CellML Cellular Electrophysiology & Physiome Modeling (.cellml)

@modelscript/cellml (languages/cellml) provides native WebAssembly parsing, 7-base SI dimensional unit consistency and component port directionality verification, Hodgkin-Huxley / cardiac action-potential and 0D microvascular Windkessel ODE integration, DAEBuilder lowering, and Modelica 3.x / SBML projections for IUPS Physiome Project CellML (1.0 / 1.1 / 2.0) physiological models.

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Supported Extensions & Standards

Extension	Format	Description
.cellml, .xml	CellML 1.0 / 1.1 / 2.0	Modular XML specification of units, component, variable, MathML math ODEs, connection, and encapsulation

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Key Capabilities

1. Modular Components, Encapsulation & 7-Base SI Units

• Parses <units> definitions (prefix, multiplier, exponent over SI base units ampere, candela, kelvin, kilogram, metre, mole, second) and verifies dimensional homogeneity across <map_variables> component connections.
• Enforces public_interface and private_interface (in / out / none) encapsulation rules.

2. Cardiac Action Potential & Microvascular Hemodynamics Solver

• Integrates membrane voltage $V_m$ and ionic gating variables ($m,h,n,d,f,x_r$) across Hodgkin-Huxley, Noble, Luo-Rudy, and ten Tusscher cardiac electrophysiology models alongside 0D Windkessel arterial/venous perfusion loops:$$C_m\frac{d{V}_m}{dt}=-(I_{\text{Na}}+I_{\text{K}}+I_{\text{CaL}}+I_{\text{leak}}-I_{\text{stim}}(t)),\frac{dy}{dt}={\alpha }_y(V_m)(1-y)-{\beta }_y(V_m)y$$

3. DAE Arena Lowering & Modelica / SBML Projection

• Lowers modular CellML equations into @modelscript/runtime's DAEBuilder arena and projects models into Modelica 3.x (cellmlToModelica) and SBML (cellmlToSbml).

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Pre-Flight Diagnostics

10 rules8 error2 warning

Code	Rule	Severity	Message
M9301	cellml-missing-model-name	error	CellML '<model>' element is missing a non-empty 'name' attribute.
M9302	cellml-unresolved-units	error	Variable '<targetName>' in component '<componentName>' references unresolved units '<unitName>'.
M9303	cellml-interface-direction-conflict	error	Variable mapping between '<comp1>.<var1>' (interface '<iface1>') and '<comp2>.<var2>' (interface '<iface2>') has incompatible interface directions.
M9304	cellml-unit-dimensional-mismatch	warning	Connected variables '<comp1>.<var1>' ('<units1>') and '<comp2>.<var2>' ('<units2>') have incompatible physical SI base dimensions.
M9305	cellml-uninitialized-state-variable	warning	Differential state variable '<varName>' in component '<compName>' has no 'initial_value' attribute.
M9306	cellml-encapsulation-hierarchy-cycle	error	Circular component reference '<compName>' detected in '<encapsulation>' hierarchy.
M9307	cellml-unresolved-connection-member	error	Connection references unknown <memberKind> '<memberName>' in '<contextName>'.
M9308	cellml-overconstrained-variable	error	Variable '<varName>' in component '<compName>' has an 'in' interface or prior assignment and cannot be assigned by an equation or ODE.
M9309	cellml-undefined-math-ci	error	Equation in component '<compName>' references undeclared variable identifier '<ciName>'.
M9310	cellml-duplicate-variable-or-component	error	Duplicate <entityKind> '<name>' declared in component '<compName>'.

Generated from languages/cellml/src/lints/rules.ts. All languages →

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CLI Usage

# Inspect CellML components, variables, units, and connections
msx cellml inspect HodgkinHuxley.cellml

# Validate SI dimensional unit compatibility and interface directions
msx cellml validate HodgkinHuxley.cellml

# Integrate cellular electrophysiology ODE trajectories
msx cellml simulate HodgkinHuxley.cellml

# Project CellML model to Modelica 3.x or SBML
msx cellml to-modelica HodgkinHuxley.cellml > HodgkinHuxley.mo
msx cellml to-sbml HodgkinHuxley.cellml > HodgkinHuxley.sbml