Welcome! This web site serves the BioNetGen user community by providing information about BioNetGen and tools for the development, annotation, and discussion of BioNetGen models.
News
- Warning MacOS users! New versions of OS X (11.5 or newer) might force you to switch your default shell to be zsh, see here. This will break the extension if you are using anaconda python since anaconda python won’t be your default python in zsh. Try renaming your
.bash_profileto.zprofile. - New VS Code extension for BioNetGen is out! (GitHub link, documentation). Click here to get started. This extension uses PyBioNetGen, which provides a Python interface for BioNetGen models. (GitHub link, documentation)
- command line tool for weighted ensemble sampling of BNGL models is released, GitHub link, documentation.
Getting Help and Reporting Problems
- The preferred way to get help, report a bug, or request a feature is to post an issue on the BioNetGen GitHub issues page.
- You may also send email to bionetgen.help@gmail.com. We will treat all help email requests, including models or model snippets, as confidential.
Citing BioNetGen
If you use BioNetGen for a project please cite
- Harris, L. A. et al. BioNetGen 2.2: advances in rule-based modeling. Bioinformatics 32, 3366–3368 (2016). In addition, consider sending us an email or tweet @bionetgen. We’d love to hear about it!
Download
- VS Code extension for BioNetGen. We encourage both new and current BioNetGen users to use this interace for developing BioNetGen models. Installation instructions are here. This extension uses PyBioNetGen, which provides a Python and command-line interfaces for BioNetGen models.
- Other interfaces for BioNetGen include:
- RuleBender provides an Eclispe-based interface for BioNetGen that includes interactive model visualization capabilities. Installation instructions are here.
- BioNetGen command line. The core BioNetGen code includes a command-line interface that may be useful to developers and advanced users. The BioNetGen code is bundled with both the PyBioNetGen and RuleBender.
Documentation
- Getting Started
- Modeling Reaction Networks with BioNetGen. Introduces basic BioNetGen block syntax, actions, and workflows for simulating models, plotting results, and parameter scanning.
- Rule-Based Modeling with BioNetGen. Introduces the concepts and syntax for modeling biochemical networks using structured molecules and rules in BioNetGen.
- BioNetGen tutorial on GitHub Provides detailed examples that demonstrate a wide range of language and modeling features.
- FAQ (Under construction)
- Reference
- Papers
Upcoming Features
- Network visualization support to VS Code extension
- A C++ based BNGL parser
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.