BioNetGen Quickstart

This quickstart gets you from installation to your first successful model run. If you are brand new to BioNetGen, start here.

Prerequisites

Complete the installation steps in Installation.
Confirm the CLI is available:

bionetgen -h

If this command fails, revisit Installation before continuing.

Run your first model

Create a file named SIR.bngl with the following content:

begin model

begin parameters
  N  1.0e2
  I0 1
  R0 2.5
  g  0.33
  b  g*R0/N
end parameters

begin species
  S() N-I0
  I() I0
end species

begin observables
  Molecules S S()
  Molecules I I()
  Molecules R R()
end observables

begin reaction rules
  R1: S + I -> I + I b
  R2: I -> R g
end reaction rules

end model

# Actions
generate_network({overwrite=>1})
simulate({method=>"ode",t_end=>30,n_steps=>200})

Run the model:

bionetgen run -i SIR.bngl -o sir_output

You should now have an output folder sir_output containing simulation results.

What to check

Verify the run completed without errors in terminal output.
Open files in sir_output and confirm time-course data was generated.
Re-run after changing parameters (for example R0) and compare results.

Run from VS Code

If you prefer the VS Code extension workflow:

Open SIR.bngl in VS Code.
Use the extension run controls or command palette actions to execute the model.
Use the built-in graphing and visualization features for quick inspection.

Where to go next

For PyBioNetGen CLI details, see Command Line Interface.
For Python library usage, see Library.
For step-by-step tutorials, see Tutorials.