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 the BioNetGen Distributions and in the Model Examples. The BioNetGen language has recently been extended to include explicit representation of compartments, as described in a recent tutorial.
Discussion and FAQ
Related Programs and Modules
- RuleBuilder
- PhiBPlot
- NFsim
- DYNSTOC
- GetBonNie
