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Owen2011OxygenBasedCellCycleModel Class Reference

#include <Owen2011OxygenBasedCellCycleModel.hpp>

+ Inheritance diagram for Owen2011OxygenBasedCellCycleModel:
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Public Member Functions

 Owen2011OxygenBasedCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
 
AbstractCellCycleModel * CreateCellCycleModel ()
 
void CheckAndLabelCell ()
 
units::quantity< unit::time > GetCurrentQuiescentDuration ()
 
units::quantity< unit::time > GetCurrentQuiescenceOnsetTime ()
 
units::quantity< unit::pressure > GetEnterQuiescenceOxygenConcentration ()
 
units::quantity< unit::time > GetCriticalQuiescentDuration ()
 
double GetSDuration () const
 
double GetG2Duration () const
 
double GetMDuration () const
 
double GetPhi ()
 
double GetVEGF ()
 
double GetP53 ()
 
units::quantity< unit::pressure > GetLeaveQuiescenceOxygenConcentration ()
 
void Initialise ()
 
void InitialiseDaughterCell ()
 
virtual void OutputCellCycleModelParameters (out_stream &rParamsFile)
 
bool ReadyToDivide ()
 
virtual void ResetForDivision ()
 
void SetMaxRandInitialPhase (units::quantity< unit::dimensionless > rand_max_phase)
 
void SetEnterQuiescenceOxygenConcentration (units::quantity< unit::pressure > enterQuiescenceOxygenConcentration)
 
void SetLeaveQuiescenceOxygenConcentration (units::quantity< unit::pressure > leaveQuiescenceOxygenConcentration)
 
void SetCriticalQuiescentDuration (units::quantity< unit::time > criticalQuiescentDuration)
 
void SetCurrentQuiescenceOnsetTime (units::quantity< unit::time > currentQuiescenceOnsetTime)
 
void SetG2Onset (units::quantity< unit::dimensionless > value)
 
void SetSOnset (units::quantity< unit::dimensionless > value)
 
void SetMOnset (units::quantity< unit::dimensionless > value)
 
void SetOdeSolverTimeStep (units::quantity< unit::time > timeStep)
 
void SetReferenceTimeScale (units::quantity< unit::time > referenceTimeScale)
 
void SetReferenceConcentrationScale (units::quantity< unit::concentration > referenceConcentrationScale)
 
void SetThresholdFractionOfNormalCellNeighbours (double value)
 
void UpdateQuiescentDuration ()
 
void UpdateCellCyclePhase ()
 

Protected Attributes

units::quantity< unit::time > mOdeIntegrationTimeStep
 
units::quantity< unit::dimensionless > sOnset
 
units::quantity< unit::dimensionless > g2Onset
 
units::quantity< unit::dimensionless > mOnset
 
units::quantity< unit::time > mReferenceTimeScale
 
units::quantity< unit::concentration > mReferenceConcentrationScale
 
units::quantity< unit::solubility > mReferenceSolubility
 
units::quantity< unit::dimensionless > mMaxRandInitialPhase
 
units::quantity< unit::time > mCurrentQuiescentDuration
 
units::quantity< unit::time > mCurrentQuiescenceOnsetTime
 
units::quantity< unit::pressure > mEnterQuiescenceOxygenConcentration
 
units::quantity< unit::pressure > mLeaveQuiescenceOxygenConcentration
 
units::quantity< unit::time > mCriticalQuiescentDuration
 
units::quantity< unit::dimensionless > mp53ThresholdForApoptosisOfNormalCellsInHealthyMicroenvironment
 
units::quantity< unit::dimensionless > mp53ThresholdForApoptosisOfNormalCellsInTumourMicroenvironment
 
units::quantity< unit::dimensionless > mthresholdFractionOfNormalCellNeighbours
 

Private Member Functions

template<class Archive >
void serialize (Archive &archive, const unsigned int version)
 
void AdjustOdeParameters (double currentTime)
 

Friends

class boost::serialization::access
 

Detailed Description

Oxygen-dependent ODE-based cell-cycle model. Published by Owen et al. 2011

Definition at line 51 of file Owen2011OxygenBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

Owen2011OxygenBasedCellCycleModel::Owen2011OxygenBasedCellCycleModel ( boost::shared_ptr< AbstractCellCycleModelOdeSolver >  pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>())

Default constructor.

