Antimony Modular Systems Biology (.ant)

@modelscript/antimony (languages/antimony) provides native WebAssembly GLR parsing, hierarchical submodel composition and port aliasing (is), rate and assignment rule evaluation, state-triggered event handling, 4th-order Runge-Kutta ODE integration, DAEBuilder lowering, and bidirectional SBML Level 3 / Modelica 3.x projection for Antimony human-readable systems biology models.

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Supported Extensions & Standards

Extension	Format	Description
.ant	Antimony Model	Modular text language (model ... end) for biochemical reactions, compartments, species, events, and submodel imports

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Key Capabilities

1. Human-Readable Biochemical Reactions & Rules

• Parses concise Antimony syntax:
  • Compartments & Species: compartment cell = 1.0; species S1 in cell = 10.0, $S_ext in cell = 5.0; (including boundary species $).
  • Reactions: J1: S1 + E -> ES; k_on * S1 * E - k_off * ES; with named reaction IDs, stoichiometric weights, and arbitrary kinetic rate laws.
  • Rate & Assignment Rules: x' = k1 * S1 - k2 * x; and totS := S1 + ES;.
  • State Events: E1: at (S1 < 0.5): S1 = 10.0, k1 = 0.2;.

2. Modular Composition (model & is)

• Supports reusable model definitions instantiated as submodels (A: Oscillator();) with shared variable bindings (A.S1 is Cytosol_S1;) and unit declarations (unit mM = 1e-3 mole / litre;).

3. RK4 Solver, DAE Lowering & SBML / Modelica Projection

• Simulates coupled reaction networks and state events (solveAntimony), lowers equations into @modelscript/runtime's DAEBuilder arena, and exports to SBML Level 3 Core (antimonyToSbml) and Modelica 3.x (antimonyToModelica).

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Pre-Flight Diagnostics

10 rules8 error2 warning

Code	Rule	Severity	Message
M9001	empty-antimony-module	error	Antimony module '<moduleName>' contains no species, reactions, or rules.
M9002	undefined-compartment-in-species	error	Species '<speciesId>' is placed in undeclared compartment '<compartmentId>'.
M9003	missing-reaction-rate-law	warning	Reaction '<reactionId>' has no kinetic rate expression.
M9004	negative-stoichiometric-coefficient	error	Species '<speciesId>' in reaction '<reactionId>' has non-positive stoichiometry '<stoichiometry>'.
M9005	undefined-rate-law-symbol	warning	Rate expression in '<reactionId>' references undeclared identifier '<symbol>'.
M9006	duplicate-reaction-id	error	Reaction identifier '<reactionId>' is defined multiple times in module '<moduleName>'.
M9007	circular-submodel-instantiation	error	Submodel hierarchy contains a cycle involving '<moduleName>'.
M9008	conflicting-species-variability	error	Species '<speciesId>' is declared both 'const' and modified by a rate rule or non-boundary reaction.
M9009	negative-compartment-volume	error	Compartment '<compartmentId>' initialized with non-positive volume '<volume>'.
M9010	invalid-event-trigger	error	Event '<eventId>' trigger condition is not a relational/boolean expression.

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

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CLI Usage

# Run pre-flight linting on an Antimony model
msx lint Repressilator.ant

# Parse and inspect Antimony model declarations
msx parse Repressilator.ant