to BioNetGen and if you are new to using BioNetGen you are probably looking for the graphical user interface, RuleBender. For more information please visit bionetgen.org.

Most users should simply download the latest BioNetGen release and get the appropriate distribution for their OS. To install BioNetGen, unzip the BioNetGen distribution file, e.g. BioNetGen-2.3-MacOSX.tar.gz, in the directory where you would like BioNetGen installed. BioNetGen requires Perl, in MacOS and most Linux flavors Perl should be installed by default, Windows users will have to install Perl (a good one is Strawberry Perl).

Download Latest Test Builds

These builds are the from the head of master and are not guaranteed to be stable. Use at your own risk.

Compilation from Source

Please see compilation instructions here

BioNetGen History and Support

The BioNetGen software package was initially developed by the Cell Signaling Team at Los Alamos National Laboratory. The current development team is based in the Department of Computational and Systems Biology at the University of Pittsburgh School of Medicine, with contributions from collaborators at the Theoretical Division and Center for Nonlinear Studies at Los Alamos National Laboratory, the Departments of Biology and Computer Science at the University of New Mexico, the Center for Cell Analysis and Modeling at the University of Connecticut Health Center, and the Department of Biological Chemistry at the Johns Hopkins University School of Medicine.

BioNetGen development is currently supported under the auspices of the Center for Multiscale Modeling of Biological Systems (MMBioS), a collaboration between the University of Pittsburgh, the Pittsburgh Supercomputing Center, Carnegie Mellon University, and the Salk Institute (NIH grant P41GM103712). BioNetGen has been supported by NIH grant GM076570 and work has been performed under DOE contract DE-AC52-06NA25396. Additional support for BioNetGen has been provided by NIH grants GM085273, AI35997, and CA109552, NSF grant 0829788, the Arizona Biomedical Research Commission, and the Department of Computational Biology at the University of Pittsburgh School of Medicine.

Distributions

The latest BioNetGen distributions, release notes, installation guides, tutorials, etc. are available at http://bionetgen.org.

RuleBender, a Java-based graphical front end for BioNetGen, is also available at http://bionetgen.org. RuleBender is supported on Linux, Mac OS/X, and Windows platforms. A compatible version of BioNetGen is included in the RuleBender distribution. If you are not sure if your version of BNG is compatible with RuleBender, please use the version distributed with RuleBender.

Contact Us

Email the developers at bionetgen.help@gmail.com

Troubleshooting

If you see the message ABORT: Could not find executable run_network, try setting the environment variable "BNGPATH" to the root directory of your BioNetGen installation. Under bash-like shells, this is done by typing: export BNGPATH=<bngpath>, where is the root directory of BNG.

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