Parameters
pOdeSolverAn optional pointer to a cell-cycle model ODE solver object (allows the use of different ODE solvers)

Definition at line 56 of file Owen2011OxygenBasedCellCycleModel.cpp.

References mOdeIntegrationTimeStep, GenericParameters::mpGasConcentrationAtStp, Secomb04Parameters::mpOxygenVolumetricSolubility, mReferenceSolubility, and mReferenceTimeScale.

Referenced by CreateCellCycleModel().

Member Function Documentation

void Owen2011OxygenBasedCellCycleModel::AdjustOdeParameters ( double  currentTime)
private

Adjust any ODE parameters needed before solving until currentTime.

Parameters
currentTimethe time up to which the system will be solved.

Definition at line 87 of file Owen2011OxygenBasedCellCycleModel.cpp.

Referenced by serialize().

void Owen2011OxygenBasedCellCycleModel::CheckAndLabelCell ( )
units::quantity< unit::time > Owen2011OxygenBasedCellCycleModel::GetCriticalQuiescentDuration ( )
Returns
mCriticalQuiescentDuration

Definition at line 237 of file Owen2011OxygenBasedCellCycleModel.cpp.

References mCriticalQuiescentDuration.

units::quantity< unit::time > Owen2011OxygenBasedCellCycleModel::GetCurrentQuiescenceOnsetTime ( )
Returns
mCurrentQuiescenceOnsetTime

Definition at line 222 of file Owen2011OxygenBasedCellCycleModel.cpp.

References mCurrentQuiescenceOnsetTime.

units::quantity< unit::time > Owen2011OxygenBasedCellCycleModel::GetCurrentQuiescentDuration ( )
Returns
mCurrentQuiescentDuration

Definition at line 217 of file Owen2011OxygenBasedCellCycleModel.cpp.

References mCurrentQuiescentDuration.

units::quantity< unit::pressure > Owen2011OxygenBasedCellCycleModel::GetEnterQuiescenceOxygenConcentration ( )
Returns
mEnterQuiescenceOxygenConcentration

Definition at line 227 of file Owen2011OxygenBasedCellCycleModel.cpp.

References mEnterQuiescenceOxygenConcentration.

double Owen2011OxygenBasedCellCycleModel::GetG2Duration ( ) const

Get the duration of the cell's G2 phase.

Returns
the duration of the cell's G2 phase.

Definition at line 186 of file Owen2011OxygenBasedCellCycleModel.cpp.

units::quantity< unit::pressure > Owen2011OxygenBasedCellCycleModel::GetLeaveQuiescenceOxygenConcentration ( )
Returns
mLeaveQuiescenceOxygenConcentration

Definition at line 232 of file Owen2011OxygenBasedCellCycleModel.cpp.

References mLeaveQuiescenceOxygenConcentration.

double Owen2011OxygenBasedCellCycleModel::GetMDuration ( ) const

Get the duration of the cell's M phase.

Returns
the duration of the cell's M phase.

Definition at line 191 of file Owen2011OxygenBasedCellCycleModel.cpp.

double Owen2011OxygenBasedCellCycleModel::GetP53 ( )

Get the value of p53.

Returns
the value of p53.

Definition at line 210 of file Owen2011OxygenBasedCellCycleModel.cpp.

Referenced by Owen2011TrackingModifier< DIM >::UpdateCellData().

double Owen2011OxygenBasedCellCycleModel::GetPhi ( )

Get the value of phi.

Returns
the value of phi.

Definition at line 196 of file Owen2011OxygenBasedCellCycleModel.cpp.

Referenced by Owen2011TrackingModifier< DIM >::UpdateCellData().

double Owen2011OxygenBasedCellCycleModel::GetSDuration ( ) const

Get the duration of the cell's S phase.

Returns
the duration of the cell's S phase.

Definition at line 181 of file Owen2011OxygenBasedCellCycleModel.cpp.

double Owen2011OxygenBasedCellCycleModel::GetVEGF ( )

Get the value of VEGF.

Returns
the value of VEGF.

Definition at line 203 of file Owen2011OxygenBasedCellCycleModel.cpp.

Referenced by Owen2011TrackingModifier< DIM >::UpdateCellData().

void Owen2011OxygenBasedCellCycleModel::Initialise ( )

Initialise the cell-cycle model at the start of a simulation.

This method will be called precisely once per cell set up in the initial cell population. It is not called on cell division; use ResetForDivision(), CreateCellCycleModel() and InitialiseDaughterCell() for that.

