Chaste
Build::
|
#include <Owen2011OxygenBasedCellCycleModel.hpp>
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 |
Oxygen-dependent ODE-based cell-cycle model. Published by Owen et al. 2011
Definition at line 51 of file Owen2011OxygenBasedCellCycleModel.hpp.
Owen2011OxygenBasedCellCycleModel::Owen2011OxygenBasedCellCycleModel | ( | boost::shared_ptr< AbstractCellCycleModelOdeSolver > | pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>() | ) |
Default constructor.
pOdeSolver | An 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().
|
private |
Adjust any ODE parameters needed before solving until currentTime.
currentTime | the time up to which the system will be solved. |
Definition at line 87 of file Owen2011OxygenBasedCellCycleModel.cpp.
Referenced by serialize().
void Owen2011OxygenBasedCellCycleModel::CheckAndLabelCell | ( | ) |
Check if the oxygen concentration of the cell is below the EnterQuiescenceOxygenConcentration. If it is true the label cells.
Definition at line 96 of file Owen2011OxygenBasedCellCycleModel.cpp.
References mCurrentQuiescenceOnsetTime, mEnterQuiescenceOxygenConcentration, mp53ThresholdForApoptosisOfNormalCellsInHealthyMicroenvironment, mp53ThresholdForApoptosisOfNormalCellsInTumourMicroenvironment, mReferenceConcentrationScale, mReferenceSolubility, mReferenceTimeScale, and mthresholdFractionOfNormalCellNeighbours.
Referenced by UpdateCellCyclePhase().
AbstractCellCycleModel * Owen2011OxygenBasedCellCycleModel::CreateCellCycleModel | ( | ) |
Overridden builder method to create new copies of this cell-cycle model.
Definition at line 136 of file Owen2011OxygenBasedCellCycleModel.cpp.
References mCriticalQuiescentDuration, mCurrentQuiescenceOnsetTime, mEnterQuiescenceOxygenConcentration, mLeaveQuiescenceOxygenConcentration, mReferenceConcentrationScale, mReferenceTimeScale, Owen2011OxygenBasedCellCycleModel(), SetCriticalQuiescentDuration(), SetCurrentQuiescenceOnsetTime(), SetEnterQuiescenceOxygenConcentration(), SetLeaveQuiescenceOxygenConcentration(), SetReferenceConcentrationScale(), and SetReferenceTimeScale().
units::quantity< unit::time > Owen2011OxygenBasedCellCycleModel::GetCriticalQuiescentDuration | ( | ) |
Definition at line 237 of file Owen2011OxygenBasedCellCycleModel.cpp.
References mCriticalQuiescentDuration.
units::quantity< unit::time > Owen2011OxygenBasedCellCycleModel::GetCurrentQuiescenceOnsetTime | ( | ) |
Definition at line 222 of file Owen2011OxygenBasedCellCycleModel.cpp.
References mCurrentQuiescenceOnsetTime.
units::quantity< unit::time > Owen2011OxygenBasedCellCycleModel::GetCurrentQuiescentDuration | ( | ) |
Definition at line 217 of file Owen2011OxygenBasedCellCycleModel.cpp.
References mCurrentQuiescentDuration.
units::quantity< unit::pressure > Owen2011OxygenBasedCellCycleModel::GetEnterQuiescenceOxygenConcentration | ( | ) |
Definition at line 227 of file Owen2011OxygenBasedCellCycleModel.cpp.
References mEnterQuiescenceOxygenConcentration.
double Owen2011OxygenBasedCellCycleModel::GetG2Duration | ( | ) | const |
Get the duration of the cell's G2 phase.
Definition at line 186 of file Owen2011OxygenBasedCellCycleModel.cpp.
units::quantity< unit::pressure > Owen2011OxygenBasedCellCycleModel::GetLeaveQuiescenceOxygenConcentration | ( | ) |
Definition at line 232 of file Owen2011OxygenBasedCellCycleModel.cpp.
References mLeaveQuiescenceOxygenConcentration.
double Owen2011OxygenBasedCellCycleModel::GetMDuration | ( | ) | const |
Get the duration of the cell's M phase.
Definition at line 191 of file Owen2011OxygenBasedCellCycleModel.cpp.
double Owen2011OxygenBasedCellCycleModel::GetP53 | ( | ) |
Get 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.
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.
Definition at line 181 of file Owen2011OxygenBasedCellCycleModel.cpp.
double Owen2011OxygenBasedCellCycleModel::GetVEGF | ( | ) |
Get 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.
|
virtual |
Outputs cell cycle model parameters to files.
rParamsFile | the file stream to which the parameters are output |
Definition at line 264 of file Owen2011OxygenBasedCellCycleModel.cpp.
