SBML feature support

This page summarises which SBML constructs chaste-sbml can translate into Chaste C++, and which it cannot. Models using explicitly unsupported constructs are rejected with a clear error during generation.

SBML levels and packages

• SBML Level 2 and Level 3 are supported. SBML Level 1 is not supported.

• Hierarchical models (the comp package) are supported by flattening the model on load. If flattening fails, generation stops with an error.

• Flux balance constraints (the fbc package) are not supported.

• Other packages are not interpreted.

Note

A model whose SBML level is outside 2-3 is not rejected outright; the generator warns and proceeds on a best-effort basis, so the output may be incorrect.

Model components

Construct	Status	Notes
Species (amount & concentration)	Supported	hasOnlySubstanceUnits, boundaryCondition, and species/model conversionFactor are all handled; both amount and concentration are exposed.
Compartments	Supported	Constant, rule-driven, and ODE-driven compartments; time-varying compartments add dilution terms to conserve amount.
Global parameters	Supported	Constant, rule-varied, event-varied, or ODE-driven.
Local (kinetic-law) parameters	Supported	Scoped per reaction; shadow globals of the same name. A local parameter with no value is an error.
Reactions & kinetic laws	Supported	Each reaction is exposed as a flux; a reaction with no kinetic law falls back to the product of its reactants.
Stoichiometry	Supported	Constant, variable (via rate/assignment rule), and stoichiometryMath.
Function definitions	Supported	Emitted as C++ functions taking double arguments.
Initial assignments	Supported	Expanded on load where possible; the remainder applied to species, parameters, compartments, and stoichiometry.

Rules

Rule type	Status	Notes
Assignment rules	Supported	Applied to species, compartments, parameters, and stoichiometry.
Rate rules	Supported	Take precedence over a species’ reaction contributions.
Algebraic rules	Not supported	Generation stops with an error.

Events

Events are supported, with some limits:

• Trigger, event assignments, priority, and the trigger’s initial value at t=0 semantics are handled.

• For CVODE root-finding, a trigger distance is derived from a single top-level relational operator with two operands. Compound boolean triggers or n-ary relationals fall back to a constant distance (they still fire, but not via smooth root-finding).

• Event delays are not supported: a non-zero (or non-numeric) delay is rejected. A zero delay is fine.

Time and units

• Time-unit scaling to Chaste’s hours is supported for time units that reduce to seconds (second, millisecond, minute, hour). See Time units for the resolution rules and the --timescale override.

• General physical units are not enforced. Numeric-literal unit annotations are stripped, and species/parameter/compartment quantities are treated as non-dimensional, so your model must be unit-consistent on its own.

MathML

Standard MathML is translated to C++:

• Arithmetic, relational, and boolean operators.

• The full set of elementary functions (sin, cos, exp, log, sqrt, pow, abs, floor, ceil, the inverse and hyperbolic trig functions, and so on), mapped to std:: or to sm:: helper functions where C++ has no direct equivalent (for example cot, factorial, piecewise, min/max).

• Constants pi, exponentiale, avogadro, and the time and rateOf csymbols; infinity and notanumber.

• Calls to a model’s own function definitions.

The delay() function is not supported and is rejected during generation.

Note

A model function may legitimately be named sin, min, log, and so on. Those calls are left as calls to your function definition and are not rerouted to the C++ built-in of the same name.

Explicitly unsupported constructs

Each of these stops generation with an error:

• Flux balance constraints (fbc package)

• Fast reactions

• Algebraic rules

• Event delays (non-zero)

• delay() MathML function

• Local parameter without a value

SBML Test Suite results

The generator is run against the SBML Test Suite semantic cases in CI (see the sbml_test_suite workflow). Of 1821 semantic cases:

Outcome	Cases	Share
Pass (generated and numerically verified against Chaste)	1345	74%
Unsupported (skipped)	476	26%

The unsupported cases break down by the feature they exercise:

Feature	Cases
delay() / event delays	262
Algebraic rules	125
Flux balance / steady-state (no time course)	34
Fast reactions	34
Random event execution	11
Event execution semantics	10

Note

These counts come from chaste_sbml/SbmlRefModels/test/data/sbml_test_suite_status.csv, which CI checks against actual generation.