By the time this is called, a CellPopulation will have been set up, so the model can know where its cell is located in space. If relevant to the simulation, any singletons will also have been initialised.

Definition at line 242 of file Owen2011OxygenBasedCellCycleModel.cpp.

References mMaxRandInitialPhase, and mReferenceConcentrationScale.

void Owen2011OxygenBasedCellCycleModel::InitialiseDaughterCell ( )

Overridden InitialiseDaughterCell() method.

Definition at line 258 of file Owen2011OxygenBasedCellCycleModel.cpp.

void Owen2011OxygenBasedCellCycleModel::OutputCellCycleModelParameters ( out_stream &  rParamsFile)
virtual

Outputs cell cycle model parameters to files.

Parameters
rParamsFilethe file stream to which the parameters are output

Definition at line 264 of file Owen2011OxygenBasedCellCycleModel.cpp.

References mCriticalQuiescentDuration, mEnterQuiescenceOxygenConcentration, and mLeaveQuiescenceOxygenConcentration.

bool Owen2011OxygenBasedCellCycleModel::ReadyToDivide ( )
Returns
whether the cell is ready to divide (enter M phase).

The intention is that this method is called precisely once at each timestep of the simulation. However this does not appear to always be the case at present, and so it can cope with more unusual usage patterns.

Definition at line 292 of file Owen2011OxygenBasedCellCycleModel.cpp.

References UpdateCellCyclePhase().

void Owen2011OxygenBasedCellCycleModel::ResetForDivision ( )
virtual

Resets the oxygen-based model to the start of the cell cycle (this model does not cycle naturally). Cells are given a new birth time and cell cycle proteins are reset. Note that the oxygen concentration maintains its current value.

Should only be called by the Cell Divide() method.

Definition at line 274 of file Owen2011OxygenBasedCellCycleModel.cpp.

Referenced by UpdateCellCyclePhase().

template<class Archive >
void Owen2011OxygenBasedCellCycleModel::serialize ( Archive &  archive,
const unsigned int  version 
)
inlineprivate

Archive the cell-cycle model and ODE system.

Parameters
archivethe archive
versionthe archive version

Definition at line 65 of file Owen2011OxygenBasedCellCycleModel.hpp.

References AdjustOdeParameters(), mCriticalQuiescentDuration, mCurrentQuiescenceOnsetTime, mCurrentQuiescentDuration, mEnterQuiescenceOxygenConcentration, and mLeaveQuiescenceOxygenConcentration.

void Owen2011OxygenBasedCellCycleModel::SetCriticalQuiescentDuration ( units::quantity< unit::time >  criticalQuiescentDuration)

Set method for mCriticalQuiescentDuration.

Parameters
criticalQuiescentDurationthe new value of mCriticalQuiescentDuration

Definition at line 369 of file Owen2011OxygenBasedCellCycleModel.cpp.

References mCriticalQuiescentDuration.

Referenced by CreateCellCycleModel().

void Owen2011OxygenBasedCellCycleModel::SetCurrentQuiescenceOnsetTime ( units::quantity< unit::time >  currentQuiescenceOnsetTime)

Set method for mCurrentQuiescenceOnsetTime.

Parameters
currentQuiescenceOnsetTimethe new value of mCurrentQuiescenceOnsetTime

Definition at line 375 of file Owen2011OxygenBasedCellCycleModel.cpp.

References mCurrentQuiescenceOnsetTime.

Referenced by CreateCellCycleModel().

void Owen2011OxygenBasedCellCycleModel::SetEnterQuiescenceOxygenConcentration ( units::quantity< unit::pressure >  enterQuiescenceOxygenConcentration)

Set method for mEnterQuiescenceOxygenConcentration.

Parameters
enterQuiescenceOxygenConcentrationthe new value of mEnterQuiescenceOxygenConcentration

Definition at line 357 of file Owen2011OxygenBasedCellCycleModel.cpp.

References mEnterQuiescenceOxygenConcentration.

Referenced by CreateCellCycleModel().

void Owen2011OxygenBasedCellCycleModel::SetG2Onset ( units::quantity< unit::dimensionless >  value)

Set the G2 onset time

Parameters
valuethe G2 onset time

Definition at line 325 of file Owen2011OxygenBasedCellCycleModel.cpp.

