Documentation

SimBiology Functions

Modeling

Import Models

sbioloadproject Load project from file
sbmlimport Import SBML-formatted file
sbiowhos Show contents of project file, library file, or SimBiology root object
load Load variables from file into workspace

Build Models

sbiomodel Construct model object
sbioroot Return SimBiology root object
sbioreset Delete all model objects
sbioselect Search for objects with specified constraints
sbiolastwarning SimBiology last warning message
sbiolasterror SimBiology last error message
addcompartment Create compartment object
addspecies Create species object and add to compartment object within model object
addparameter Create parameter object and add to model or kinetic law object
addreaction Create reaction object and add to model object
addrule Create rule object and add to model object
addevent Add event object to model object
verify Validate and verify SimBiology model
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

Export Models

sbiosaveproject Save all models in root object
sbmlexport Export SimBiology model to SBML file

Extend Modeling Environment

sbioaddtolibrary Add to user-defined library
sbioremovefromlibrary Remove kinetic law, unit, or unit prefix from library
sbiocopylibrary Copy library to disk
sbioroot Return SimBiology root object
sbioreset Delete all model objects
sbioabstractkineticlaw Create kinetic law definition
sbiounit Create user-defined unit
sbiounitprefix Create user-defined unit prefix
sbioshowunits Show units in library
sbioshowunitprefixes Show unit prefixes in library
sbioconvertunits Convert unit and unit value to new unit
sbiounitcalculator Convert value between units
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

sbiovariant Construct variant object
addvariant Add variant to model
sbiosimulate Simulate SimBiology model
sbioaccelerate Prepare model object for accelerated simulations
sbiosampleparameters Generate parameters by sampling covariate model
sbiosampleerror Sample error based on error model and add noise to simulation data
createSimFunction Create SimFunction object
sbioplot Plot simulation results in one figure
sbiosubplot Plot simulation results in subplots
sbiotrellis Plot data or simulation results in trellis plot
sbioensemblerun Multiple stochastic ensemble runs of SimBiology model
sbioensembleplot Show results of ensemble run using 2-D or 3-D plots
sbioensemblestats Get statistics from ensemble run data
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

sbiosimulate Simulate SimBiology model
adddose Add dose object to model
sbiodose Construct dose object
sbioaccelerate Prepare model object for accelerated simulations
sbiosampleparameters Generate parameters by sampling covariate model
sbiosampleerror Sample error based on error model and add noise to simulation data
createSimFunction Create SimFunction object
sbioplot Plot simulation results in one figure
sbiosubplot Plot simulation results in subplots
sbiotrellis Plot data or simulation results in trellis plot
sbioensemblerun Multiple stochastic ensemble runs of SimBiology model
sbioensembleplot Show results of ensemble run using 2-D or 3-D plots
sbioensemblestats Get statistics from ensemble run data
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

sbiosimulate Simulate SimBiology model
sbioaccelerate Prepare model object for accelerated simulations
sbiosampleparameters Generate parameters by sampling covariate model
sbiosampleerror Sample error based on error model and add noise to simulation data
addconfigset Create configuration set object and add to model object
getconfigset Get configuration set object from model object
createSimFunction Create SimFunction object
sbioplot Plot simulation results in one figure
sbiosubplot Plot simulation results in subplots
sbiotrellis Plot data or simulation results in trellis plot
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

sbiosimulate Simulate SimBiology model
sbioaccelerate Prepare model object for accelerated simulations
sbiosampleparameters Generate parameters by sampling covariate model
sbiosampleerror Sample error based on error model and add noise to simulation data
addconfigset Create configuration set object and add to model object
getconfigset Get configuration set object from model object
createSimFunction Create SimFunction object
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

sbionmimport Import NONMEM-formatted data
sbionmfiledef NONMEM file definition object for sbionmimport
sbiotrellis Plot data or simulation results in trellis plot
GroupedData object Table-like collection of data and metadata

Nonlinear Regression

groupedData Create groupedData object
sbiofit Perform nonlinear least-squares regression
sbionlinfit Perform nonlinear least-squares regression using SimBiology models
sbioparamestim Perform parameter estimation
sbiosampleparameters Generate parameters by sampling covariate model
sbiosampleerror Sample error based on error model and add noise to simulation data
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

groupedData Create groupedData object
sbiofitmixed Fit nonlinear mixed-effects model
sbionlmefit Estimate nonlinear mixed effects using SimBiology models
sbionlmefitsa Estimate nonlinear mixed effects with stochastic EM algorithm
sbiosampleparameters Generate parameters by sampling covariate model
sbiosampleerror Sample error based on error model and add noise to simulation data
sbiofitstatusplot Plot status of sbionlmefit or sbionlmefitsa
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

export Export SimBiology models for deployment and standalone applications
SimBiology.export.Model.simulate Simulate exported SimBiology model
SimBiology.export.Model.accelerate Prepare exported SimBiology model for acceleration
SimBiology.export.Model Exported SimBiology model object
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