main configuration /
compartment types
Event Actions
Event actions describe what happens with a cell in a discrete compartment. In the eventActions
section all event actions that can occur in a specific discrete compartment are parametrized. It is a mandatory
part of the discreteCompartmentType tag in the compartmentTypes section. Every
event action has to state the tag generationInfo which defines all information that are necessary
to create a new event action of this specific type:
Following event actions can be parametrized:
You will find an example for the eventActions section with different defined event actions at
the bottom of the page.
GenerationInfo
The
GenerationInfo has to be stated for every event action in the
eventActions
section. It defines all information that are necessary to create a new event of the corresponding event
action type.
<generationInfo>
<meanTimeToNextEvent functionRef="functionID"/>
<distribution distRef="distID"/>
<probability> </probability>
</generationInfo>
meanTimeToNextEvent |
Refers to a beforehand defined function that computes the mean time until an event of this
type occurs depending on the current number of cells in the corresponding compartment. |
distRef |
Refers to a beforehand defined distribution that describes the time until an event of this
type occurs. Please not that the values in the distribution are given in minutes! |
probability |
The probability with which this event action occurs in the corresponding discrete compartment.
The value has to be in the interval [0,1]. Note, that the sum of all probabilities in an
eventActions section has to be one. Else, CaTSiT will abort with
a corresponding error. |
CellDeath
The cell death event action decreases the number of cells in the compartment by one. No new cell progression
events are created. Please note that the elements have to be stated in exactly the same order as listed below.
<cellDeath>
<name> </name>
<generationInfo>
<meanTimeToNextEvent functionRef="functionID"/>
<distribution distRef="distID"/>
<probability> </probability>
</generationInfo>
</cellDeath>
CellDivision
The cell division event action increases the number of cells in the compartment by one. Two new cell progression
events are created afterwards (one for the 'old' cell and one for 'new' cell) to describe what happens next
to both cells involved. Please note that the elements have to be stated in exactly the same order as listed below.
<cellDivision>
<name> </name>
<generationInfo>
<meanTimeToNextEvent functionRef="functionID"/>
<distribution distRef="distID"/>
<probability> </probability>
</generationInfo>
</cellDivision>
TransferToNewContinuousCompartment
This event action decreases the number of cells in the compartment by one and creates a new continuous compartment
using the given parameter for host organ, growth function, colonization rate and successor. Please note that the
elements have to be stated in exactly the same order as listed below.
<transferToNewContinuousCompartment>
<name> </name>
<generationInfo>
<meanTimeToNextEvent functionRef="functionID"/>
<distribution distRef="distID"/>
<probability> </probability>
</generationInfo>
<newName> </newName>
<newHostOrgan organRef="organID"/>
<newGrowthFunction functionRef="functionID"/>
<newColonizationRate functionRef="functionID"/>
<newSuccessor compartmentRef="compartmentID"/>
</transferToNewContinuousCompartment>
name |
The name of the event action. |
generationInfo |
The generation information for this event action. |
newName |
The name of the newly created compartment. |
newHostOrgan |
The host organ in which new compartment will be situated in. Refers to a beforehand defined host
organ. |
newGrowthFunction |
The growth function of the new compartment. Refers to a beforehand defined function. |
newColonizationRate |
Optional. The colonization rate of the new compartment. If not stated, the new compartment will
not spread metastases. Refers to a beforehand defined colonization rate. |
newSuccessor |
The successor of the new compartment. Has to be a discrete compartment. Mostly it will be the
blood compartment. Refers to a later in the configuration file defined compartment. |
TransferToNewDiscreteCompartment
This event action decreases the number of cells in the compartment by one and creates a new discrete compartment
using the given parameter for host organ, compartment type and successor. Please note that the elements have to
be stated in exactly the same order as listed below.
<transferToNewDiscreteCompartment>
<name> </name>
<generationInfo>
<meanTimeToNextEvent functionRef="functionID"/>
<distribution distRef="distID"/>
<probability> </probability>
</generationInfo>
<hostOrgan organRef="organID"/>
<newCompartmentType typeRef="typeID"/>
<newSuccessor compartmentRef="compartmentID"/>
</transferToNewDiscreteCompartment>
name |
The name of the event action. |
generationInfo |
The generation information for this event action. |
newHostOrgan |
The host organ the new compartment will be situated in. Refers to a beforehand defined host
organ. |
newCompartmentType |
The compartment type of the new compartment. Refers to a beforehand defined compartment type. |
newSuccessor |
The successor of the new compartment. Has to be a discrete compartment. Mostly it will be the
blood compartment. Refers to a later in the configuration file defined compartment. |
TransferToNext
The transfer to next event action decreases the number of cells in the current compartment by one and increases
the number of cells in the successor compartment by one. This event action can only be applied if both, the current
and the successor, compartment are discrete compartments. The
transferToNext event action cannot be
applied between a discrete and a continuous compartment. Please note that the elements have to be stated in exactly
the same order as listed below.
<transferToNext>
<name> </name>
<generationInfo>
<meanTimeToNextEvent functionRef="functionID"/>
<distribution distRef="distID"/>
<probability> </probability>
</generationInfo>
</transferToNext>
Sample configuration of the eventActions section
In this sample configuration of an eventActions section three event actions are defined: one
cell death event action with the probability of 0.9 and two TransferToNewContinuousCompartment
event actions to create lung and liver metastases. Lung metastases are created with a probability of 0.06. New
lung metastases growth with the beforehand defined growth function lungMetastasis and do not
spread further metastases, since no colonization rate was defined. Liver metastases are created with a
probability of 0.04. New liver metastases growth with the beforehand defined growth function liverMetastasis
and spread metastases with the beforehand defined colonization rate colonizationLiverMetastasis.
The successor of all new lung and liver metastases is the discrete compartment blood which is
defined later in the configuration file. The sum of all probabilities is 1.
<eventActions>
<cellDeath>
<name>cell death</name>
<generationInfo>
<meanTimeToNextEvent functionRef="identity"/>
<!-- The values of the distribution are given in minutes! -->
<distribution distRef="normal"/>
<probability>0.9</probability>
</generationInfo>
</cellDeath>
<transferToNewContinuousCompartment>
<name>create lung metastasis</name>
<generationInfo>
<meanTimeToNextEvent functionRef="identity"/>
<!-- The values of the distribution are given in minutes! -->
<distribution distRef="normal"/>
<probability>0.06</probability>
</generationInfo>
<newName>lung metastasis</newName>
<newHostOrgan organRef="lung"/>
<newGrowthFunction functionRef="lungMetastasis"/>
<!-- This is the ID of a later in the file configured compartment.
Not a host organ or compartment type! -->
<newSuccessor compartmentRef="blood"/>
</transferToNewContinuousCompartment>
<transferToNewContinuousCompartment>
<name>create liver metastasis</name>
<generationInfo>
<meanTimeToNextEvent functionRef="identity"/>
<!-- The values of the distribution are given in minutes! -->
<distribution distRef="normal"/>
<probability>0.04</probability>
</generationInfo>
<newName>liver metastasis</newName>
<newHostOrgan organRef="lung"/>
<newGrowthFunction functionRef="liverMetastasis"/>
<newColonizationRate functionRef="colonizationLiverMetastasis">
<!-- This is the ID of a later in the file configured compartment.
Not a host organ or compartment type! -->
<newSuccessor compartmentRef="blood"/>
</transferToNewContinuousCompartment>
</eventActions>
