XML-Schema Documentation

Go to the XML-Tag Index page for direct access. You can download the complete XML-Schema here and various sample configurations at the sample configurations page.

The configuration consists of of two parts:
  • the configuration of simulation setup that shall be simulated (mostly referred to as main configuration file) and
  • the configuration of technical details of the simulation (mostly referred to as technical file)

If not explicitly stated otherwise, all time values are given in days.


Technical configuration

The technical configuration file is structured as follows: 
    <configuration>

        <technical>
            <duration> </duration>
            <timeStepsForSaving> </timeStepsForSaving>
            <debug-mode> </debug-mode>
        </technical>

    </configuration>
duration Defines the time span the simulation shall cover. Please also adjust the value for the tag timeStepsForSaving accordingly when you increase or decrease the duration.
Unit: days
timeStepsForSaving Defines the interval for saving the current status of the simulated system. This value, together with the duration, directly influences the size of the resulting output file. For fast growing tumours use small values to keep track of the progress. For slowly growing tumours user bigger values (e.g. 10-30) to avoid unnecessary big output files.
Unit: days
debug-mode Enables or disables the debug mode. In the debug mode more information are printed during the simulation. Valid values are true or false.



Main configuration

The main configuration file is structured as follows: 
    <configuration>

        <functions></functions>

        <distributions></distributions>

        <hostOrgans></hostOrgans>

        <compartmentTypes></compartmentTypes>

        <compartments></compartments>

        <globalTreatments></globalTreatments>

    </configuration>

The tag <metastatic-Cascade> is the main tag and surrounds the whole configuration. It includes the sections functions, distributions, hostOrgans, compartmentTypes, compartments and the optional globalTreatments which are described in detail below.

Functions

In the functions section the growth functions (Constant, Linear, Exponential, Power, Logarithmic or Gompertz) and the colonization rates are defined. For parametrization details of each function or an example configuration of the functions section please see the function page.

Distributions

In the distributions section the distributions (Gaussian or Uniform) are defined. For parametrization details of each distribution or an example configuration of the distributions section please see the distribution page.

Host organs

In the hostOrgans section the different host organs for the primary tumor and metastases are defined. Please note that the bloodstream is also handled as an organ. For parametrization details please see the host organ page.

Compartment types

In the compartmentTypes section the characteristics of a discrete compartment are defined in a discreteCompartmentType element including the set off possible event actions that may occur in a discrete compartment. By using compartment types the same characteristics can be applied for multiple discrete compartments. For parametrization details please see the compartment types and event actions page.

Compartments

In the compartments section the initial compartments that are present at the start of the simulation are defined. At least the primary tumor has to be defined. Mostly also the bloodstream is defined in this section. Metastases are not defined in this section since they are created during the course of the simulation according to the parametrized characteristics. For parametrization details please see the compartments page.

Global Treatments

In the globalTreatments section therapies such as chemotherapy, external beam radiation, radioimmunotherapy and radioembolization are parametrized. For details please see the global treatments page.