This web site serves the BioNetGen user community by providing information about BioNetGen and tools for the development, annotation, and discussion of BioNetGen models.
Please send questions, comments, and account requests to email@example.com. We will treat all help requests, including models or model snippets, as confidential.
If you use BioNetGen in a work submitted for publication, please cite:
Harris, L. A. et al. BioNetGen 2.2: advances in rule-based modeling. Bioinformatics 32, 3366–3368 (2016).
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.
- RuleBender – the graphical interface for BioNetGen that includes BioNetGen and NFsim source code and executables.
- BioNetGen – command-line only version that includes BioNetGen and NFsim source code. The latest releases and release notes can be found on our GitHub releases page.
Documentation and Tutorials
- Introduction to rule-based modeling with BioNetGen and RuleBender- slides
- Getting started with RuleBender (video)
- BioNetGen Tutorial on GitHub
- Application Note (open access)
- BioNetGen Primer (pdf – free)
- BioNetGen Bible (pdf – free)
- Published BioNetGen models