#include <WntCellCycleOdeSystem.hpp>

Inheritance diagram for WntCellCycleOdeSystem:

Collaboration diagram for WntCellCycleOdeSystem:

Public Member Functions
	WntCellCycleOdeSystem (double wntLevel=0.0, boost::shared_ptr< AbstractCellMutationState > pMutationState=boost::shared_ptr< AbstractCellMutationState >(), std::vector< double > stateVariables=std::vector< double >())

	~WntCellCycleOdeSystem ()

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)

bool	CalculateStoppingEvent (double time, const std::vector< double > &rY)

double	CalculateRootFunction (double time, const std::vector< double > &rY)

double	GetWntLevel () const

Public Member Functions inherited from AbstractOdeSystem
	AbstractOdeSystem (unsigned numberOfStateVariables)

virtual	~AbstractOdeSystem ()

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	mk2d

double	mk3d

double	mk34d

double	mk43d

double	mk23d

double	mad

double	mJ11d

double	mJ12d

double	mJ13d

double	mJ61d

double	mJ62d

double	mJ63d

double	mKm1d

double	mkpd

double	mphi_r

double	mphi_i

double	mphi_j

double	mphi_p

double	ma2d

double	ma3d

double	ma4d

double	ma5d

double	mk16d

double	mk61d

double	mPhiE2F1

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< double >	mStateVariables

std::vector< double >	mParameters

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

0. r = pRb 1. e = E2F1 2. i = CycD (inactive) 3. j = CycD (active) 4. p = pRb-p 5. c = destruction complex (Active) 6. b1 = Beta-Catenin (from 1st allele) 7. b2 = Beta-Catenin (from 1st allele) 8. WntLevel

Definition at line 66 of file WntCellCycleOdeSystem.hpp.

Constructor & Destructor Documentation

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

Constructor.

Parameters

wntLevel	is a non-dimensional Wnt value between 0 and 1. This sets up the Wnt pathway in its steady state.
pMutationState	optional mutation state (affects the ODE system)
stateVariables	optional initial conditions for state variables (only used in archiving)

State variables.

0. r = pRb 1. e = E2F1 (This is the S-phase indicator) 2. i = CycD (inactive) 3. j = CycD (active) 4. p = pRb-p 5. c = APC (Active) 6. b1 = Beta-Catenin (1st allele's copy) 7. b2 = Beta-Catenin (2nd allele's copy) 8. wntLevel

Definition at line 45 of file WntCellCycleOdeSystem.cpp.

References Init(), ma2d, ma3d, ma4d, ma5d, mpMutationState, AbstractUntemplatedParameterisedSystem::mpSystemInfo, AbstractParameterisedSystem< std::vector< double > >::SetDefaultInitialCondition(), and AbstractParameterisedSystem< std::vector< double > >::SetStateVariables().

WntCellCycleOdeSystem::~WntCellCycleOdeSystem ( )

Destructor.

Definition at line 122 of file WntCellCycleOdeSystem.cpp.

Member Function Documentation

double WntCellCycleOdeSystem::CalculateRootFunction	(	double	time,
		const std::vector< double > &	rY
	)

virtual

When using CVODE this function is called instead of CalculateStoppingEvent. It allows the point at which rY[1] reaches 1 to be found to greater precision.

Parameters

time	at which to calculate whether the stopping event has occurred
rY	value of the solution vector used to evaluate the RHS

Returns: function value - giving CVODE an estimate of how close we are to the root.

Reimplemented from AbstractOdeSystem.

Definition at line 305 of file WntCellCycleOdeSystem.cpp.

bool WntCellCycleOdeSystem::CalculateStoppingEvent	(	double	time,
		const std::vector< double > &	rY
	)

virtual

This also contains a calculation of dY[1], copied from EvaluateYDerivatives. Ensure they do not get out of sync!

Parameters

time	at which to calculate whether the stopping event has occurred
rY	value of the solution vector used to evaluate the RHS

Returns: whether we have reached the stopping event

Reimplemented from AbstractOdeSystem.

Definition at line 291 of file WntCellCycleOdeSystem.cpp.

References mad, mJ12d, mJ62d, mk2d, mkpd, and mPhiE2F1.

void WntCellCycleOdeSystem::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

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 194 of file WntCellCycleOdeSystem.cpp.

References ma2d, ma3d, ma4d, ma5d, mad, mJ11d, mJ12d, mJ13d, mJ61d, mJ62d, mJ63d, mk16d, mk23d, mk2d, mk34d, mk3d, mk43d, mk61d, mKm1d, mkpd, mphi_i, mphi_j, mphi_p, mphi_r, mPhiE2F1, and mpMutationState.