SOSDesign-class            package:rsbml            R Documentation

_S_O_S_D_e_s_i_g_n

_D_e_s_c_r_i_p_t_i_o_n:

     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.

_D_e_t_a_i_l_s:

     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.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

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

_S_l_o_t_s:


     '._D_a_t_a': Object of class '"matrix"', holding the parameter
          settings. 

     '_r_e_a_c_t_i_o_n_s': Object of class '"character"' of length the number of
          columns, holding the reaction IDs for parameters local to a
          reaction (i.e. 'KineticLaw' 'Parameter's). For global
          parameters, the corresponding value should be the empty
          string.

_E_x_t_e_n_d_s:

     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.

_M_e_t_h_o_d_s:


     _r_e_a_c_t_i_o_n_s 'signature(object = "SOSDesign")': gets the 'reactions'
          slot. 

     _r_e_a_c_t_i_o_n_s<- 'signature(object = "SOSDesign")': sets the
          'reactions' slot.

_A_u_t_h_o_r(_s):

     Michael Lawrence

_R_e_f_e_r_e_n_c_e_s:

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

_S_e_e _A_l_s_o:

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

