Documentation
From BioNetWiki
Contents |
Key Documents
Review of Rule-based Modeling
A recent 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.
The BioNetGen Bible
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. 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.
The BioNetGen Primer
The Primer provides a gentle introduction to rule-based modeling with BioNetGen.
Compartmental BioNetGen
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.
Technical Documentation
- Reaction Rule Semantics: how reactant molecules are mapped to product molecules.
Discussion and FAQ
Related Programs and Modules
- RuleBuilder
- PhiBPlot
- BioNetGen to SSC translator
- NFsim
- DYNSTOC
- GetBonNie
