BioNetGen Rule-Based Biochemical Networks (.bngl)

@modelscript/bngl (languages/bngl) provides native WebAssembly GLR parsing, rule-based site-specific biochemical network expansion, observable pattern aggregation, 4th-order Runge-Kutta ODE integration, DAEBuilder lowering, and SBML / Modelica projections for BioNetGen Language (BNGL) multiprotein signaling, receptor oligomerization, and post-translational modification models.

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Supported Extensions & Standards

Extension	Format	Description
.bngl	BioNetGen Model	Block-structured rule-based biochemical specification (parameters, molecule types, seed species, observables, reaction rules, actions)

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Key Capabilities

1. Site-Specific Molecule Types & Bond Graphs

• Parses structured BNGL blocks:
  • molecule types: Multi-component proteins with internal phosphorylation/conformational states (e.g., EGFR(L,CR1,Y1068~U~P)).
  • seed species: Initial molecular complexes with explicit site bonds (!1, !+, !?, !.).
  • observables: Molecules and Species pattern queries aggregating phosphorylated or bound sub-complexes.
  • reaction rules: Unidirectional (->) and bidirectional (<->) site-transformation and binding rules without combinatorial manual enumeration.

2. Automated Network Expansion & ODE Simulation

• Iteratively applies reaction rules to seed species to generate the reachable species and elementary reaction network (generateNetwork / solveBngl).
• Integrates species concentration trajectories and observable outputs, and lowers the expanded network into @modelscript/runtime's DAEBuilder arena, SBML (bnglToSbml), and Modelica 3.x (bnglToModelica).

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Pre-Flight Diagnostics

10 rules8 error2 warning

Code	Rule	Severity	Message
M9051	molecule-type-undeclared	error	Molecule type '<moleculeName>' referenced in '<context>' is not declared in 'molecule types'.
M9052	component-site-undeclared	error	Component site '<siteName>' is not declared on molecule type '<moleculeName>'.
M9053	invalid-internal-state	error	Internal state '~<stateName>' is not allowed for component '<siteName>' of molecule type '<moleculeName>'.
M9054	dangling-bond-label	error	Bond label '!<bondLabel>' in complex pattern '<patternText>' appears '<count>' times; each bond must connect exactly 2 sites.
M9055	undefined-rate-parameter	warning	Reaction rule '<ruleId>' references undeclared rate parameter '<parameterName>'.
M9056	reversible-rule-missing-reverse-rate	error	Reversible reaction rule '<ruleId>' ('<->') is missing a reverse rate constant.
M9057	negative-seed-concentration	error	Seed species '<speciesPattern>' has negative initial concentration '<concentration>'.
M9058	empty-bionetgen-model	error	BioNetGen model '<modelName>' contains no molecule types, seed species, or reaction rules.
M9059	duplicate-observable-name	error	Observable '<observableName>' is defined multiple times in 'observables'.
M9060	unbounded-polymerization-rule	warning	Reaction rule '<ruleId>' forms intermolecular bonds on multi-site molecule '<moleculeName>' that can cause unbounded polymerization.

Generated from languages/bngl/src/errors.ts. All languages →

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CLI Usage

# Validate molecule site states, bond indices, and reaction rate constants
msx lint EgfrSignaling.bngl

# Parse and inspect BioNetGen blocks
msx parse EgfrSignaling.bngl