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SimBiology Functions

Alphabetical List By Category

SimBiology Desktop

simbiologyOpen SimBiology desktop for modeling and simulation

Modeling

Import Models

sbioloadprojectLoad project from file
sbmlimportImport SBML-formatted file
sbiowhosShow contents of project file, library file, or SimBiology root object
loadLoad variables from file into workspace

Build Models

sbiomodelConstruct model object
sbiorootReturn SimBiology root object
sbioresetDelete all model objects
sbioselectSearch for objects with specified constraints
sbiolastwarningSimBiology last warning message
sbiolasterrorSimBiology last error message
verifyValidate and verify SimBiology model
addcompartmentCreate compartment object
addspeciesCreate species object and add to compartment object within model object
addparameterCreate parameter object and add to model or kinetic law object
addreactionCreate reaction object and add to model object
addruleCreate rule object and add to model object
addeventAdd event object to model object
findUnusedComponentsFind unused species, parameters, and compartments in a model
findUsages(species,parameter,compartment)Find out how a species, parameter, or compartment is used in a model
findUsages(unit,unitprefix)Find out how a unit or unit prefix is used
findUsages(AbstractKineticLaw)Find out how an AbstractKineticLaw object is used
updateInitialAssignmentsUpdate initial assignment rules to remove order dependencies
Model objectModel and component information
Compartment objectOptions for compartments
Species objectOptions for compartment species
Parameter objectParameter and scope information
Reaction objectOptions for model reactions
KineticLaw objectKinetic law information for reaction
Rule objectHold rule for species and parameters
Event objectStore event information
Root objectHold models, unit libraries, and abstract kinetic law libraries
PKModelDesign objectHelper object to construct pharmacokinetic model
PKCompartment objectUsed by PKModelDesign to create SimBiology model
PKModelMap objectDefine SimBiology model components’ roles
constructConstruct SimBiology model from PKModelDesign object
addCompartmentAdd compartment to PKModelDesign object

Export Models

sbiosaveprojectSave all models in root object
sbmlexportExport SimBiology model to SBML file

Extend Modeling Environment

sbioaddtolibraryAdd to user-defined library
sbioremovefromlibrary Remove kinetic law, unit, or unit prefix from library
sbiocopylibraryCopy library to disk
sbiorootReturn SimBiology root object
sbioresetDelete all model objects
sbioabstractkineticlawCreate kinetic law definition
sbiounitCreate user-defined unit
sbiounitprefixCreate user-defined unit prefix
sbioshowunitsShow units in library
sbioshowunitprefixesShow unit prefixes in library
sbioconvertunitsConvert unit and unit value to new unit
sbiounitcalculatorConvert value between units
Root objectHold models, unit libraries, and abstract kinetic law libraries
AbstractKineticLaw objectKinetic law information in library
Unit objectHold information about user-defined unit
UnitPrefix objectHold information about user-defined unit prefix

Simulation

Simulate Responses to Biological Variability and Doses

sbiosimulateSimulate SimBiology model
createSimFunctionCreate SimFunction object
sbiodoseConstruct dose object
adddoseAdd dose object to model
sbiovariantConstruct variant object
addvariantAdd variant to model
sbiosteadystate Find steady state of SimBiology model
sbioacceleratePrepare model object for accelerated simulations
sbiosampleparametersGenerate parameters by sampling covariate model (requires Statistics and Machine Learning Toolbox software)
sbiosampleerrorSample error based on error model and add noise to simulation data
sbioplotPlot simulation results in one figure
sbiosubplotPlot simulation results in subplots
sbiotrellisPlot data or simulation results in trellis plot
sbioensemblerunMultiple stochastic ensemble runs of SimBiology model
sbioensembleplotShow results of ensemble run using 2-D or 3-D plots
sbioensemblestatsGet statistics from ensemble run data
SimFunction objectFunction-like interface to execute SimBiology models
ScheduleDose objectDefine drug dosing protocol
RepeatDose objectDefine drug dosing protocol
Variant objectStore alternate component values
SimData objectSimulation data storage
Configset objectSolver settings information for model simulation
SolverOptionsSpecify model solver options
RuntimeOptionsOptions for logged species
CompileOptionsDimensional analysis and unit conversion options

