main configuration

Compartment Types

In the compartmentTypes section all discrete compartment types that are required for the configuration are parametrized. It is a mandatory part of the main configuration section. In a discrete compartment type all characteristics of a discrete compartment are defined. You will find an example for the compartmentTypes section with different defined discrete compartment types at the bottom of the page.

The discrete compartment type is structured as follows:

    <discreteCompartmentType typeID="name">
        <name> </name>
        <eventActions> </eventActions>
    </discreteCompartmentType>

The mandatory attribute typeID 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 compartment type. (Please do not confuse this with typeID)
eventActions In the eventActions section all event actions that may occur in the specified compartment type are defined together with their respective probability of occurrence. For a detailed list of all available event actions please see the corresponding event actions page. Please note, that the sum of all probabilities in an eventActions section has to be one! Else, the CaTSiT will abort with a corresponding error.



Sample configuration of the compartmentTypes section

In this sample configuration of a compartmentTypes section two different discrete compartment types are defined: the lung_metastasis_type and the blood_type. In a discrete compartment with the compartment type lung_metastasis_type cells do either divide, die or transfer to the successor compartment. In a discrete compartment with the compartment type blood_type cells do either die or found a new discrete compartment of the type lung_metastasis_type. The sum of all probabilities in each eventActions section is 1. 

    <compartmentTypes>
        <discreteCompartmentType typeID="lung_metastasis_type">
            <name>lung metastasis</name>
            <eventActions>
                <cellDivision>
                    <name>cell division</name>
                    <generationInfo>
                        <meanTimeToNextEvent functionRef="identity"/>
                        <distribution distRef="normal"/>
                        <probability>0.55</probability>
                    </generationInfo>
                </cellDivision>
                <cellDeath>
                    <name>cell death</name>
                    <generationInfo>
                        <meanTimeToNextEvent functionRef="identity"/>
                        <distribution distRef="normal"/>
                        <probability>0.4</probability>
                    </generationInfo>
                </cellDeath>
                <transferToNext>
                    <name>spread to blood</name>
                    <generationInfo>
                        <meanTimeToNextEvent functionRef="identity"/>
                        <distribution distRef="normal"/>
                        <probability>0.05</probability>
                    </generationInfo>
                </transferToNext>
            </eventActions>
        </discreteCompartmentType>

        <discreteCompartmentType typeID="blood_Type">
            <name>blood stream</name>
            <eventActions>
                <cellDeath>
                    <name>cell death</name>
                    <generationInfo>
                        <meanTimeToNextEvent functionRef="identity"/>
                        <distribution distRef="normal"/>
                        <probability>0.99</probability>
                    </generationInfo>
                </cellDeath>
                <transferToNewDiscreteCompartment>
                    <name>create lung metastasis</name>
                    <generationInfo>
                        <meanTimeToNextEvent functionRef="identity"/>
                        <distribution distRef="normal"/>
                        <probability>0.01</probability>
                    </generationInfo>
                    <newHostOrgan organRef="lung"/>
                    <newCompartmentType typeRef="lung_metastasis_type"/>
                    <newSuccessor compartmentRef="blood"/>
                </transferToNewDiscreteCompartment>
            </eventActions>
        </discreteCompartmentType>

    </compartmentTypes>