Documentation

SimBiology Classes

Modeling

Build Models

Model object Model and component information
Compartment object Options for compartments
Species object Options for compartment species
Parameter object Parameter and scope information
Reaction object Options for model reactions
KineticLaw object Kinetic law information for reaction
Rule object Hold rule for species and parameters
Event object Store event information
Root object Hold models, unit libraries, and abstract kinetic law libraries
PKModelDesign object Helper object to construct pharmacokinetic model
PKCompartment object Used by PKModelDesign to create SimBiology model
PKModelMap object Define SimBiology model components' roles
construct Construct SimBiology model from PKModelDesign object
addCompartment Add compartment to PKModelDesign object

Extend Modeling Environment

Root object Hold models, unit libraries, and abstract kinetic law libraries
AbstractKineticLaw object Kinetic law information in library
Unit object Hold information about user-defined unit
UnitPrefix object Hold information about user-defined unit prefix

Simulation

Simulate Responses to Biological Variability

SimData object Simulation data storage
Configset object Solver settings information for model simulation
SolverOptions Specify model solver options
RuntimeOptions Options for logged species
CompileOptions Dimensional analysis and unit conversion options
SimFunction object Function-like interface to execute SimBiology models
SimFunctionSensitivity object SimFunctionSensitivity object, subclass of SimFunction object

Simulate Responses to Different Doses

SimData object Simulation data storage
ScheduleDose object Define drug dosing protocol
RepeatDose object Define drug dosing protocol
Configset object Solver settings information for model simulation
SolverOptions Specify model solver options
RuntimeOptions Options for logged species
CompileOptions Dimensional analysis and unit conversion options
SimFunction object Function-like interface to execute SimBiology models
SimFunctionSensitivity object SimFunctionSensitivity object, subclass of SimFunction object

Scan Parameter Ranges

SimData object Simulation data storage
Configset object Solver settings information for model simulation
SolverOptions Specify model solver options
RuntimeOptions Options for logged species
CompileOptions Dimensional analysis and unit conversion options
SimFunction object Function-like interface to execute SimBiology models
SimFunctionSensitivity object SimFunctionSensitivity object, subclass of SimFunction object

Calculate Sensitivities

SensitivityAnalysisOptions Specify sensitivity analysis options
SimData object Simulation data storage
Configset object Solver settings information for model simulation
SolverOptions Specify model solver options
RuntimeOptions Options for logged species
CompileOptions Dimensional analysis and unit conversion options
SimFunction object Function-like interface to execute SimBiology models
SimFunctionSensitivity object SimFunctionSensitivity object, subclass of SimFunction object

Estimation

Import Data

GroupedData object Table-like collection of data and metadata

Nonlinear Regression

GroupedData object Table-like collection of data and metadata
EstimatedInfo object Object containing information about estimated model quantities
LeastSquaresResults object Results object containing estimation results from least-squares regression
OptimResults object Estimation results object, subclass of LeastSquaresResults
NLINResults object Estimation results object, subclass of LeastSquaresResults

Nonlinear Mixed-Effects Modeling

CovariateModel object Define relationship between parameters and covariates
GroupedData object Table-like collection of data and metadata
EstimatedInfo object Object containing information about estimated model quantities
NLMEResults object Results object containing estimation results from nonlinear mixed-effects modeling

Deployment

SimBiology.export.Model Exported SimBiology model object
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