main configuration

Functions

In the functions section all functions that are required for the configuration are parametrized. It is a mandatory part of the main configuration section. Following functions can be parametrized:

Every function has the mandatory attribute functionID 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.

The colonization rate has to be stated at the end of the function block. No other function definitions are allowed after a colonization rate. You will find an example for the functions section with different defined functions at the bottom of the page.

Constant function

    <constantFunction functionID="name">
        <constant> </constant>
    </constantFunction>

A function with the form f(x) = constant.

Linear function

    <linearFunction functionID="name">
        <m> </m>
        <n> </n>
    </linearFunction>

A function with the form f(x) = m * x + n. If used as a growth function m displays the growth rate of the tumor (unit: 1/day) and n the start size (unit: number of cells). The start size must be bigger or equal than 1 for the primary tumor and 1 for metastases.

Exponential function

    <exponentialFunction functionID="name">
        <a> </a>
        <b> </b>
        <c> </c>
    </exponentialFunction>

A function with the form f(x) = a * e^( b*x ) + c. If used as a growth function b displays the growth rate of the tumor (unit: 1/day) and n=a+c the start size (unit: number of cells). The start size must be bigger or equal than 1 for the primary tumor and 1 for metastases.

Power function

    <powerFunction functionID="name">
        <a> </a>
        <b> </b>
        <c> </c>
    </powerFunction>

A function with the form f(x) = a * x^b + c. If used as a growth function b displays the growth rate of the tumor (unit: 1/day), c the start size (unit: number of cells) and a serves as a scaling factor. The start size must be bigger or equals 1 for the primary tumor and 1 for metastases.

Logarithmic function

    <logFunction functionID="name">
        <a> </a>
        <b> </b>
        <startSize> </startSize>
    </logFunction>

A function with the form f(x) = a * log ( b*x ). If used as a growth function b displays the growth rate of the tumor (unit: 1/day). The start size is optional but must be bigger or equals 1 for the primary tumor or 1 for metastases.

Gompertz function

    <gompertzFunction functionID="name">
        <growthRate> </growthRate>
        <tumorSize> </tumorSize>
        <startSize> </startSize>
    </gompertzFunction>

A function with the form x(t) = b * (b/n)^-e^( -a*t ), where

a = growthRate The growth rate constant. Unit: 1/day
b = tumorSize The maximum tumor size. Unit: number of cells
n = startSize Optional. The start size of the tumor must be bigger or equals 1 for the primary tumor and 1 for metastases. If not stated, this value is set to 1. Unit: number of cells.

ColonizationRate function

    <colonizationRate functionID="name">
        <colonizationCoefficient> </colonizationCoefficient>
        <fractalDim> </fractalDim>
    </colonizationRate>

The colonization rate with the form g(x) = m * x(t)^a, where x(t) is the growth function of the tumor, which is automatically set by the tumor compartment, and

m = colonizationCoefficient The colonization coefficient. Unit: 1/(cell*day)
a = fractalDim The fractal dimension describes the distribution of the blood vessels in or on the surface of a tumor. A value of 1 describes a complete vascularization of the tumor, while a value of 2/3 describes a superficial blood supply.



Sample configuration of the functions section

In this sample configuration of a functions section three different Gompertz growth functions are defined: for the primary tumor, liver metastases and lung metastases. A constant function with the return value of 1 is defined and two different colonization rates. 

    <functions>

        <gompertzFunction functionID="primaryTumor">
            <growthRate>0.00286</growthRate>
            <tumorSize>7.3e10</tumorSize>
            <startSize>1e6</startSize>
        </gompertzFunction>

        <gompertzFunction functionID="liverMetastasis">
            <growthRate>0.00123</growthRate>
            <tumorSize>6.2e9</tumorSize>
            <startSize>1</startSize>
        </gompertzFunction>

        <gompertzFunction functionID="lungMetastasis">
            <growthRate>0.00321</growthRate>
            <tumorSize>5.1e10</tumorSize>
            <startSize>1</startSize>
        </gompertzFunction>

        <constantFunction functionID="identity">
            <constant>1</constant>
        </constantFunction>

        <colonizationRate functionID="colonizationPrimaryTumor">
            <colonizationCoefficient>5.3e-8</colonizationCoefficient>
            <fractalDim>0.663</fractalDim>
        </colonizationRate>

        <colonizationRate functionID="colonizationLiverMetastasis">
            <colonizationCoefficient>2.3e-5</colonizationCoefficient>
            <fractalDim>0.663</fractalDim>
        </colonizationRate>

    </functions>