MoBi Project — MoBiProject • ospsuite

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

Super classes

rSharp::NetObject -> DotNetWrapper -> 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

`MoBiProject$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: Underlying reference to the MoBi project in the simulation engine.
sourceFile: (Optional) File used to load the project

Returns

A new MoBiProject object.

`MoBiProject$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.

Returns

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.

`MoBiProject$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.

Returns

A named list of DataSet objects.

`MoBiProject$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.

Returns

A named list of MoBiModule objects.

`MoBiProject$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.

Returns

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

`MoBiProject$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.

Returns

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

`MoBiProject$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. Names that do not match any module in modulesNames raise an error.
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. Names that do not match any module in modulesNames raise an error.
settings: Optional, a SimulationSettings object defining the simulation settings. If NULL (default), the default simulation settings of the project will be used.

Returns

A SimulationConfiguration object.

`MoBiProject$print()`

Print the object to the console

Usage

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

Arguments

printClassProperties: Whether to print class properties.
...: Rest arguments.