Announcements

• New VS Code extension for BioNetGen is out! (GH link)
• New Python BioNetGen package is out! (GH link)

Upcoming Features

• 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 bionetgen.help@gmail.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).

In addition, please send us an email or send a tweet to @bionetgen. We’d love to hear about it!

Download

• RuleBender – 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.
• FAQ (Under construction)

Reference

• Quick Reference Guide
• Actions and Arguments Guide

Papers

• Application Note (open access)
• BioNetGen Primer (pdf – free)
• BioNetGen Bible (pdf – free)
• Published BioNetGen models

Contact

• Email: bionetgen.help@gmail.com
• GitHub repositories.
• Twitter: @bionetgen

Acknowledgements

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.

BioNetGen and this web site are maintained by the Lab of James Faeder in the Department of Computational and Systems Biology and the University of Pittsburgh School of Medicine.