Learn more about SimBiology

Method Reference

Alphabetical List

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Objects SimBiology objects Abstract Kinetic Laws Work with abstract kinetic law objects Compartments Work with compartment objects Configuration Sets Work with configuration set objects Events Work with event objects Kinetic Laws Create parameter objects and work with kinetic law objects Models Create SimBiology objects and work with model objects Parameters Work with parameter objects Pharmacokinetic Modeling Create SimBiology objects Reactions Create kinetic law and species objects and work with reaction objects Root Work with the root object Rules Work with rule objects SimData Methods for SimData objects Species Methods for species objects Units and Unit Prefixes Methods for unit and prefix objects Variants Methods for variant objects Using Object Methods Command-line syntax for using methods with SimBiology objects

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Objects

AbstractKineticLaw object	Kinetic law information in library
Compartment object	Options for compartments
Configset object	Solver settings information for model simulation
Event object	Store event information
KineticLaw object	Kinetic law information for reaction
Model object	Model and component information
Parameter object	Parameter and scope information
PKCompartment object	Used by PKModelDesign to create SimBiology model
PKData object	Define roles of data set columns
PKModelDesign object	Helper object to construct pharmacokinetic model
PKModelMap object	Define SimBiology model components roles
Reaction object	Options for model reactions
Root object	Hold models, unit libraries, and abstract kinetic law libraries
Rule object	Hold rule for species and parameters
SimData object	Simulation data storage
Species object	Options for compartment species
Unit object	Hold information about user-defined unit
UnitPrefix object	Hold information about user-defined unit prefix
Variant object	Store alternate component values

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Abstract Kinetic Laws

delete (any object)	Delete SimBiology object
display (any object)	Display summary of SimBiology object
get (any object)	Get object properties
set (any object)	Set object properties

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Compartments

addcompartment (model, compartment)	Create compartment object
addspecies (compartment)	Create species object and add to compartment object
copyobj (any object)	Copy SimBiology object and its children
delete (any object)	Delete SimBiology object
display (any object)	Display summary of SimBiology object
get (any object)	Get object properties
rename (compartment, parameter, species)	Rename object and update expressions
reorder (model, compartment)	Reorder component lists
set (any object)	Set object properties

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Configuration Sets

copyobj (any object)	Copy SimBiology object and its children
delete (any object)	Delete SimBiology object
display (any object)	Display summary of SimBiology object
set (any object)	Set object properties

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Events

copyobj (any object)	Copy SimBiology object and its children
delete (any object)	Delete SimBiology object
display (any object)	Display summary of SimBiology object
get (any object)	Get object properties
set (any object)	Set object properties

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Kinetic Laws

addparameter (model, kineticlaw)	Create parameter object and add to model or kinetic law object
copyobj (any object)	Copy SimBiology object and its children
delete (any object)	Delete SimBiology object
display (any object)	Display summary of SimBiology object
get (any object)	Get object properties
getparameters (kineticlaw)	Get specific parameters in kinetic law object
getspecies (kineticlaw)	Get specific species in kinetic law object
set (any object)	Set object properties
setparameter (kineticlaw)	Specify specific parameters in kinetic law object
setspecies (kineticlaw)	Specify species in kinetic law object

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Models

addcompartment (model, compartment)	Create compartment object
addconfigset (model)	Create configuration set object and add to model object
addevent (model)	Add event object to model object
addparameter (model, kineticlaw)	Create parameter object and add to model or kinetic law object
addreaction (model)	Create reaction object and add to model object
addrule (model)	Create rule object and add to model object
addvariant (model)	Add variant to model
copyobj (any object)	Copy SimBiology object and its children
delete (any object)	Delete SimBiology object
display (any object)	Display summary of SimBiology object
get (any object)	Get object properties
getadjacencymatrix (model)	Get adjacency matrix from model object
getconfigset (model)	Get configuration set object from model object
getstoichmatrix (model)	Get stoichiometry matrix from model object
getvariant (model)	Get variant from model
removeconfigset (model)	Remove configuration set from model
removevariant (model)	Remove variant from model
reorder (model, compartment)	Reorder component lists
set (any object)	Set object properties
setactiveconfigset (model)	Set active configuration set for model object
verify (model, variant)	Validate and verify SimBiology model

