matrix; each column
corresponds to a parameter in the model and each row should hold the
parameter settings for one run of the experiment.new("SOSDesign", data,
nrow, ncol, byrow, dimnames, ...). This is the same as initializing a
matrix..Data:"matrix", holding the
parameter settings. reactions:"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."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.signature(object = "SOSDesign"): gets the
reactions slot. signature(object = "SOSDesign"): sets the
reactions slot.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.
SOSExperiment, the container of this class, for
configuring and running a simulation.