A comprehensive introduction to modeling with BioNetGen including a complete description of the syntax and semantics of the BioNetGen language and tutorial examples was published in the volume Systems Biology, which is part of the popular Methods in Molecular Biology series. If this volume is not available to you in either online or print format, please download the preprint version of this chapter. Alternatively, check out the The BioNetGen Online Manual for a more up-to-date summary of the BioNetGen software and supported methods. For further examples of BioNetGen models and usage see the models found in Model Examples and in the Models2 directory of the BioNetGen distribution.
Errata are listed here, including updates on minor BNGL syntax changes in newer releases.
Quick Reference Guide
The Quick Reference Guide provides easy access to both the basic and advanced features of the BioNetGen language.
Navigable documentation of the BioNetGen software and supported methods. (under construction)
The Primer provides a gentle introduction to rule-based modeling with BioNetGen. Section 6.1 contains a very brief introduction to the use of Functions to create user-defined rate laws. The full reference is
J. A. Sekar and J.R. Faeder (2012) Rule-based modeling of signal transduction: a primer. Methods Mol. Biol. 880, 139-218. doi: 10.1007/978-1-61779-833-7_9. link
A preprint is available here.
New and Improved! The most comprehensive listing of BioNetGen actions and arguments ever compiled. This is an invaluable reference for users of all levels.
A review in Science Signaling (formerly known as Science's STKE) provides a general overview of the rule-based approach and surveys the available tools (as of 2006) for rule-based modeling. A more recent survey of the available tools is provided in the paper describing the compartmental extension of BioNetGen.
BioNetGen 2.2.4+ includes features for modeling free energy in a rule-based framework. Documentation and examples are found here.
The BioNetGen language has recently been extended to include explicit representation of compartments. A tutorial, example files, and a paper describing the extension can be found here.
New BioNetGen features
- Simulate BNGL network models within MATLAB using the Mex code generator action.
- Improve memory efficiency of Network-Free simulations with the Hybrid particle-population model generator.
- Accelerated-stochastic simulations with the partitioned-leaping algorithm .
- Reaction Rule Semantics: how reactant molecules are mapped to product molecules.
Discussion and FAQ
Related Programs and Modules
- RuleBuilder, a graphical IDE for BioNetGen.
- PhiBPlot, a simple plotting utility.
- BioNetGen-to-SSC translator
- NFsim, a BNGL-compatible network-free stochastic simulator.