References g2Onset.

void Owen2011OxygenBasedCellCycleModel::SetLeaveQuiescenceOxygenConcentration ( units::quantity< unit::pressure >  leaveQuiescenceOxygenConcentration)

Set method for mLeaveQuiescenceOxygenConcentration.

Parameters
leaveQuiescenceOxygenConcentrationthe new value of mLeaveQuiescenceOxygenConcentration

Definition at line 363 of file Owen2011OxygenBasedCellCycleModel.cpp.

References mLeaveQuiescenceOxygenConcentration.

Referenced by CreateCellCycleModel().

void Owen2011OxygenBasedCellCycleModel::SetMaxRandInitialPhase ( units::quantity< unit::dimensionless >  rand_max_phase)

Set maximum phase of cell upon initialisation.

Parameters
rand_max_phasethe maximum phase value at initialization

Definition at line 351 of file Owen2011OxygenBasedCellCycleModel.cpp.

References mMaxRandInitialPhase.

void Owen2011OxygenBasedCellCycleModel::SetMOnset ( units::quantity< unit::dimensionless >  value)

Set the M onset time

Parameters
valuethe M onset time

Definition at line 330 of file Owen2011OxygenBasedCellCycleModel.cpp.

References mOnset.

void Owen2011OxygenBasedCellCycleModel::SetOdeSolverTimeStep ( units::quantity< unit::time >  timeStep)

Set the ODE solver time step

Parameters
timeStepthe ODE solver time step

Definition at line 335 of file Owen2011OxygenBasedCellCycleModel.cpp.

References mOdeIntegrationTimeStep, and mReferenceTimeScale.

void Owen2011OxygenBasedCellCycleModel::SetReferenceConcentrationScale ( units::quantity< unit::concentration >  referenceConcentrationScale)

Set the reference concentration scale

Parameters
referenceConcentrationScalethe reference concentration scale

Definition at line 346 of file Owen2011OxygenBasedCellCycleModel.cpp.

References mReferenceConcentrationScale.

Referenced by CreateCellCycleModel().

void Owen2011OxygenBasedCellCycleModel::SetReferenceTimeScale ( units::quantity< unit::time >  referenceTimeScale)

Set the reference timescale

Parameters
referenceTimeScalethe reference timescale

Definition at line 341 of file Owen2011OxygenBasedCellCycleModel.cpp.

References mReferenceTimeScale.

Referenced by CreateCellCycleModel().

void Owen2011OxygenBasedCellCycleModel::SetSOnset ( units::quantity< unit::dimensionless >  value)

Set the S2 onset time

Parameters
valuethe S2 onset time

Definition at line 320 of file Owen2011OxygenBasedCellCycleModel.cpp.

References sOnset.

void Owen2011OxygenBasedCellCycleModel::SetThresholdFractionOfNormalCellNeighbours ( double  value)

Set method for mthresholdFractionOfNormalCellNeighbours.

Parameters
valuethe new value of mthresholdFractionOfNormalCellNeighbours

Definition at line 381 of file Owen2011OxygenBasedCellCycleModel.cpp.

References mthresholdFractionOfNormalCellNeighbours.

void Owen2011OxygenBasedCellCycleModel::UpdateCellCyclePhase ( )

Update cell-cycle phase.

Definition at line 386 of file Owen2011OxygenBasedCellCycleModel.cpp.

References CheckAndLabelCell(), g2Onset, mOnset, ResetForDivision(), sOnset, and UpdateQuiescentDuration().

Referenced by ReadyToDivide().

void Owen2011OxygenBasedCellCycleModel::UpdateQuiescentDuration ( )

Friends And Related Function Documentation

friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 57 of file Owen2011OxygenBasedCellCycleModel.hpp.

Member Data Documentation

units::quantity<unit::dimensionless> Owen2011OxygenBasedCellCycleModel::g2Onset
protected

Cell cycle fraction at which G2 phase begins

Definition at line 97 of file Owen2011OxygenBasedCellCycleModel.hpp.

Referenced by SetG2Onset(), and UpdateCellCyclePhase().

units::quantity<unit::time> Owen2011OxygenBasedCellCycleModel::mCriticalQuiescentDuration
protected
units::quantity<unit::time> Owen2011OxygenBasedCellCycleModel::mCurrentQuiescenceOnsetTime
protected
units::quantity<unit::time> Owen2011OxygenBasedCellCycleModel::mCurrentQuiescentDuration
protected

How long the current period of quiescence has lasted.

