Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
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#include <Alarcon2004OxygenBasedCellCycleOdeSystem.hpp>
Public Member Functions | |
Alarcon2004OxygenBasedCellCycleOdeSystem (double oxygenConcentration, bool isLabelled, std::vector< double > stateVariables=std::vector< double >()) | |
~Alarcon2004OxygenBasedCellCycleOdeSystem () | |
void | Init () |
void | EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY) |
bool | CalculateStoppingEvent (double time, const std::vector< double > &rY) |
void | SetIsLabelled (bool isLabelled) |
bool | IsLabelled () const |
double | GetOxygenConcentration () const |
Public Member Functions inherited from AbstractOdeSystem | |
AbstractOdeSystem (unsigned numberOfStateVariables) | |
virtual | ~AbstractOdeSystem () |
virtual double | CalculateRootFunction (double time, const std::vector< double > &rY) |
bool | GetUseAnalyticJacobian () |
const std::vector< double > & | rGetConstStateVariables () const |
Public Member Functions inherited from AbstractParameterisedSystem< std::vector< double > > | |
AbstractParameterisedSystem (unsigned numberOfStateVariables) | |
std::vector< double > & | rGetStateVariables () |
std::vector< double > | GetStateVariables () |
void | SetStateVariables (const std::vector< double > &rStateVariables) |
double | GetStateVariable (unsigned index) const |
double | GetStateVariable (const std::string &rName) const |
void | SetStateVariable (unsigned index, double newValue) |
void | SetStateVariable (const std::string &rName, double newValue) |
virtual void | VerifyStateVariables () |
void | SetDefaultInitialConditions (const std::vector< double > &rInitialConditions) |
void | SetDefaultInitialCondition (unsigned index, double initialCondition) |
std::vector< double > | GetInitialConditions () const |
void | ResetToInitialConditions () |
double | GetParameter (unsigned index) const |
double | GetParameter (const std::string &rName) const |
void | SetParameter (const std::string &rName, double value) |
void | SetParameter (unsigned index, double value) |
double | GetAnyVariable (unsigned index, double time=0.0, std::vector< double > *pDerivedQuantities=NULL) |
double | GetAnyVariable (const std::string &rName, double time=0.0, std::vector< double > *pDerivedQuantities=NULL) |
void | SetAnyVariable (unsigned index, double value) |
void | SetAnyVariable (const std::string &rName, double value) |
virtual std::vector< double > | ComputeDerivedQuantities (double time, const std::vector< double > &rState) |
std::vector< double > | ComputeDerivedQuantitiesFromCurrentState (double time) |
Public Member Functions inherited from AbstractUntemplatedParameterisedSystem | |
AbstractUntemplatedParameterisedSystem (unsigned numberOfStateVariables) | |
virtual | ~AbstractUntemplatedParameterisedSystem () |
boost::shared_ptr< const AbstractOdeSystemInformation > | GetSystemInformation () const |
std::string | GetSystemName () const |
unsigned | GetNumberOfAttributes () const |
bool | HasAttribute (const std::string &rName) const |
double | GetAttribute (const std::string &rName) const |
unsigned | GetNumberOfStateVariables () const |
const std::vector< std::string > & | rGetStateVariableNames () const |
const std::vector< std::string > & | rGetStateVariableUnits () const |
unsigned | GetStateVariableIndex (const std::string &rName) const |
bool | HasStateVariable (const std::string &rName) const |
std::string | GetStateVariableUnits (unsigned index) const |
unsigned | GetNumberOfParameters () const |
const std::vector< std::string > & | rGetParameterNames () const |
const std::vector< std::string > & | rGetParameterUnits () const |
unsigned | GetParameterIndex (const std::string &rName) const |
bool | HasParameter (const std::string &rName) const |
std::string | GetParameterUnits (unsigned index) const |
unsigned | GetNumberOfDerivedQuantities () const |
