#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::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 44 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::~WntCellCycleOdeSystem ( )

Destructor.

Definition at line 121 of file WntCellCycleOdeSystem.cpp.

Member Function Documentation

◆ CalculateRootFunction()

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 304 of file WntCellCycleOdeSystem.cpp.

◆ CalculateStoppingEvent()

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 290 of file WntCellCycleOdeSystem.cpp.

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

◆ EvaluateYDerivatives()

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 193 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.

◆ GetMutationState()

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

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

Returns: mpMutationState the mutation state of the cell.

Definition at line 285 of file WntCellCycleOdeSystem.cpp.

References mpMutationState.

◆ GetWntLevel()

double WntCellCycleOdeSystem::GetWntLevel ( ) const

Returns: mWntLevel.

Definition at line 351 of file WntCellCycleOdeSystem.cpp.

References mWntLevel.

◆ Init()

void WntCellCycleOdeSystem::Init ( )

Initialise parameter values.

Definition at line 126 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, and mPhiE2F1.

Referenced by WntCellCycleOdeSystem().

◆ serialize()

template<class Archive >

void WntCellCycleOdeSystem::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Serialize the object and its member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 139 of file WntCellCycleOdeSystem.hpp.

◆ SetMutationState()

void WntCellCycleOdeSystem::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

pMutationState the mutation state.

Definition at line 116 of file WntCellCycleOdeSystem.cpp.

References mpMutationState.

Friends And Related Symbol Documentation

◆ boost::serialization::access

friend class boost::serialization::access

friend

Definition at line 131 of file WntCellCycleOdeSystem.hpp.

Member Data Documentation

◆ ma2d

double WntCellCycleOdeSystem::ma2d

private

Dimensional parameter a_2.

Definition at line 111 of file WntCellCycleOdeSystem.hpp.

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

◆ ma3d

double WntCellCycleOdeSystem::ma3d

private

Dimensional parameter a_3.

Definition at line 113 of file WntCellCycleOdeSystem.hpp.

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

◆ ma4d

double WntCellCycleOdeSystem::ma4d

private

Dimensional parameter a_4.

Definition at line 115 of file WntCellCycleOdeSystem.hpp.

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

◆ ma5d

double WntCellCycleOdeSystem::ma5d

private

Dimensional parameter a_5.

Definition at line 117 of file WntCellCycleOdeSystem.hpp.

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

◆ mad

double WntCellCycleOdeSystem::mad

private

Dimensional parameter a.

Definition at line 85 of file WntCellCycleOdeSystem.hpp.

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

◆ mJ11d

double WntCellCycleOdeSystem::mJ11d

private

Dimensional parameter J_11.

Definition at line 87 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mJ12d

double WntCellCycleOdeSystem::mJ12d

private

Dimensional parameter J_12.

Definition at line 89 of file WntCellCycleOdeSystem.hpp.

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

◆ mJ13d

double WntCellCycleOdeSystem::mJ13d

private

Dimensional parameter J_13.

Definition at line 91 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mJ61d

double WntCellCycleOdeSystem::mJ61d

private

Dimensional parameter J_13.

Definition at line 93 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mJ62d

double WntCellCycleOdeSystem::mJ62d

private

Dimensional parameter J_62.

Definition at line 95 of file WntCellCycleOdeSystem.hpp.

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

◆ mJ63d

double WntCellCycleOdeSystem::mJ63d

private

Dimensional parameter J_63.

Definition at line 97 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mk16d

double WntCellCycleOdeSystem::mk16d

private

Dimensional parameter k_16.

Definition at line 119 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mk23d

double WntCellCycleOdeSystem::mk23d

private

Dimensional parameter k_23.

Definition at line 83 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mk2d

double WntCellCycleOdeSystem::mk2d

private

Parameters for the Swat et al. (2004) model Dimensional parameter k_2.

Definition at line 75 of file WntCellCycleOdeSystem.hpp.

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

◆ mk34d

double WntCellCycleOdeSystem::mk34d

private

Dimensional parameter k_34.

Definition at line 79 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mk3d

double WntCellCycleOdeSystem::mk3d

private

Dimensional parameter k_3.

Definition at line 77 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mk43d

double WntCellCycleOdeSystem::mk43d

private

Dimensional parameter k_2.

Definition at line 81 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mk61d

double WntCellCycleOdeSystem::mk61d

private

Dimensional parameter k_61.

Definition at line 121 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mKm1d

double WntCellCycleOdeSystem::mKm1d

private

Dimensional parameter K_m1.

Definition at line 99 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mkpd

double WntCellCycleOdeSystem::mkpd

private

Dimensional parameter k_p.

Definition at line 101 of file WntCellCycleOdeSystem.hpp.

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

◆ mphi_i

double WntCellCycleOdeSystem::mphi_i

private

Dimensionless parameter phi_i.

Definition at line 105 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mphi_j

double WntCellCycleOdeSystem::mphi_j

private

Dimensionless parameter phi_j.

Definition at line 107 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mphi_p

double WntCellCycleOdeSystem::mphi_p

private

Dimensionless parameter phi_p.

Definition at line 109 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mphi_r

double WntCellCycleOdeSystem::mphi_r

private

Dimensionless parameter phi_r.

Definition at line 103 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mPhiE2F1

double WntCellCycleOdeSystem::mPhiE2F1

private

Dimensionless parameter phi_E2F1.

Definition at line 123 of file WntCellCycleOdeSystem.hpp.

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

◆ mpMutationState

boost::shared_ptr<AbstractCellMutationState> WntCellCycleOdeSystem::mpMutationState

private

The mutation state of the cell - Wnt pathway behaviour (and hence cell cycle time) changes depending on this

Definition at line 126 of file WntCellCycleOdeSystem.hpp.

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

◆ mWntLevel

double WntCellCycleOdeSystem::mWntLevel

private

The Wnt level (this affects the ODE system).

Definition at line 129 of file WntCellCycleOdeSystem.hpp.

Referenced by GetWntLevel().

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

crypt/src/odes/WntCellCycleOdeSystem.hpp
crypt/src/odes/WntCellCycleOdeSystem.cpp

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ WntCellCycleOdeSystem()

◆ ~WntCellCycleOdeSystem()

Member Function Documentation

◆ CalculateRootFunction()

◆ CalculateStoppingEvent()

◆ EvaluateYDerivatives()

◆ GetMutationState()

◆ GetWntLevel()

◆ Init()

◆ serialize()

◆ SetMutationState()

Friends And Related Symbol Documentation

◆ boost::serialization::access

Member Data Documentation

◆ 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

◆ mpMutationState

◆ mWntLevel