Phenotype

Note

The Phenotype class is a nested object within the Cell and CellDefinition classes.

The Phenotype class is used to work with various cell properties.

To import this class use:

import ru.biosoft.physicell.core.Phenotype

In this class, there are 12 separate classes, each of which is used to work with a specific set of cell properties.

Phenotype classes

Class	Description
Cycle cycle	Used to describe the life cycle of a cell. All members of this class are presented in Table 1.1.
death death	Used to describe a model of cell death. All members of this class are presented in Table 1.2.
volume volume	Used to describe the volumetric properties of a cell. All members of this class are presented in Table 1.3.
Geometry geometry	Used to describe the size of a cell. All members of this class are presented in Table 1.4.
Mechanics mechanics	Used to describe the mechanical properties of a cell. All members of this class are presented in Table 1.5.
Motility motility	Used to describe cell motility. All members of this class are presented in Table 1.6.
Secretion secretion	Used to describe the secretion and consumption of substances by a cell. All members of this class are presented in Table 1.7.
Molecular molecular	Used to describe the content of substances inside a cell. All members of this class are presented in Table 1.8.
CellInteractions cellInteractions	Used to describe interactions between different types of cells.
CellTransformations cellTransformations	Used to describe the transformation of a cell from one type to another. All members of this class are presented in Table 1.10.
Intracellular intracellular	Used to describe intracellular processes of a cell using ordinary differential equations or a flow model. All members of this class are presented in Table 1.11.
CellIntegrity cellIntegrity	Used to describe the integrity of a cell.

Table 1.1. Members of the Cycle class

Class member	Description
int code	Contains a numerical code for the cell’s life cycle. Example of usage.
Phase currentPhase()	Returns the current phase of the life cycle of this cell. Example of usage.
int currentPhase().code	Contains the numerical code of the current phase of the life cycle of a given cell. Example of usage.
int currentPhase().index	Contains the internal current phase of the life cycle of a given cell.
boolean currentPhase().divisionAtExit	Contains true if the cell divides when leaving this phase of the cell cycle.
boolean currentPhase().removalAtExit	Contains true if the cell disappears when leaving this phase of the cell cycle.
String currentPhase().name	Contains the name of the current phase of the life cycle of a given cell. Example of usage.
CycleData data	Contains an object of the CycleData class that stores numerical data of the life cycle of this particular cell. Example of usage.
double data.elapsedTimePhase	Contains the time spent by a cell in the current phase of its life cycle. Example of usage.
double data.getTransitionRate(int phase1, int phase2)	phase1 - life cycle phase number. phase2 - life cycle phase number. Returns the transition speed between life cycle phases numbered phase1 and phase2. Example of usage.
void data.setTransitionRate(int phase1, int phase2, double speed)	phase1 - life cycle phase number. phase2 - life cycle phase number. speed - speed of transition between life cycle phases. Sets the transition speed between life cycle phases with numbers phase1 and phase2 equal to speed. Example of usage.
double data.getExitRate(int phase)	phase - life cycle phase number. Returns the probability of exiting phase numbered phase*. *Used if a cell can move from phase to only one other phase. Example of usage.
void data.setExitRate(int phase, double probability)	phase - life cycle phase number. probability - probability. Sets the probability of leaving the phase with phase number equal to probability. Example of usage.

Table 1.2. Members of the Death class

Class member	Description
boolean dead	Contains true if the cell is dead. Example of usage.
double[] rates	Contains an array of probabilities of all types of cell deaths. Example of usage.
int rates.size()	Returns the number of probabilities of all possible cell deaths. Example of usage.
void rates.set(int index, double probability)	index - index of the type of cell death. probability - probability. Sets the probability of the type of cell death with index index equal to probability. Example of usage.
double rates.get(int index)	index - index of the type of cell death. Returns the probability of the type of cell death with index index. Example of usage.
int findDeathModelIndex(String name)	name - name of the type of cell death. Returns an index of the cell death type called name. Example of usage.

Table 1.3. Members of the Volume class

Class member	Description
double total	Contains the total volume of the cell. Example of usage.

Table 1.4. Members of the Geometry class

Class member	Description
double radius	Contains the radius of the cell. Example of usage.

Table 1.5. Members of the Mechanics class

Class member	Description
double attachmentElasticConstant	Contains the coefficient with which a cell is attracted to other cells. Example of usage.
double cellCellAdhesionStrength	Contains the force of intercellular adhesion. Example of usage.
double cellCellRepulsionStrength	Contains the force of intercellular repulsion. Example of usage.
double relDetachmentDistance	Contains the relative distance (radius multiplier) at which a cell separates from an attached cell. Example of usage.

Table 1.6. Members of the Motility class

Class member	Description
boolean isMotile	Contains true if the cell is motile. Example of usage.
double migrationBias	Contains a number from the interval [0,1], where 0 means that the cell moves completely randomly, and 1 means it moves completely purposefully. Example of usage.
double[] migrationBiasDirection	Contains a normalized vector describing the direction in which the cell is moving purposefully at a given time. Example of usage.
double migrationSpeed	Contains the speed of cell movement. Example of usage.
double persistenceTime	Contains the time during which the cell maintains one direction of movement. Example of usage.
int chemotaxisDirection	Contains “1” if the cell is moving towards the substrate during chemotaxis, or “-1” if the cell is moving away from it. Example of usage.

Table 1.7. Members of the Secretion class

Class member	Description
double[] secretionRates	Contains an array of secretion rates of each substrate by a given cell. Example of usage.
double[] uptakeRates	Contains an array of rates of consumption of each substrate by a given cell. Example of usage.
double[] netExportRates	Contains an array containing constant (independent of cell volume) secretion/consumption rates of all possible substrates for a given cell. Example of usage.
void setSecretionToZero()	Sets the secretion rate to 0 for all substrates in the model for a given cell. Example of usage.
void setUptakeToZero()	Sets the consumption rate to 0 for all substrates in the model for a given cell. Example of usage.

Table 1.8. Members of the Molecular class

Class member	Description
double[] internSubstrates	Contains an array consisting of the quantities of all possible substances inside the cell. Example of usage.
double fractionReleasedDeath	Contains a fraction of internal substances that are released from the cell at the time of its death. Example of usage.
double fractionTransferredIngested	Contains the fraction of internal substances that a cell receives that has absorbed a cell of a given type. Example of usage.

Table 1.10. Members of the CellTransformations class

Class member	Description
double[] transformationRates	Contains an array of probabilities of transformation of cells of a given type into all other cell types. Example of usage.

Table 1.11. Members of the class Intracellular

Class member	Description
void start()	Runs intracellular model calculations. Example of usage.
void setParameterValue(String name, double value)	name - name of the intracellular model parameter. value - value. Sets the numerical value value to the name parameter in the intracellular model. Example of usage.
double getParameterValue(String name)	name - name of the intracellular model parameter. Returns the value of the name parameter in the intracellular model. Example of usage.