Definition at line 127 of file Owen2011OxygenBasedCellCycleModel.hpp.

Referenced by GetCurrentQuiescentDuration(), serialize(), and UpdateQuiescentDuration().

units::quantity<unit::pressure> Owen2011OxygenBasedCellCycleModel::mEnterQuiescenceOxygenConcentration
protected

Oxygen concentration below which cancerous cells enter quiescence. A prolonged period of quiescence causes the cell to become apoptotic.

Definition at line 138 of file Owen2011OxygenBasedCellCycleModel.hpp.

Referenced by CheckAndLabelCell(), CreateCellCycleModel(), GetEnterQuiescenceOxygenConcentration(), OutputCellCycleModelParameters(), serialize(), and SetEnterQuiescenceOxygenConcentration().

units::quantity<unit::pressure> Owen2011OxygenBasedCellCycleModel::mLeaveQuiescenceOxygenConcentration
protected

Oxygen concentration above which cancerous cells leave their state of being quiescent

Definition at line 143 of file Owen2011OxygenBasedCellCycleModel.hpp.

Referenced by CreateCellCycleModel(), GetLeaveQuiescenceOxygenConcentration(), OutputCellCycleModelParameters(), serialize(), SetLeaveQuiescenceOxygenConcentration(), and UpdateQuiescentDuration().

units::quantity<unit::dimensionless> Owen2011OxygenBasedCellCycleModel::mMaxRandInitialPhase
protected

Maximum initial value allocated to phi.

Definition at line 122 of file Owen2011OxygenBasedCellCycleModel.hpp.

Referenced by Initialise(), and SetMaxRandInitialPhase().

units::quantity<unit::time> Owen2011OxygenBasedCellCycleModel::mOdeIntegrationTimeStep
protected

ODE integration time-step

Definition at line 87 of file Owen2011OxygenBasedCellCycleModel.hpp.

Referenced by Owen2011OxygenBasedCellCycleModel(), and SetOdeSolverTimeStep().

units::quantity<unit::dimensionless> Owen2011OxygenBasedCellCycleModel::mOnset
protected

Cell cycle fraction at which M phase begins

Definition at line 102 of file Owen2011OxygenBasedCellCycleModel.hpp.

Referenced by SetMOnset(), and UpdateCellCyclePhase().

units::quantity<unit::dimensionless> Owen2011OxygenBasedCellCycleModel::mp53ThresholdForApoptosisOfNormalCellsInHealthyMicroenvironment
protected

p53 threshold above which normal cells become apoptotic in a healthy environment.

Definition at line 153 of file Owen2011OxygenBasedCellCycleModel.hpp.

Referenced by CheckAndLabelCell().

units::quantity<unit::dimensionless> Owen2011OxygenBasedCellCycleModel::mp53ThresholdForApoptosisOfNormalCellsInTumourMicroenvironment
protected

p53 threshold above which normal cells become apoptotic in a tumour environment.

Definition at line 158 of file Owen2011OxygenBasedCellCycleModel.hpp.

Referenced by CheckAndLabelCell().

units::quantity<unit::concentration> Owen2011OxygenBasedCellCycleModel::mReferenceConcentrationScale
protected
units::quantity<unit::solubility> Owen2011OxygenBasedCellCycleModel::mReferenceSolubility
protected

The reference solubility

Definition at line 117 of file Owen2011OxygenBasedCellCycleModel.hpp.

Referenced by CheckAndLabelCell(), Owen2011OxygenBasedCellCycleModel(), and UpdateQuiescentDuration().

units::quantity<unit::time> Owen2011OxygenBasedCellCycleModel::mReferenceTimeScale
protected
units::quantity<unit::dimensionless> Owen2011OxygenBasedCellCycleModel::mthresholdFractionOfNormalCellNeighbours
protected

Threshold which defines the proportion of neighbours which must be normal in order for a cell's micro-environment to be considered normal.

Definition at line 164 of file Owen2011OxygenBasedCellCycleModel.hpp.

Referenced by CheckAndLabelCell(), and SetThresholdFractionOfNormalCellNeighbours().

units::quantity<unit::dimensionless> Owen2011OxygenBasedCellCycleModel::sOnset
protected

Cell cycle fraction at which S phase begins

Definition at line 92 of file Owen2011OxygenBasedCellCycleModel.hpp.

Referenced by SetSOnset(), and UpdateCellCyclePhase().


The documentation for this class was generated from the following files: