3. Simulation Configuration.XML File

All properties of a simulation, including definitions of the initial population, fitness functions, replication and mutation operators, and sampling information, are defined in a single XML file.

The overall format of a configuration file is defined by the following structure:

<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
       xsi:noNamespaceSchemaLocation="santa.xsd">

    <!-- How many times should the simulation be run ?
         Optional (default = 1) -->
    <replicates>100</replicates>

    <simulation>
        <!-- Description of the genome: properties, example sequences, and features -->
        <genome>
            ...
        </genome>

        <!-- Definition of the initial population -->
        <population>
            ...
        </population>

        <!-- Description of the (default) fitness function -->
        <fitnessFunction>
            ...
        </fitnessFunction>

        <!-- Description of the (default) replicator -->
        <replicator>
            ...
        </replicator>

        <!-- Description of the (default) mutator -->
        <mutator>
            ...
        </mutator>

        <!-- Definition of a first epoch -->
        <epoch>
            <!-- A name for the epoch (used only to display simulator progress) -->
            <name>epoch 1</name>

            <!-- Duration of the epoch in number of generations -->
            <generations>1000</generations>

            <!-- Optionally, override the default fitness function, replicator, or mutator -->
            <fitnessFunction>
                 ...
            </fitnessFunction>

            <replicator>
                 ...
            </replicator>

            <mutator>
                 ...
            </mutator>
        </epoch>

        <!-- Optionally, additional epochs... -->
        <epoch>
            ...
        </epoch>

        <!-- Define when and how information must be sampled from the simulation -->
        <samplingSchedule>
            ...
        </samplingSchedule>
    </simulation>
</santa>

In the next subsections it is described how each of the variables in this configuration file can be edited to define different simulation scenarios.