SOSExperiment-class {rsbml} | R Documentation

## SOS Experiment

### Description

Implementation of `Experiment` for simulating SBML models using the SOS: (S)BML (O)DE (S)olver library.

### Details

The general workflow for running a simulation:

1. Create or import an SBML DOM.

2. Customize the model, for example by adding perturbation `Event`s.

3. Wrap the SBML DOM in a `SOSSubject`, e.g. `new("SOSSubject", dom)`.

4. Optionally construct a `SOSDesign` for running the experiment in batch over several sets of model parameter settings.

5. Optionally construct a `SOSProtocol` for specifying the time points and other parameters controlling the simulation.

6. Construct an instance of this class that groups the subject, design and protocol.

7. Run `simulate` on the `SOSExperiment`, optionally specifying the number of iterations and the random seed.

8. Analyze the returned `SOSResult`, perhaps starting by converting it to a time series with `as.ts` and making some plots.

### Objects from the Class

Objects can be created by calls of the form `new("SOSExperiment", ...)`.

### Slots

`protocol`:

  Object of class `SOSProtocol`, where the simulation parameters are specified.

`design`:

  Object of class `SOSDesign`, specifying model parameters for each run of a batch experiment.

`subject`:

  Object of class `SOSSubject`, containing the `Model` to be simulated.

`result`:

  Object of class `SOSResult` containing the result of the simulation.

### Extends

Class `Experiment`, directly.

### Methods

simulate

  `signature(object = "SOSExperiment")`: `simulate(object, nsim = 10, seed, ...)`: Simulates the SBML document in the `subject` slot according to the design points in `design` and parameters in `protocol` for `nsim` iterations, using `seed` as the random seed. Returns an instance of `SOSExperiment`, which now should include a `SOSResult` for analysis.

### 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

The `simulate` method on `SBMLDocument` is a shortcut, but most users will probably find the above approach most useful.

[Package rsbml version 2.48.0 Index]