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Functions in SimBiology

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  • 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

    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

    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

    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

    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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