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Property Reference

Alphabetical List

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Abstract Kinetic Law Properties for abstract kinetic law objects Compartments Properties for compartment objects Configuration Sets Properties for configuration set objects Events Properties for event objects Kinetic Laws Properties for kinetic law objects Models Properties for model objects Parameters Properties for parameter objects PKCompartment Properties for parameter objects PKData Properties for parameter objects PKModelDesign Properties for parameter objects PKModelMap Properties for parameter objects Reactions Properties for reaction objects Root Properties for the root object Rules Properties for rule objects SimData Properties for SimData objects Species Properties for species objects Unit Properties for unit objects Unit Prefix Properties for unit objects Variant Properties for variant objects Using Object Properties Command-line syntax for entering and retrieving property values

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Abstract Kinetic Law

Annotation	Store link to URL or file
Expression	Expression to determine reaction rate equation
Name	Specify name of object
Notes	HTML text describing SimBiology object
ParameterVariables	Parameters in kinetic law definition
Parent	Indicate parent object
SpeciesVariables	Species in abstract kinetic law
Tag	Specify label for SimBiology object
Type	Display top-level SimBiology object type
UserData	Specify data to associate with object

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Compartments

Annotation	Store link to URL or file
Capacity	Compartment capacity
CapacityUnits	Compartment capacity units
Compartments	Array of compartments in model or compartment
ConstantCapacity	Specify variable or constant compartment capacity
Name	Specify name of object
Notes	HTML text describing SimBiology object
Owner	Owning compartment
Parent	Indicate parent object
Species	Array of species in compartment object
Tag	Specify label for SimBiology object
Type	Display top-level SimBiology object type
UserData	Specify data to associate with object

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Configuration Sets

Active	Indicate object in use during simulation
CompileOptions	Dimensional analysis and unit conversion options
Name	Specify name of object
Notes	HTML text describing SimBiology object
RuntimeOptions	Options for logged species
SensitivityAnalysisOptions	Specify sensitivity analysis options
SolverOptions	Specify model solver options
SolverType	Select solver type for simulation
StopTime	Set stop time for simulation
StopTimeType	Specify type of stop time for simulation
TimeUnits	Show stop time units for simulation
Type	Display top-level SimBiology object type

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Events

Properties for event objects

Active	Indicate object in use during simulation
Annotation	Store link to URL or file
EventFcns	Event expression
Name	Specify name of object
Notes	HTML text describing SimBiology object
Parent	Indicate parent object
Tag	Specify label for SimBiology object
Trigger	Event trigger
Type	Display top-level SimBiology object type
UserData	Specify data to associate with object

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Kinetic Laws

Annotation	Store link to URL or file
Expression	Expression to determine reaction rate equation
KineticLawName	Name of kinetic law applied to reaction
Name	Specify name of object
Notes	HTML text describing SimBiology object
Parameters	Array of parameter objects
ParameterVariableNames	Cell array of reaction rate parameters
ParameterVariables	Parameters in kinetic law definition
Parent	Indicate parent object
SpeciesVariableNames	Cell array of species in reaction rate equation
SpeciesVariables	Species in abstract kinetic law
Tag	Specify label for SimBiology object
Type	Display top-level SimBiology object type
UserData	Specify data to associate with object

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Models

Annotation	Store link to URL or file
Compartments	Array of compartments in model or compartment
Events	Contain all event objects
Models	Contain all model objects
Name	Specify name of object
Notes	HTML text describing SimBiology object
Parameters	Array of parameter objects
Parent	Indicate parent object
Reactions	Array of reaction objects
Rules	Array of rules in model object
Tag	Specify label for SimBiology object
Type	Display top-level SimBiology object type
UserData	Specify data to associate with object

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Parameters

Annotation	Store link to URL or file
ConstantValue	Specify variable or constant parameter value
Name	Specify name of object
Notes	HTML text describing SimBiology object
Parent	Indicate parent object
Tag	Specify label for SimBiology object
Type	Display top-level SimBiology object type
UserData	Specify data to associate with object
Value	Assign value to parameter object
ValueUnits	Parameter value units

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PKCompartment

DosingType	Drug dosing type in compartment
EliminationType	Drug elimination type from compartment
HasResponseVariable	Compartment drug concentration reported
Name	Specify name of object

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PKData

CovariateLabels	Identify covariate columns in data set
DataSet	Dataset object containing imported data
DependentVarLabel	Identify dependent variable column in data set
DoseLabel	Identify dose column in data set
GroupID	Integer identifying each group in data set
GroupLabel	Identify group column in data set
GroupNames	Unique values from GroupLabel in data set
IndependentVarLabel	Identify independent variable column in data set
RateLabel	Identify rate of infusion column in data set