References mCriticalQuiescentDuration, mEnterQuiescenceOxygenConcentration, and mLeaveQuiescenceOxygenConcentration.
bool Owen2011OxygenBasedCellCycleModel::ReadyToDivide | ( | ) |
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().
|
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().
|
inlineprivate |
Archive the cell-cycle model and ODE system.
archive | the archive |
version | the 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.
criticalQuiescentDuration | the 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.
currentQuiescenceOnsetTime | the 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.
enterQuiescenceOxygenConcentration | the 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
value | the 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.
leaveQuiescenceOxygenConcentration | the 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.
rand_max_phase | the 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
value | the 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
timeStep | the 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
referenceConcentrationScale | the 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
referenceTimeScale | the 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
value | the S2 onset time |
Definition at line 320 of file Owen2011OxygenBasedCellCycleModel.cpp.
References sOnset.
void Owen2011OxygenBasedCellCycleModel::SetThresholdFractionOfNormalCellNeighbours | ( | double | value | ) |
Set method for mthresholdFractionOfNormalCellNeighbours.
value | the 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 | ( | ) |
Update the duration for which the cell has been quiescent.
Definition at line 449 of file Owen2011OxygenBasedCellCycleModel.cpp.
References mCriticalQuiescentDuration, mCurrentQuiescenceOnsetTime, mCurrentQuiescentDuration, mLeaveQuiescenceOxygenConcentration, mReferenceConcentrationScale, mReferenceSolubility, and mReferenceTimeScale.
Referenced by UpdateCellCyclePhase().
|
friend |
Needed for serialization.
Definition at line 57 of file Owen2011OxygenBasedCellCycleModel.hpp.
|
protected |
Cell cycle fraction at which G2 phase begins
Definition at line 97 of file Owen2011OxygenBasedCellCycleModel.hpp.
Referenced by SetG2Onset(), and UpdateCellCyclePhase().
|
protected |
Critical quiescent duration.
Definition at line 148 of file Owen2011OxygenBasedCellCycleModel.hpp.
Referenced by CreateCellCycleModel(), GetCriticalQuiescentDuration(), OutputCellCycleModelParameters(), serialize(), SetCriticalQuiescentDuration(), and UpdateQuiescentDuration().
|
protected |
The time when the current period of quiescence began.
Definition at line 132 of file Owen2011OxygenBasedCellCycleModel.hpp.
Referenced by CheckAndLabelCell(), CreateCellCycleModel(), GetCurrentQuiescenceOnsetTime(), serialize(), SetCurrentQuiescenceOnsetTime(), and UpdateQuiescentDuration().
|
protected |
How long the current period of quiescence has lasted.
Definition at line 127 of file Owen2011OxygenBasedCellCycleModel.hpp.
Referenced by GetCurrentQuiescentDuration(), serialize(), and UpdateQuiescentDuration().
|
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().
|
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().
|
protected |
Maximum initial value allocated to phi.
Definition at line 122 of file Owen2011OxygenBasedCellCycleModel.hpp.
Referenced by Initialise(), and SetMaxRandInitialPhase().
|
protected |
ODE integration time-step
Definition at line 87 of file Owen2011OxygenBasedCellCycleModel.hpp.
Referenced by Owen2011OxygenBasedCellCycleModel(), and SetOdeSolverTimeStep().
|
protected |
Cell cycle fraction at which M phase begins
Definition at line 102 of file Owen2011OxygenBasedCellCycleModel.hpp.
Referenced by SetMOnset(), and UpdateCellCyclePhase().
|
protected |
p53 threshold above which normal cells become apoptotic in a healthy environment.
Definition at line 153 of file Owen2011OxygenBasedCellCycleModel.hpp.
Referenced by CheckAndLabelCell().
|
protected |
p53 threshold above which normal cells become apoptotic in a tumour environment.
Definition at line 158 of file Owen2011OxygenBasedCellCycleModel.hpp.
Referenced by CheckAndLabelCell().
|
protected |
The reference concentration scale
Definition at line 112 of file Owen2011OxygenBasedCellCycleModel.hpp.
Referenced by CheckAndLabelCell(), CreateCellCycleModel(), Initialise(), SetReferenceConcentrationScale(), and UpdateQuiescentDuration().
|
protected |
The reference solubility
Definition at line 117 of file Owen2011OxygenBasedCellCycleModel.hpp.
Referenced by CheckAndLabelCell(), Owen2011OxygenBasedCellCycleModel(), and UpdateQuiescentDuration().
|
protected |
The reference time scale
Definition at line 107 of file Owen2011OxygenBasedCellCycleModel.hpp.
Referenced by CheckAndLabelCell(), CreateCellCycleModel(), Owen2011OxygenBasedCellCycleModel(), SetOdeSolverTimeStep(), SetReferenceTimeScale(), and UpdateQuiescentDuration().
|
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().
|
protected |
Cell cycle fraction at which S phase begins
Definition at line 92 of file Owen2011OxygenBasedCellCycleModel.hpp.
Referenced by SetSOnset(), and UpdateCellCyclePhase().