const std::vector< std::string > & | rGetDerivedQuantityNames () const |
const std::vector< std::string > & | rGetDerivedQuantityUnits () const |
unsigned | GetDerivedQuantityIndex (const std::string &rName) const |
bool | HasDerivedQuantity (const std::string &rName) const |
std::string | GetDerivedQuantityUnits (unsigned index) const |
unsigned | GetAnyVariableIndex (const std::string &rName) const |
bool | HasAnyVariable (const std::string &rName) const |
std::string | GetAnyVariableUnits (unsigned index) const |
std::string | GetAnyVariableUnits (const std::string &rName) const |
Private Member Functions | |
template<class Archive > | |
void | serialize (Archive &archive, const unsigned int version) |
Private Attributes | |
double | ma1 |
double | ma2 |
double | ma3 |
double | ma4 |
double | mb3 |
double | mb4 |
double | mc1 |
double | mc2 |
double | md1 |
double | md2 |
double | mJ3 |
double | mJ4 |
double | mEta |
double | mMstar |
double | mB |
double | mxThreshold |
double | myThreshold |
double | mOxygenConcentration |
bool | mIsLabelled |
Friends | |
class | boost::serialization::access |
Additional Inherited Members | |
Protected Member Functions inherited from AbstractParameterisedSystem< std::vector< double > > | |
std::string | DumpState (const std::string &rMessage) |
std::string | DumpState (const std::string &rMessage, std::vector< double > Y) |
std::string | DumpState (const std::string &rMessage, std::vector< double > Y, double time) |
void | CheckParametersOnLoad (const std::vector< double > &rParameters, const std::vector< std::string > &rParameterNames) |
Protected Attributes inherited from AbstractOdeSystem | |
bool | mUseAnalyticJacobian |
Protected Attributes inherited from AbstractParameterisedSystem< std::vector< double > > | |
std::vector< double > | mStateVariables |
std::vector< double > | mParameters |
Protected Attributes inherited from AbstractUntemplatedParameterisedSystem | |
unsigned | mNumberOfStateVariables |
boost::shared_ptr< AbstractOdeSystemInformation > | mpSystemInfo |
Represents the Alarcon et al. (2004) system of ODEs (see ticket #461). [doi:10.1016/j.jtbi.2004.04.016]
The variables are
0. x = Cdh1-APC complexes 1. y = cyclin-CDK 2. z = p27 3. m = mass 4. u = RBNP 5. P = oxygen concentration
Definition at line 59 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Alarcon2004OxygenBasedCellCycleOdeSystem::Alarcon2004OxygenBasedCellCycleOdeSystem | ( | double | oxygenConcentration, |
bool | isLabelled, | ||
std::vector< double > | stateVariables = std::vector<double>() |
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) |
Constructor.
oxygenConcentration | is a non-dimensional oxygen concentration value between 0 and 1 |
isLabelled | whether the cell associated with this cell cycle ODE system is labelled (this affects the ODE system) |
stateVariables | optional initial conditions for state variables (only used in archiving) |
State variables
0. x = Cdh1-APC complexes 1. y = cyclin-CDK 2. z = p27 3. m = mass 4. u = RBNP 5. oxygenConcentration
Definition at line 39 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.
References Init(), ma1, mc1, mIsLabelled, mMstar, AbstractUntemplatedParameterisedSystem::mpSystemInfo, mxThreshold, myThreshold, AbstractParameterisedSystem< std::vector< double > >::SetDefaultInitialCondition(), and AbstractParameterisedSystem< std::vector< double > >::SetStateVariables().
Alarcon2004OxygenBasedCellCycleOdeSystem::~Alarcon2004OxygenBasedCellCycleOdeSystem | ( | ) |
Destructor.
Definition at line 86 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.
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virtual |
Calculate whether the conditions for the cell cycle to finish have been met.
time | at which to calculate whether the stopping event has occurred |
rY | value of the solution vector used to evaluate the RHS. |
Reimplemented from AbstractOdeSystem.
Definition at line 158 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.
