SOSExperiment-class          package:rsbml          R Documentation

_S_O_S _E_x_p_e_r_i_m_e_n_t

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

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

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

     The general workflow for running a simulation:

        1.  Create or import an SBML 'Model'.

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

        3.  Wrap the model in a 'SOSSubject', e.g. 'new("SOSSubject",
           model)'.

        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.

_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("SOSExperiment",
     ...)'.

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


     '_p_r_o_t_o_c_o_l': Object of class 'SOSProtocol', where  the simulation
          parameters are specified.

     '_d_e_s_i_g_n': Object of class 'SOSDesign',  specifying model
          parameters for each run of a batch experiment.

     '_s_u_b_j_e_c_t': Object of class 'SOSSubject', containing the 'Model' to
          be simulated.

     '_r_e_s_u_l_t': Object of class 'SOSResult' containing the result of the
          simulation. 

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

     Class 'Experiment', directly.

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


     _s_i_m_u_l_a_t_e 'signature(object = "SOSExperiment")': 'simulate(object,
          nsim = 10, seed, ...)': Simulates the model 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.

_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:

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

