Chaste  Release::2018.1
Mirams2010WntOdeSystem Class Reference

#include <Mirams2010WntOdeSystem.hpp>

+ Inheritance diagram for Mirams2010WntOdeSystem:
+ Collaboration diagram for Mirams2010WntOdeSystem:

Public Member Functions

 Mirams2010WntOdeSystem (double wntLevel=0.0, boost::shared_ptr< AbstractCellMutationState > pMutationState=boost::shared_ptr< AbstractCellMutationState >(), std::vector< double > stateVariables=std::vector< double >())
 
 ~Mirams2010WntOdeSystem ()
 
void Init ()
 
void SetMutationState (boost::shared_ptr< AbstractCellMutationState > pMutationState)
 
const boost::shared_ptr
< AbstractCellMutationState
GetMutationState () const
 
void EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY)
 
double GetWntLevel () const
 
- Public Member Functions inherited from AbstractOdeSystem
 AbstractOdeSystem (unsigned numberOfStateVariables)
 
virtual ~AbstractOdeSystem ()
 
virtual bool CalculateStoppingEvent (double time, const std::vector< double > &rY)
 
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< doubleGetStateVariables ()
 
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< doubleGetInitialConditions () 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< doubleComputeDerivedQuantities (double time, const std::vector< double > &rState)
 
std::vector< doubleComputeDerivedQuantitiesFromCurrentState (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 mA
 
double mB
 
double mC
 
double mD
 
double mE
 
double mF
 
boost::shared_ptr
< AbstractCellMutationState
mpMutationState
 
double mWntLevel
 

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< doublemStateVariables
 
std::vector< doublemParameters
 
- Protected Attributes inherited from AbstractUntemplatedParameterisedSystem
unsigned mNumberOfStateVariables
 
boost::shared_ptr
< AbstractOdeSystemInformation
mpSystemInfo
 

Detailed Description

Represents the Mirams et al. system of ODEs, based on Swat et al. (2004) [doi:10.1093/bioinformatics/bth110] and a simple Wnt model (unpublished)

The variables are

6. b1 = Beta-Catenin (from 1st allele) 7. b2 = Beta-Catenin (from 1st allele) 8. WntLevel

Definition at line 60 of file Mirams2010WntOdeSystem.hpp.

Constructor & Destructor Documentation

Mirams2010WntOdeSystem::Mirams2010WntOdeSystem ( double  wntLevel = 0.0,
boost::shared_ptr< AbstractCellMutationState pMutationState = boost::shared_ptr<AbstractCellMutationState>(),
std::vector< double stateVariables = std::vector<double>() 
)

Constructor.

Parameters
wntLevelis a non-dimensional Wnt value between 0 and 1. This sets up the Wnt pathway in its steady state.
pMutationStateoptional mutation state (affects the ODE system)
stateVariablesoptional initial conditions for state variables (only used in archiving)

State variables.

0. b1 = Beta-Catenin (1st allele's copy) 1. b2 = Beta-Catenin (2nd allele's copy) 2. wntLevel

Definition at line 45 of file Mirams2010WntOdeSystem.cpp.

References Init(), mA, mB, mC, mD, mF, mpMutationState, AbstractUntemplatedParameterisedSystem::mpSystemInfo, AbstractParameterisedSystem< std::vector< double > >::SetDefaultInitialCondition(), and AbstractParameterisedSystem< std::vector< double > >::SetStateVariables().

Mirams2010WntOdeSystem::~Mirams2010WntOdeSystem ( )

Destructor.

Definition at line 96 of file Mirams2010WntOdeSystem.cpp.

Member Function Documentation

void Mirams2010WntOdeSystem::EvaluateYDerivatives ( double  time,
const std::vector< double > &  rY,
std::vector< double > &  rDY 
)
virtual

Compute the RHS of the WntCellCycle 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].

Parameters
timeused to evaluate the RHS.
rYvalue of the solution vector used to evaluate the RHS.
rDYfilled in with the resulting derivatives (using Alarcons et al. (2004) system of equations).

Implements AbstractOdeSystem.

Definition at line 112 of file Mirams2010WntOdeSystem.cpp.

References mA, mB, mC, mD, mE, mF, and mpMutationState.

const boost::shared_ptr< AbstractCellMutationState > Mirams2010WntOdeSystem::GetMutationState ( ) const

Called by the archive function on the Wnt cell-cycle model.

Returns
mpMutationState

Definition at line 157 of file Mirams2010WntOdeSystem.cpp.

References mpMutationState.

double Mirams2010WntOdeSystem::GetWntLevel ( ) const
Returns
mWntLevel.

Definition at line 180 of file Mirams2010WntOdeSystem.cpp.

References mWntLevel.

void Mirams2010WntOdeSystem::Init ( )

Initialise parameter values.

Definition at line 101 of file Mirams2010WntOdeSystem.cpp.

References mA, mB, mC, mD, mE, and mF.

Referenced by Mirams2010WntOdeSystem().

template<class Archive >
void Mirams2010WntOdeSystem::serialize ( Archive &  archive,
const unsigned int  version 
)
inlineprivate

Serialize the object and its member variables.

Parameters
archivethe archive
versionthe current version of this class

Definition at line 95 of file Mirams2010WntOdeSystem.hpp.

void Mirams2010WntOdeSystem::SetMutationState ( boost::shared_ptr< AbstractCellMutationState pMutationState)

Set the mutation state of the cell.

This should be called by the relevant cell-cycle model before any solving of the ODE system (as it is used to evaluate the Y derivatives).

Parameters
pMutationStatethe mutation state.

Definition at line 91 of file Mirams2010WntOdeSystem.cpp.

References mpMutationState.

Member Data Documentation

double Mirams2010WntOdeSystem::mA
private

Parameters for the Mirams et al. (2010) modelDimensional parameter a.

Definition at line 69 of file Mirams2010WntOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and Mirams2010WntOdeSystem().

double Mirams2010WntOdeSystem::mB
private

Dimensional parameter b.

Definition at line 71 of file Mirams2010WntOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and Mirams2010WntOdeSystem().

double Mirams2010WntOdeSystem::mC
private

Dimensional parameter c.

Definition at line 73 of file Mirams2010WntOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and Mirams2010WntOdeSystem().

double Mirams2010WntOdeSystem::mD
private

Dimensional parameter d.

Definition at line 75 of file Mirams2010WntOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and Mirams2010WntOdeSystem().

double Mirams2010WntOdeSystem::mE
private

Dimensional parameter e.

Definition at line 77 of file Mirams2010WntOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Mirams2010WntOdeSystem::mF
private

Dimensional parameter f.

Definition at line 79 of file Mirams2010WntOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and Mirams2010WntOdeSystem().

boost::shared_ptr<AbstractCellMutationState> Mirams2010WntOdeSystem::mpMutationState
private

The mutation state of the cell (this affects the ODE system).

Definition at line 82 of file Mirams2010WntOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), GetMutationState(), Mirams2010WntOdeSystem(), and SetMutationState().

double Mirams2010WntOdeSystem::mWntLevel
private

The Wnt level (this affects the ODE system).

Definition at line 85 of file Mirams2010WntOdeSystem.hpp.

Referenced by GetWntLevel().


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