COMBINE SED-ML Simulation Experiments (.sedml)

@modelscript/sedml (languages/sedml) provides native WebAssembly parsing, KiSAO solver algorithm validation, multi-task simulation protocol execution (UniformTimeCourse, OneStep, SteadyState, RepeatedTask), DataGenerator post-processing, DAEBuilder lowering, and Modelica experiment projection for Simulation Experiment Description Markup Language (SED-ML Level 1 Version 3/4) reproducible simulation studies.

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Supported Extensions & Standards

Extension	Format	Description
.sedml, .xml	COMBINE SED-ML	XML specification of listOfModels, listOfSimulations, listOfTasks, listOfDataGenerators, and listOfOutputs

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Key Capabilities

1. Reproducible Simulation Protocols & KiSAO Solvers

• Parses SED-ML elements:
  • Models & Changes (model, changeAttribute, computeChange): Base model references (SBML, CellML, Modelica) and parameter overrides.
  • Simulations (uniformTimeCourse, oneStep, steadyState): Initial time, output start/end times, number of points, and KiSAO algorithm identifiers (KISAO:0000019 CVODE, KISAO:0000032 RK4, KISAO:0000029 Gillespie SSA).
  • Tasks & Data Generators (task, repeatedTask, dataGenerator): MathML/infix normalization and scaling of raw simulation variables for plot2D, plot3D, and report outputs.

2. Protocol Execution & Modelica Experiment Projection

• Executes time-course and parameter-sweep tasks (executeSedml), lowers the experiment schedule into @modelscript/runtime's DAEBuilder arena, and generates Modelica models annotated with annotation(experiment(StartTime=..., StopTime=..., NumberOfIntervals=..., Tolerance=...)) (sedmlToModelica).

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Pre-Flight Diagnostics

10 rules8 error2 warning

Code	Rule	Severity	Message
M9151	invalid-time-course-bounds	error	UniformTimeCourse simulation '<simId>' defines invalid time course bounds ('<details>').
M9152	invalid-kisao-id	error	Simulation '<simId>' specifies missing or malformed algorithm KiSAO identifier '<kisaoId>'; expected 'KISAO:xxxxxxx'.
M9153	unresolved-model-reference	error	SED-ML element '<ownerId>' references undefined model '<modelRef>'.
M9154	unresolved-simulation-reference	error	Task '<taskId>' references undefined simulation '<simRef>'.
M9155	unresolved-task-reference	error	SED-ML variable or subTask in '<ownerId>' references undefined task '<taskRef>'.
M9156	unresolved-data-generator-reference	error	Output '<outputId>' element '<itemId>' references undefined dataGenerator '<dataGenRef>'.
M9157	circular-model-source	error	Model '<modelId>' source reference chain '<chain>' forms a circular dependency.
M9158	undefined-data-generator-math-variable	warning	DataGenerator '<dataGenId>' math expression references identifier '<symbolName>' not declared in listOfVariables or listOfParameters.
M9159	empty-sedml-experiment	warning	SED-ML document defines an empty experiment with no simulations or tasks.
M9160	duplicate-sedml-id	error	SED-ML identifier '<id>' on '<elementKind>' is declared multiple times within the document.

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

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CLI Usage

# Validate time-course bounds, KiSAO IDs, and model/task/dataGenerator references
msx lint OscillatoryProtocol.sedml

# Parse and inspect SED-ML simulation experiment definitions
msx parse OscillatoryProtocol.sedml