main configuration

Compartments

In the compartments section all compartments that are already existing at the start of the simulation are defined. This will most probably be the primary tumor and the blood stream. Metastases are not defined in this section since they are created during the course of the simulation according to the parametrized characteristics. The compartments section is a mandatory part of the main configuration section. Following compartments can be parametrized:

Every compartment has the mandatory attribute compartmentID which 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.

You will find an example for the compartments section with different defined compartments at the bottom of the page.

Continuous compartment

The continuous compartment is structured as follows. Please note that all elements have to be stated in exactly the same order as listed below.

    <continuousCompartment compartmentID="name">
        <hostOrgan organRef="organID"/>
        <successor compartmentRef="compartmentID"/>
        <isPrimaryTumor>true</isPrimaryTumor>
        <resectionTime> </resectionTime>
        <remnantFraction> </remnantFraction>
        <name> </name>
        <growthFunction functionRef="functionID"/>
        <colonizationRate functionRef="functionID"/>
    </continuousCompartment>
hostOrgan The host organ in which compartment will be situated in. Refers to a beforehand defined host organ.
successor optional The successor of the compartment to were cells are spread (mostly the blood stream). If not stated, the compartment will not be able to spread metastases. Refers to a beforehand or later defined compartment.
isPrimaryTumor optional Tags this compartment as the primary tumor. Can be used only once in the complete list of compartments.
resectionTime optional The time point when this compartment shall be resected. Unit: days
remnantFraction optional The fraction of cells that is/can not be removed by the surgeons during resection of the primary tumor and therefore remains in the tissue. If no resection time is stated, then this parameter will have no effect. Has to be stated in the interval [0,1] (e.g. 0.001 if 0.1% of the cells remain in the tissue).
name The name of the compartment. (Please do not confuse this with compartmentID)
growthFunction The growth function of the compartment. Refers to a beforehand defined function.
colonizationRate optional Optional. The colonization rate of the compartment. If not stated, the compartment will not spread metastases. Refers to a beforehand defined colonization rate.


Discrete compartment

The discrete compartment is structured as follows. Please note that all elements have to be stated in exactly the same order as listed below.

    <discreteCompartment compartmentID="name">
        <hostOrgan organRef="organID"/>
        <successor compartmentRef="compartmentID"/>
        <isPrimaryTumor>true</isPrimaryTumor>
        <resectionTime> </resectionTime>
        <remnantFraction> </remnantFraction>
        <startSize> </startSize>
        <discreteCompartmentType typeRef="typeID" />
        <localTreatments> </localTreatments>
    </discreteCompartment>
hostOrgan The host organ in which compartment will be situated in. Refers to a beforehand defined host organ.
successor optional The successor of the compartment to were cells are spread (mostly the blood stream). If not stated, the compartment will not be able to spread metastases. Refers to a beforehand or later defined compartment.
isPrimaryTumor optional Tags this compartment as the primary tumor. Can be used only once in the complete list of compartments.
resectionTime optional The time point when this compartment shall be resected. Unit: days
remnantFraction optional The fraction of cells that is/can not be removed by the surgeons during resection of the primary tumor and therefore remains in the tissue. If no resection time is stated, then this parameter will have no effect. Has to be stated in the interval [0,1] (e.g. 0.001 if 0.1% of the cells remain in the tissue).
startSize optional The number of cells the compartment will start. If not stated the initial number of cells will be zero. Unit: number of cells
discreteCompartmentType The compartment type of the discrete compartment where its characteristics are defined. Refers to a beforehand defined discrete compartment type.
localTreatments optional If the characteristics of the discrete compartment change during the course of the simulation, for instance due to medication/treatment, than further discrete compartment types can be applied for this compartment in the localTreatments section. Please see the local treatments page for details.



Sample configuration of the compartmentTypes section

In this sample configuration of a compartments section two different compartments are defined: the primary_tumor and the blood. The blood compartment has no successor. Cells leave the compartment by the transferToNewContinuousCompartment event action. Due to e.g. medication that is given for a time span of 200 days the probability for cell death in the blood compartment is increased. Therefore, for this time span another discrete compartment type is applied to the blood compartment. 

    <compartmentTypes>
        <discreteCompartmentType typeID="blood_Type">
            <name>blood stream</name>
            <eventActions>
                <cellDeath>
                    <name>cell death</name>
                    <generationInfo>
                        <meanTimeToNextEvent functionRef="identity"/>
                        <distribution distRef="normal"/>
                        <probability>0.8</probability>
                    </generationInfo>
                </cellDeath>
                <transferToNewContinuousCompartment>
                    <name>create lung metastasis</name>
                    <generationInfo>
                        <meanTimeToNextEvent functionRef="identity"/>
                        <distribution distRef="normal"/>
                        <probability>0.2</probability>
                    </generationInfo>
                    <newName>lung metastasis</newName>
                    <newHostOrgan organRef="lung"/>
                    <newGrowthFunction functionRef="lungMetastasis"/>
                </transferToNewContinuousCompartment>
            </eventActions>
        </discreteCompartmentType>

        <discreteCompartmentType typeID="blood_treated_Type">
            <name>blood stream</name>
            <eventActions>
                <cellDeath>
                    <name>cell death</name>
                    <generationInfo>
                        <meanTimeToNextEvent functionRef="identity"/>
                        <distribution distRef="normal"/>
                        <probability>0.999</probability>
                    </generationInfo>
                </cellDeath>
                <transferToNewContinuousCompartment>
                    <name>create lung metastasis</name>
                    <generationInfo>
                        <meanTimeToNextEvent functionRef="identity"/>
                        <distribution distRef="normal"/>
                        <probability>0.001</probability>
                    </generationInfo>
                    <newName>lung metastasis</newName>
                    <newHostOrgan organRef="lung"/>
                    <newGrowthFunction functionRef="lungMetastasis"/>
                </transferToNewContinuousCompartment>
            </eventActions>
        </discreteCompartmentType>
    </compartmentTypes>

    <compartments>
        <continuousCompartment compartmentID="primary_tumor">
            <hostOrgan organRef="colon"/>
            <successor compartmentRef="blood"/>
            <isPrimaryTumor>true</isPrimaryTumor>
            <!-- The primary tumor is completely resected without any remnants at day 1300-->
            <resectionTime>1300</resectionTime>
            <name>primary tumor</name>
            <growthFunction functionRef="growthFunction"/>
            <colonizationRate functionRef="colonizationRate"/>
        </continuousCompartment>

        <discreteCompartment compartmentID="blood">
            <hostOrgan organRef="blood_vessels"/>
            <discreteCompartmentType typeRef="blood_Type"/>
            <!-- In the time span of day 1000 and day 1200 an adapted
                 discrete compartment type is applied that describes
                 the effects of medication. -->
            <localTreatments>
                <localTreatment>
                    <start>
                        <timeCondition>1000</timeCondition>
                    </start>
                    <end>
                        <timeCondition>1200</timeCondition>
                    </end>
                    <compartmentType typeRef="blood_treated_Type"/>
                </localTreatment>
            </localTreatments>
        </discreteCompartment>
    </compartments>