Scan Parameter Ranges

sbiosimulateSimulate SimBiology model
sbioacceleratePrepare model object for accelerated simulations
sbiosampleparametersGenerate parameters by sampling covariate model (requires Statistics and Machine Learning Toolbox software)
sbiosampleerrorSample error based on error model and add noise to simulation data
addconfigsetCreate configuration set object and add to model object
getconfigsetGet configuration set object from model object
createSimFunctionCreate SimFunction object
sbioplotPlot simulation results in one figure
sbiosubplotPlot simulation results in subplots
sbiotrellisPlot data or simulation results in trellis plot
SimData objectSimulation data storage
Configset objectSolver settings information for model simulation
SolverOptionsSpecify model solver options
RuntimeOptionsOptions for logged species
CompileOptionsDimensional analysis and unit conversion options
SimFunction objectFunction-like interface to execute SimBiology models
SimFunctionSensitivity objectSimFunctionSensitivity object, subclass of SimFunction object

Calculate Sensitivities

sbiosimulateSimulate SimBiology model
sbioacceleratePrepare model object for accelerated simulations
sbiosampleparametersGenerate parameters by sampling covariate model (requires Statistics and Machine Learning Toolbox software)
sbiosampleerrorSample error based on error model and add noise to simulation data
addconfigsetCreate configuration set object and add to model object
getconfigsetGet configuration set object from model object
createSimFunctionCreate SimFunction object
SensitivityAnalysisOptionsSpecify sensitivity analysis options
SimData objectSimulation data storage
Configset objectSolver settings information for model simulation
SolverOptionsSpecify model solver options
RuntimeOptionsOptions for logged species
CompileOptionsDimensional analysis and unit conversion options
SimFunction objectFunction-like interface to execute SimBiology models
SimFunctionSensitivity objectSimFunctionSensitivity object, subclass of SimFunction object

Estimation

Import Data

sbionmimportImport NONMEM-formatted data
sbionmfiledefNONMEM file definition object for sbionmimport
sbiotrellisPlot data or simulation results in trellis plot
sbioncaCompute noncompartmental analysis (NCA) parameters (requires Statistics and Machine Learning Toolbox)
sbioncaoptionsSpecify options to calculate noncompartmental analysis (NCA) parameters
groupedData Table-like collection of data and metadata

Nonlinear Regression

sbiofitPerform nonlinear least-squares regression
sbionlinfitPerform nonlinear least-squares regression using SimBiology models (requires Statistics and Machine Learning Toolbox software)
sbioparamestimPerform parameter estimation
sbiosampleparametersGenerate parameters by sampling covariate model (requires Statistics and Machine Learning Toolbox software)
sbiosampleerrorSample error based on error model and add noise to simulation data
sbioparameterciCompute confidence intervals for estimated parameters (requires Statistics and Machine Learning Toolbox)
sbiopredictionciCompute confidence intervals for model predictions (requires Statistics and Machine Learning Toolbox)
groupedData Table-like collection of data and metadata
EstimatedInfo objectObject containing information about estimated model quantities
LeastSquaresResults objectResults object containing estimation results from least-squares regression
OptimResults objectEstimation results object, subclass of LeastSquaresResults
NLINResults objectEstimation results object, subclass of LeastSquaresResults
ParameterConfidenceIntervalObject containing confidence interval results for estimated parameters
PredictionConfidenceIntervalObject containing confidence interval results for model predictions

Nonlinear Mixed-Effects Modeling

sbiofitmixedFit nonlinear mixed-effects model (requires Statistics and Machine Learning Toolbox software)
sbionlmefitEstimate nonlinear mixed effects using SimBiology models (requires Statistics and Machine Learning Toolbox software)
sbionlmefitsaEstimate nonlinear mixed effects with stochastic EM algorithm (requires Statistics and Machine Learning Toolbox software)
sbiosampleparametersGenerate parameters by sampling covariate model (requires Statistics and Machine Learning Toolbox software)
sbiosampleerrorSample error based on error model and add noise to simulation data
sbiofitstatusplotPlot status of sbionlmefit or sbionlmefitsa
CovariateModel objectDefine relationship between parameters and covariates
groupedData Table-like collection of data and metadata
EstimatedInfo objectObject containing information about estimated model quantities
NLMEResults objectResults object containing estimation results from nonlinear mixed-effects modeling

Deployment

exportExport SimBiology models for deployment and standalone applications
SimBiology.export.Model.simulateSimulate exported SimBiology model
SimBiology.export.Model.acceleratePrepare exported SimBiology model for acceleration
SimBiology.export.ModelExported SimBiology model object
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