BioNetGen (BNG) VS Code Extension

A VS Code extension for the BioNetGen rule-based modeling platform. Write, validate, simulate, and visualize BioNetGen models without leaving the editor. See the starter guide for an introduction.

Features

Syntax Highlighting: Scoping for all BNGL constructs, with dark, light, and high-contrast themes.
Language Server: Real-time diagnostics (mismatched blocks, duplicate definitions, unused parameters), autocomplete for block types, actions, parameters, molecule types, and built-in functions, go-to-definition, find references, and hover information.
Intelligent Folding: Fold begin/end blocks and metadata sections.
Simulation: Run BioNetGen simulations directly from the editor and monitor processes in a sidebar tree view.
Network Visualization: Generate contact maps, rule visualizations, and regulatory graphs.
Interactive Plotting: Plot .gdat/.cdat/.scan results with a built-in viewer featuring variable selection, axis scale toggles, line style controls, and image export.
Snippets: Expand block skeletons, line templates, action calls, and math functions with Tab.

Usage

Open or create a .bngl file. Syntax highlighting and language server features activate automatically.
Click the BioNetGen icon in the editor title bar to open the command menu. From the dropdown you can:
- Run Simulation (Ctrl/Cmd+Shift+F1 on .bngl files)
- Visualize Network
- Open Plot / Viewer (Ctrl/Cmd+Shift+F1 on .gdat/.cdat/.scan files)
- Install/Check PyBioNetGen
- Upgrade PyBioNetGen
After a simulation completes, the resulting .gdat file opens automatically. Click the BioNetGen icon to launch the interactive plot viewer.
Use the sidebar controls in the plot viewer to toggle variables on/off, switch axis scales (linear/log), change line styles, toggle the legend, and export images.

Requirements

The editing features (highlighting, diagnostics, autocomplete, navigation) work out of the box. To run simulations and visualizations you also need:

Python 3 (we recommend Anaconda)
PyBioNetGen (pip install bionetgen)
Perl (Windows users: conda install -c conda-forge perl)

Installation

The extension is available on the VS Code Marketplace: search for BioNetGen in the Extensions tab.

For installation from a VSIX package or running from source, see the installation guide.

Snippets

Type a prefix and press Tab to expand. All snippets are available in .bngl files.

Block Snippets

Prefix	Description
`begin model`	Full model skeleton with all standard blocks
`begin parameters`	Parameters block
`begin molecule types`	Molecule types block
`begin compartments`	Compartments block
`begin seed species`	Seed species block
`begin species`	Species block
`begin observables`	Observables block
`begin functions`	Functions block
`begin reaction rules`	Reaction rules block
`begin population maps`	Population maps block
`begin energy patterns`	Energy patterns block

Line Snippets

Prefix	Description
`Molecule`	Molecule with component and state
`MoleculeType`	Molecule type definition with two states
`Species`	Species pattern with bond
`CompartmentLine`	Compartment definition
`ParameterLine`	Parameter name/value pair
`SpeciesLine`	Species with amount
`ObservableLine`	Observable (Molecules or Species)
`FunctionLine`	Function definition
`RuleLine`	Reaction rule with rate
`EnergyPatternLine`	Energy pattern with expression
`PopulationMapLine`	Population map rule

Action Snippets

Prefix	Description
`generate_network`	Generate network action
`generate_hybrid_model`	Generate hybrid model action
`simulate`	Simulate with method, t_end, n_steps
`parameter_scan`	Parameter scan with all options
`bifurcate`	Bifurcation analysis
`readFile`	Read file action
`writeFile`	Write file (bngl/net/xml)
`writeModel`	Write model
`writeNetwork`	Write network
`writeXML`	Write XML
`writeSBML`	Write SBML
`writeMfile`	Write M-file
`writeMexfile`	Write MEX-file
`writeMDL`	Write MDL
`visualize`	Visualize action
`setConcentrations`	Set species concentration
`addConcentration`	Add to species concentration
`saveConcentrations`	Save current concentrations
`resetConcentrations`	Reset concentrations
`setParameter`	Set parameter value
`saveParameters`	Save current parameters
`resetParameters`	Reset parameters
`setModelName`	Set model name
`substanceUnits`	Set substance units
`version`	Set version
`setOption`	Set option
`quit`	Quit action

Math Functions

abs, sin, cos, tan, exp, ln, log10, floor, ceil, sqrt, asin, acos, atan, sinh, cosh, tanh, asinh, acosh, atanh

Settings

Setting	Description	Default
`bngl.general.auto_install`	Automatically install PyBioNetGen on activation	`true`
`bngl.general.enable_terminal_runner`	Use the old terminal-based runner instead of spawning processes	`false`
`bngl.general.auto_open`	Automatically open result files (e.g. `.gdat`) after a simulation run	`true`
`bngl.general.result_folder`	Absolute path to a default results folder (used when no workspace is open)	`null`
`bngl.plotting.legend`	Show the plot legend by default	`true`
`bngl.plotting.max_series_count`	Maximum number of time series to display initially	`50`

Development

See the developer guide for architecture details and build instructions. Quick start:

npm install
npm run watch   # start build in watch mode
# Press F5 to launch the Extension Development Host

Please submit issues and feature requests at GitHub.

BioNetGen