SOSDesign-class: SOSDesign

In rsbml: R support for SBML, using libsbml

Description

Specifies the reaction names and their parameter settings for each run in a batch experiment. It extends matrix; each column corresponds to a parameter in the model and each row should hold the parameter settings for one run of the experiment.

Details

It is often desirable to explore the state space of a model by adjusting its initial parameter settings. One could do this by modifying the model itself for each experiment, but this class aims to provide a more convenient and systematic means of running experiments in batch, over a range of parameter settings. The results of the experiment will then contain the output from each run, which may then be compared.

The design is specified as a matrix, and each column in the matrix should correspond to a parameter defined in an SBML model. The column names should identify the parameters. These are not to be confused with the simulation parameters specified in SOSProtocol, which control how the simulation is executed. These should be and are designed to be kept constant across the runs.

There are two different types of parameters: global and local (reaction) parameters. Global parameters may correspond to a Species quantity, Compartment size, or model-level Parameter value. These should be identified in the column names by the id of the corresponding SBML element. The element in the reactions slot for one of these parameters should be the empty string.

The second type of parameter specifies the value of a Parameter element within the KineticLaw of a reaction. These should be named by the id of the Parameter. They also should be namespaced by the containing Reaction id, which is stored in the corresponding element of the reactions slot.

Objects from the Class

Objects can be created by calls of the form new("SOSDesign", data, nrow, ncol, byrow, dimnames, ...). This is the same as initializing a matrix.

Slots

.Data:

Object of class "matrix", holding the parameter settings.

reactions:

Object of class "character" of length the number of columns, holding the reaction IDs for parameters local to a reaction (i.e. KineticLaw Parameters). For global parameters, the corresponding value should be the empty string.

Extends

Class "matrix", from data part. Class "ExperimentDesign", directly. Class "array", by class "matrix", distance 2. Class "structure", by class "matrix", distance 3. Class "vector", by class "matrix", distance 4, with explicit coerce.

Methods

reactions

signature(object = "SOSDesign"): gets the reactions slot.

reactions<-

signature(object = "SOSDesign"): sets the reactions slot.

Author(s)

Michael Lawrence

References

See http://www.tbi.univie.ac.at/~raim/odeSolver/ for more information on the SBML ODE Solver library.

See Also

SOSExperiment, the container of this class, for configuring and running a simulation.

rsbml documentation built on Nov. 8, 2020, 8:09 p.m.