- New VS Code extension for BioNetGen is out! (GitHub link, documentation)
- New Python BioNetGen package is out! (GitHub link, documentation)
- Alpha version of a command line tool for weighted ensemble sampling of BNGL models is released, GitHub link, documentation.
- Upcoming hands-on workshop on computational biophysics, workshop Dates: June 28 – July 1, 2021, application deadline: June 11, 2021. For more details, or to apply visit here.
- Upcoming cell modeling workshop, workshop dates: July 12 - July 16, 2021, application deadline: June 25, 2021. For more details, or to apply visit here.
- New BioNetGen release is coming out with time dependent parameter support soon.
- Network visualization support to VS Code extension is being worked on.
- A python package to simplify BioNetGen (SSA only)/WESTPA simulations is in progress.
BioNetGen Modelling Language
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).
– the graphical interface for BioNetGen that includes BioNetGen and
NFsim source code and executables for Mac, Windows, and Linux.
- Step-by-step installation guide can be found here.
- BioNetGen – command-line only version that includes BioNetGen and NFsim source code plus executables for Mac, Windows, and Linux.
Documentation and Tutorials
- Getting started with RuleBender (video)
- Slide-based introduction to rule-based modeling with BioNetGen and RuleBender
- BioNetGen tutorial on GitHub Detailed examples that demonstrate a wide range of language and modeling features.
- MMBioS - Cell Modeling Virtual Workshop 2020 A YouTube playlist of all Cell Modelling workshop lectures including BioNetGen and RuleBender lessons.
- FAQ (Under construction)
- Application Note (open access)
- BioNetGen Primer (pdf – free)
- BioNetGen Bible (pdf – free)
- Published BioNetGen models
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.