The developers of BioNetGen are dedicated to making dependable software tools for rule-based modeling available to the scientific community and helping researchers learn how to use these tools. We often present tutorials about rule-based modeling and BioNetGen at conferences and summer schools.
Before proceeding, be sure that you have downloaded the latest version of the software from the Download page.
Questions about anything in the tutorial or related to rule-based modeling? Comments? Send email to firstname.lastname@example.org.
The Quick Reference Guide may be helpful in going through the examples below.
- birth-death.bngl - A simple model that introduces the basic syntax of the BioNetGen language.
- logistic.bngl - A simple model of logistic growth with unstructured molecules.
- Lotka-Volterra.bngl - Simple predator-prey model. Demonstrates BNG with unstructured molecules.
- density.bngl - Another simple model that demonstrates a density-dependent threshold for activation based on positive feedback.
- MMexact.bngl - Demonstrates parameterization of binding and catalytic reactions.
- MMapprox.bngl - Demonstrates use of global functions to define rate laws.
- LR.bngl - Simple ligand-binding receptor system. Demonstrates parameter_scan.
- LRdim.bngl - Demonstrates scaling of 3D reaction constants for surface reactions and use of the visualize command.
- BLBR.bngl - Bivalent ligand bivalent receptor. A simple example of a polymerizing system that can be simulated effectively using the network-free simulation algorithm.
- Fceri_ji.bngl - A more complex immunoreceptor signaling network. Demonstrates use of simulation protocol.
- CircadianOscillator.bngl - Simple model of Circadian oscillator that exhibits robustness to noise.
- PB2015-SupplementaryfileS7.bngl - Example of a model specified using Compartmental BNGL (cBNGL).
- loew_6_state_2sub_camkii.bngl - Model of CaMKII activation from Michalski and Loew (2012). PMC
Here are some additional exercises based on the examples above.
Start with these:
- Application note on BioNetGen 2.2. (link) (pdf)
- BioNetGen Actions and Arguments - A handy reference for advanced actions.
- Rule-Based Modeling for (Physical) Biologists - Motivation and extended tutorial
- Models from the Supplement - Many additional useful example models.
- Recent Review of Rule-Based Modeling
Older references that are still useful:
- BioNetGen Introduction and Reference - The BNG "Bible"
- BioNetGen Primer - How to model any signaling process in BNG
- NFsim Paper - Network-free simulation for BNG
- RuleBender Application Note - RuleBender paper
- Compartmental BioNetGen Tutorial