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Parameters

copyobj (any object)	Copy SimBiology object and its children
delete (any object)	Delete SimBiology object
display (any object)	Display summary of SimBiology object
get (any object)	Get object properties
rename (compartment, parameter, species)	Rename object and update expressions
set (any object)	Set object properties

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Pharmacokinetic Modeling

addCompartment (PKModelDesign)	Add compartment to PKModelDesign object
construct (PKModelDesign)	Construct SimBiology model from PKModelDesign object
get (any object)	Get object properties
PKCompartment object	Used by PKModelDesign to create SimBiology model
PKData object	Define roles of data set columns
PKModelDesign object	Helper object to construct pharmacokinetic model
PKModelMap object	Define SimBiology model components roles
set (any object)	Set object properties

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Reactions

addkineticlaw (reaction)	Create kinetic law object and add to reaction object
addproduct (reaction)	Add product species object to reaction object
addreactant (reaction)	Add species object as reactant to reaction object
copyobj (any object)	Copy SimBiology object and its children
delete (any object)	Delete SimBiology object
display (any object)	Display summary of SimBiology object
get (any object)	Get object properties
rmproduct (reaction)	Remove species object from reaction object products
rmreactant (reaction)	Remove species object from reaction object reactants
set (any object)	Set object properties

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Root

copyobj (any object)	Copy SimBiology object and its children
get (any object)	Get object properties
reset (root)	Delete all model objects from root object
set (any object)	Set object properties

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Rules

copyobj (any object)	Copy SimBiology object and its children
delete (any object)	Delete SimBiology object
display (any object)	Display summary of SimBiology object
get (any object)	Get object properties
set (any object)	Set object properties

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SimData

delete (any object)	Delete SimBiology object
display (any object)	Display summary of SimBiology object
get (any object)	Get object properties
getdata (SimData)	Get data from SimData object array
getsensmatrix (SimData)	Get 3-D sensitivity matrix from SimData array
resample (SimData)	Resample SimData object array onto new time vector
select (SimData)	Select data from SimData object
selectbyname (SimData)	Select data by name from SimData object array
set (any object)	Set object properties

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Species

copyobj (any object)	Copy SimBiology object and its children
delete (any object)	Delete SimBiology object
display (any object)	Display summary of SimBiology object
get (any object)	Get object properties
rename (compartment, parameter, species)	Rename object and update expressions
set (any object)	Set object properties

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Units and Unit Prefixes

delete (any object)	Delete SimBiology object
display (any object)	Display summary of SimBiology object
get (any object)	Get object properties
set (any object)	Set object properties

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Variants

addcontent (variant)	Append content to variant object
commit (variant)	Commit variant contents to model
copyobj (any object)	Copy SimBiology object and its children
delete (any object)	Delete SimBiology object
display (any object)	Display summary of SimBiology object
get (any object)	Get object properties
rmcontent (variant)	Remove contents from variant object
set (any object)	Set object properties
verify (model, variant)	Validate and verify SimBiology model

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Using Object Methods

Command-line syntax for using methods with SimBiology objects

Constructing (Creating) Objects Using Object Methods Help for Objects, Methods, and Properties

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Constructing (Creating) Objects

Create an object that is not referenced by a model using the constructor functions sbioabstractkineticlaw, sbiomodel, sbioparameter, sbioreaction, sbioroot, sbiorule, and sbiospecies.

ObjectName = ConstructorFunction(RequiredParameters,...
                                 'PropertyName',  PropertyValue')

To create objects referenced by a model, use the model object methods addconfigset, addmodel, addparameter, addreaction, addrule, and addspecies.

ObjectName = ModelName.Method(Arguments)

To create objects referenced by a reaction, use the reaction object methods addkineticlaw, addparameter, addproduct, and addreactant.

ObjectName = ReactionName.Method(Arguments)

Note that ObjectName is not a copy of the object, but a pointer to the created object.

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Using Object Methods

Using MATLAB function notation:

MethodName(ObjectName, arguments, ...)

Using object dot notation:

ObjectName.MethodName(arguments, ...)

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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.

simbiology

Methods — Alphabetical List

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