main configuration

Host Organs

In the hostOrgans section all host organs that are required for the configuration are parametrized. It is a mandatory part of the main configuration section.
The host organ is structured as follows: 

    <hostOrgan organID="name">
        <name> </name>
        <dormancy distRef="distID"/>
        <lateDormancy>
            <size distRef="distID"/>
            <duration distRef="distID"/>
        </lateDormancy>
        <printHostOrgan> </printHostOrgan>
    </hostOrgan>

The mandatory attribute organID is the name under which it will be referenced in the configuration file. This name has to be unique throughout the whole configuration file. The name has to start with a letter and can consist of letters, digits and underscores.

name The name of the host organ. (Please do not confuse this with organID)
dormancy optional Defines the duration of the dormancy as a distribution (Gaussian or uniform). Refer to the corresponding distribution by its distID. The values in the distribution have to be given in days.
lateDormancy optional Optional. Defines the start size and the duration of the late dormancy as distributions. If a late dormancy is defined both child elements (size and duration) have to be stated. Refer to the corresponding distributions by their distID. The size is given in number of cells and the duration in days.
printHostOrgan optional Defines whether a separate output file shall be created for this host organ. In this output file only the metastases that are situated in the defined host organ are included.
Valid values: true or false
If not stated, no separate output file will be created.



Sample configuration of the hostOrgans section

In this sample configuration of a hostOrgans section four different host organs are defined: the colon, the blood_vessels, the lung and the liver. The dormancy, size and duration parameter refer to the corresponding distributions that were defined in the distributions section. A separate output file is created for the lung but not for the other host organs. 

    <distributions>
        <gaussianDistribution distID="dormancy">
            <!-- given in days -->
            <mean>21</mean>
            <stdDev>7</stdDev>
        </gaussianDistribution>

        <uniformDistribution distID="ldSize">
            <!-- given in number of cells -->
            <min>10</min>
            <max>100</max>
        </uniformDistribution>

        <gaussianDistribution distID="ldTime">
            <!-- given in days -->
            <mean>21</mean>
            <stdDev>7</stdDev>
        </gaussianDistribution>
    </distributions>

    <hostOrgans>
        <hostOrgan organID="colon">
            <name>colon (primary tumor)</name>
        </hostOrgan>

        <hostOrgan organID="blood_vessels">
            <name>blood</name>
        </hostOrgan>

        <hostOrgan organID="lung">
            <name>lung</name>
            <dormancy distRef="dormancy"/>
            <printHostOrgan>true</printHostOrgan>
        </hostOrgan>

        <hostOrgan organID="liver">
            <name>lung</name>
            <lateDormancy>
                <size distRef="ldSize"/>
                <duration distRef="ldTime"/>
            </lateDormancy>
        </hostOrgan>
    </hostOrgans>