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, the Department of Biological Chemistry at the Johns Hopkins University School of Medicine, and the Department of Cancer Biology at the Vanderbilt University School of Medicine.
Current development of BioNetGen is supported in part by the NIGMS-funded (P41GM103712) National Center for Multiscale Modeling of Biological Systems (MMBioS). Past support has been provided by NIH grants (GM076570, GM103712, GM085273, AI35997, CA109552), NSF grant 0829788, the Arizona Biomedical Research Commission, and the Department of Computational Biology at the University of Pittsburgh School of Medicine.