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This wiki serves the BioNetGen user community by providing information about BioNetGen and tools for the development, annotation, and discussion of BioNetGen models.

BioNetWiki is read-only unless you obtain a username and password by sending email to bionetgen.help@gmail.com. In addition, pdf files and downloads are only accessible when logged in.

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  • Confidentiality. Often it is necessary for us to look at a model in order to provide help. If the model has not yet been published this can cause angst on the part of the modeler. We understand this and pledge complete confidentiality to our users. Any models, or model snippets, that you send us will never be shared outside of the direct BNG developers group.
  • Group registration. If you are teaching a course that requires use of BioNetGen, please feel free to send a list of the email addresses of your students to bionetgen.help@gmail.com so that we can setup wiki accounts for all of your students at the same time.

--The BNG team

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About BioNetGen

BioNetGen is software for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks. A comprehensive introduction to modeling with BioNetGen is available and is augmented by the models found in the BioNetGen distribution and in the Model Examples. 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 Science Signaling (formerly known as Science's STKE).

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 is 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.

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