MoBi Project

A MoBi project, containing modules, building blocks, simulations, etc.

Value

A new MoBiProject object.

A Simulation object, if the simulation with the given name is present in the project. NULL if no such simulation is available and stopIfNotFound = FALSE.

A named list of DataSet objects.

A named list of MoBiModule objects.

An object of the type BuildingBlock. NULL if the project does not contain such an individual and stopIfNotFound = FALSE.

A named list of objects of the type BuildingBlock. If stopIfNotFound = FALSE, only the expression profiles that are present in the project are returned.

A SimulationConfiguration object.

Super classes

rSharp::NetObject -> ospsuite::DotNetWrapper -> ospsuite::ObjectBase -> MoBiProject

Active bindings

sourceFile

Path to the file the project was loaded from (read-only)

simulationNames

Names of the simulations that are present in the project (read-only)

moduleNames

Names of the modules that are present in the project (read-only)

parameterIdentificationNames

Names of the parameter identifications that are present in the project (read-only)

individualNames

Names of the individuals that are present in the project (read-only)

expressionProfilesNames

Names of the expression profiles that are present in the project (read-only)

defaultSimulationSettings

Default simulation settings of the project (read-only)

Methods

Public methods

• MoBiProject$new()

• MoBiProject$getSimulation()

• MoBiProject$getObservedData()

• MoBiProject$getModules()

• MoBiProject$getIndividual()

• MoBiProject$getExpressionProfiles()

• MoBiProject$createSimulationConfiguration()

• MoBiProject$print()

Inherited methods

• rSharp::NetObject$.printClass()
• rSharp::NetObject$.printLine()
• rSharp::NetObject$call()
• rSharp::NetObject$get()
• rSharp::NetObject$getFields()
• rSharp::NetObject$getMemberSignature()
• rSharp::NetObject$getMethods()
• rSharp::NetObject$getProperties()
• rSharp::NetObject$getStaticFields()
• rSharp::NetObject$getStaticMethods()
• rSharp::NetObject$getStaticProperties()
• rSharp::NetObject$set()

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Method new()

Initialize a new instance of the class

Should not be directly used. Instead, use function loadMoBiProject() to load a project.

Usage

MoBiProject$new(netObject, sourceFile = NULL)

Arguments

netObject

Reference to NetObject .NET MoBi-project object

sourceFile

(Optional) File used to load the project

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Method getSimulation()

Load a simulation from the project

Usage

MoBiProject$getSimulation(simulationName, stopIfNotFound = TRUE)

Arguments

simulationName

Name of the simulation.

stopIfNotFound

If TRUE (default), an error is thrown if the simulation with the given name is not present in the project. If FALSE, NULL is returned.

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Method getObservedData()

Get observed data present in the project.

Usage

MoBiProject$getObservedData(dataSetNames = NULL, stopIfNotFound = TRUE)

Arguments

dataSetNames

Optional. List of names of observed data sets to retrieve from project. If NULL, all data sets are returned.

stopIfNotFound

If TRUE (default), an error is thrown if any of the specified data sets is not present in the project. Otherwise, NULL is returned for the data sets that are not found.

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Method getModules()

Get modules present in the project.

Usage

MoBiProject$getModules(names = NULL, stopIfNotFound = TRUE)

Arguments

names

Optional. Names of the modules to retrieve. If NULL, all modules are returned.

stopIfNotFound

If TRUE (default), an error is thrown if any of the specified modules is not present in the project. Otherwise, NULL is returned for the modules that are not found.

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Method getIndividual()

Get a specified individual from the project

Usage

MoBiProject$getIndividual(name, stopIfNotFound = TRUE)

Arguments

name

Name of the individual

stopIfNotFound

If TRUE (default), an error is thrown if the specified individual is not present in the project.

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Method getExpressionProfiles()

Get specified expression profiles from the project.

Usage

MoBiProject$getExpressionProfiles(names, stopIfNotFound = TRUE)

Arguments

names

List of names of the expression profiles to retrieve.

stopIfNotFound

If TRUE (default), an error is thrown if any of the specified expression profiles is not present in the project.

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Method createSimulationConfiguration()

Create a simulation configuration.

Usage

MoBiProject$createSimulationConfiguration(
  modulesNames,
  individualName = NULL,
  expressionProfilesNames = NULL,
  selectedInitialConditions = NULL,
  selectedParameterValues = NULL,
  settings = NULL
)

Arguments

modulesNames

A list of the modules from which to create the simulation. All defined modules must be present in the project. The order of module names defines the order in which the modules will be combined to a simulation!

individualName

Optional, name of the individual.

expressionProfilesNames

Optional, list of expression profiles to apply to the simulation.

selectedInitialConditions

By default, the first Initial Conditions (IC) building block (BB) of each module will be selected. If a module has multiple IC BBs, it is possible to specify which IC BB to apply by providing a named list, where the name should be the name of the module and the value the name of the IC BB. By explicitly setting the value for a specific module to NULL, no IC BB from the specified module will be applied. If the list contains a module name that is not part of the provided modules, it will be ignored.

selectedParameterValues

By default, the first Parameter Values (PV) building block (BB) of each module will be selected. If a module has multiple PV BBs, it is possible to specify which PV BB to apply by providing a named list, where the name should be the name of the module and the value the name of the PV BB. By explicitly setting the value for a specific module to NULL, no PV BB from the specified module will be applied. If the list contains a module name that is not part of the provided modules, it will be ignored.

settings

Optional, a SimulationSettings object defining the simulation settings. If NULL (default), the default simulation settings of the project will be used.

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Method print()

Print the object to the console

Usage

MoBiProject$print(printClassProperties = FALSE, ...)

Arguments

printClassProperties

Whether to print class properties.

...

Rest arguments.