References mxThreshold, and myThreshold.
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virtual |
Compute the RHS of the Alarcon et al. (2004) system of ODEs.
Returns a vector representing the RHS of the ODEs at each time step, y' = [y1' ... yn']. An ODE solver will call this function repeatedly to solve for y = [y1 ... yn].
time | used to evaluate the RHS. |
rY | value of the solution vector used to evaluate the RHS. |
rDY | filled in with the resulting derivatives (using Alarcons et al. (2004) system of equations). |
Implements AbstractOdeSystem.
Definition at line 109 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.
References ma1, ma2, ma3, ma4, mB, mb3, mb4, mc1, mc2, md1, md2, mEta, mIsLabelled, mJ3, mJ4, and mMstar.
double Alarcon2004OxygenBasedCellCycleOdeSystem::GetOxygenConcentration | ( | ) | const |
Definition at line 203 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.
References mOxygenConcentration.
void Alarcon2004OxygenBasedCellCycleOdeSystem::Init | ( | ) |
bool Alarcon2004OxygenBasedCellCycleOdeSystem::IsLabelled | ( | ) | const |
Definition at line 198 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.
References mIsLabelled.
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inlineprivate |
Serialize the object and its member variables.
archive | the archive |
version | the current version of this class |
Definition at line 116 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
void Alarcon2004OxygenBasedCellCycleOdeSystem::SetIsLabelled | ( | bool | isLabelled | ) |
Set mIsLabelled.
isLabelled | whether the cell associated with this cell cycle ODE system is labelled (this affects the ODE system) |
Definition at line 193 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.
References mIsLabelled.
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friend |
Definition at line 108 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
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private |
Constants for the Alarcon et al. (2004) model Dimensionless parameter a_1.
Definition at line 68 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), and EvaluateYDerivatives().
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private |
Dimensionless parameter a_2.
Definition at line 70 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Referenced by EvaluateYDerivatives(), and Init().
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Dimensionless parameter a_3.
Definition at line 72 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Referenced by EvaluateYDerivatives(), and Init().
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Dimensionless parameter a_4.
Definition at line 74 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Referenced by EvaluateYDerivatives(), and Init().
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Dimensionless parameter B.
Definition at line 96 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Referenced by EvaluateYDerivatives(), and Init().
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Dimensionless parameter b_3.
Definition at line 76 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Referenced by EvaluateYDerivatives(), and Init().
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Dimensionless parameter b_4.
Definition at line 78 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Referenced by EvaluateYDerivatives(), and Init().
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Dimensionless parameter c_1.
Definition at line 80 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), and EvaluateYDerivatives().
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Dimensionless parameter c_2.
Definition at line 82 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Referenced by EvaluateYDerivatives(), and Init().
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Dimensionless parameter d_1.
Definition at line 84 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Referenced by EvaluateYDerivatives(), and Init().
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Dimensionless parameter d_2.
Definition at line 86 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Referenced by EvaluateYDerivatives(), and Init().
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Dimensionless parameter eta.
Definition at line 92 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Referenced by EvaluateYDerivatives(), and Init().
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Whether the cell associated with this cell cycle ODE system is labelled (this affects the ODE system).
Definition at line 106 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), EvaluateYDerivatives(), IsLabelled(), and SetIsLabelled().
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Dimensionless parameter J_3.
Definition at line 88 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Referenced by EvaluateYDerivatives(), and Init().
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Dimensionless parameter J_4.
Definition at line 90 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Referenced by EvaluateYDerivatives(), and Init().
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Dimensionless parameter m_star.
Definition at line 94 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), EvaluateYDerivatives(), and Init().
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The oxygen concentration (this affects the ODE system).
Definition at line 103 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Referenced by GetOxygenConcentration().
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Dimensionless parameter x_THR.
Definition at line 98 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), and CalculateStoppingEvent().
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Dimensionless parameter y_THR.
Definition at line 100 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.
Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), and CalculateStoppingEvent().