Outline

The program SBMLevolver has been written entirely in C/C++ and can be used from the commandline (details on the usage are given in the next section). The program has been implemented as a set of modules or classes. The main modules include the user interface, population management, fitness evaluation, fitting of model parameters, and the creation of new models via mutation and recombination. An overview of the classes is given here.

These are the main module classes:

• BuildingBlocks

  : stores and provides the elements from which the models are build

• CentralControl

  : starts and stops the program, provides user interface

• Individual

  : encapsulates a model together with its additional attributes and methods

• Mutator

  : generates new models by mutation and recombination

• ObjectiveFunction

  : stores the evolutionary objective and provides functions to calculate the fitness of a model regarding this objective

• ParameterFitter

  : fits model parameters w.r.t. the given objective

• ParamObj

  : stores and provides all parameters of the current run

• Population

  : handles a population of models, manages selection and reproduction

• RandomNumberGenerator

  : facilitates the generation of random numbers

• sbmltools

  : contains all methods manipulating SBML structures