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PKModelDesign

PKCompartments

Hold compartments in PK model

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PKModelMap

Dosed	Dosed object name
DosingType	Drug dosing type in compartment
Estimated	Names of parameters to estimate
Observed	Measured response object name

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Reactions

Active	Indicate object in use during simulation
Annotation	Store link to URL or file
KineticLaw	Show kinetic law used for ReactionRate
Name	Specify name of object
Notes	HTML text describing SimBiology object
Parent	Indicate parent object
Products	Array of reaction products
Reactants	Array of reaction reactants
Reaction	Reaction object reaction
ReactionRate	Reaction rate equation in reaction object
Reversible	Specify whether reaction is reversible or irreversible
Stoichiometry	Species coefficients in reaction
Tag	Specify label for SimBiology object
Type	Display top-level SimBiology object type
UserData	Specify data to associate with object

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Root

BuiltInLibrary	Library of built-in components
Models	Contain all model objects
Type	Display top-level SimBiology object type
UserDefinedLibrary	Library of user-defined components

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Rules

Active	Indicate object in use during simulation
Annotation	Store link to URL or file
Name	Specify name of object
Notes	HTML text describing SimBiology object
Parent	Indicate parent object
Rule	Specify species and parameter interactions
RuleType	Specify type of rule for rule object
Tag	Specify label for SimBiology object
Type	Display top-level SimBiology object type
UserData	Specify data to associate with object

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SimData

Data	Store simulation data
DataCount	Numbers of species, parameters, sensitivities
DataInfo	Metadata labels for simulation data
DataNames	Show names in SimData object
ModelName	Name of model simulated
Name	Specify name of object
Notes	HTML text describing SimBiology object
RunInfo	Information about simulation
Time	Show simulation time steps
TimeUnits	Show stop time units for simulation
UserData	Specify data to associate with object

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Species

Annotation	Store link to URL or file
BoundaryCondition	Indicate species boundary condition
ConstantAmount	Specify variable or constant species amount
InitialAmount	Species initial amount
InitialAmountUnits	Species initial amount units
Name	Specify name of object
Notes	HTML text describing SimBiology object
Parent	Indicate parent object
Tag	Specify label for SimBiology object
Type	Display top-level SimBiology object type
UserData	Specify data to associate with object

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Unit

Annotation	Store link to URL or file
Composition	Unit composition
Multiplier	Relationship between defined unit and base unit
Name	Specify name of object
Notes	HTML text describing SimBiology object
Offset	Unit composition modifier
Parent	Indicate parent object
Tag	Specify label for SimBiology object
Type	Display top-level SimBiology object type
UserData	Specify data to associate with object

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Unit Prefix

Annotation	Store link to URL or file
Exponent	Exponent value of unit prefix
Name	Specify name of object
Notes	HTML text describing SimBiology object
Parent	Indicate parent object
Tag	Specify label for SimBiology object
Type	Display top-level SimBiology object type
UserData	Specify data to associate with object

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Variant

Active	Indicate object in use during simulation
Annotation	Store link to URL or file
Content	Contents of variant object
Name	Specify name of object
Notes	HTML text describing SimBiology object
Parent	Indicate parent object
Tag	Specify label for SimBiology object
Type	Display top-level SimBiology object type
UserData	Specify data to associate with object

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Using Object Properties

Command-line syntax for entering and retrieving property values.

Entering Property Values Use either MATLAB functions or object dot notation to enter or change property values. Retrieving Property Values Use either MATLAB functions or object dot notation to get property values. Help for Objects, Methods, and Properties Use the command sbiohelp to get information about properties.

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Entering Property Values

Enter or change a single property value using dot notation.

ObjectName.PropertyName = PropertyValue

Enter or change one or more property values using the MATLAB function set.

set(ObjectName, 'Propertyname', PropertyValue, ...)

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Retrieving Property Values

Retrieve a single property value using dot notation.

PropertyValue = ObjectName.PropertyName

Retrieve one or more property values using the MATLAB function get.

PropertyValue(s) = get(ObjectName, 'PropertyName', ...)

Retrieve one or more property values using the object method get.

PropertyValue(s) = ObjectName.get('PropertyName', ...)

List or retrieve all property values using one of the following commands:

get(ObjectName)
AllPropertyValues = get(ObjectName)

ObjectName.get

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Help for Objects, Methods, and Properties

Display information for SimBiology object methods and properties in the MATLAB Command Window.

help sbio	Display a list of functions and methods.
help FunctionName	Display function information.
sbiohelp('MethodName')	Display method information.
sbiohelp('PropertyName')	Display property information.

verify (model, variant)

Properties — Alphabetical List

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