WntCellCycleOdeSystem Class Reference

#include <WntCellCycleOdeSystem.hpp>

Inheritance diagram for WntCellCycleOdeSystem:

Collaboration diagram for WntCellCycleOdeSystem:

List of all members.

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

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

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 (2004) [doi:10.1093/bioinformatics/bth110] and a simple Wnt model (unpublished)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 63 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 32 of file WntCellCycleOdeSystem.cpp.

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

WntCellCycleOdeSystem::~WntCellCycleOdeSystem ( )

Destructor.

Definition at line 109 of file WntCellCycleOdeSystem.cpp.

Member Function Documentation

template<class Archive>

void WntCellCycleOdeSystem::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Serialize the object and its member variables.

Parameters:

	archive	the archive
	version	the current version of this class

Definition at line 136 of file WntCellCycleOdeSystem.hpp.

void WntCellCycleOdeSystem::Init ( )

Initialise parameter values.

Definition at line 114 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().

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 104 of file WntCellCycleOdeSystem.cpp.

References mpMutationState.

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 273 of file WntCellCycleOdeSystem.cpp.

References mpMutationState.

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 181 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.

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 278 of file WntCellCycleOdeSystem.cpp.

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

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 292 of file WntCellCycleOdeSystem.cpp.

double WntCellCycleOdeSystem::GetWntLevel ( ) const

Get method for mWntLevel.

Definition at line 339 of file WntCellCycleOdeSystem.cpp.

References mWntLevel.

Member Data Documentation

double WntCellCycleOdeSystem::mk2d [private]

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

Definition at line 72 of file WntCellCycleOdeSystem.hpp.

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

double WntCellCycleOdeSystem::mk3d [private]

Dimensional parameter k_3.

Definition at line 74 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mk34d [private]

Dimensional parameter k_34.

Definition at line 76 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mk43d [private]

Dimensional parameter k_2.

Definition at line 78 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mk23d [private]

Dimensional parameter k_23.

Definition at line 80 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mad [private]

Dimensional parameter a.

Definition at line 82 of file WntCellCycleOdeSystem.hpp.

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

double WntCellCycleOdeSystem::mJ11d [private]

Dimensional parameter J_11.

Definition at line 84 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mJ12d [private]

Dimensional parameter J_12.

Definition at line 86 of file WntCellCycleOdeSystem.hpp.

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

double WntCellCycleOdeSystem::mJ13d [private]

Dimensional parameter J_13.

Definition at line 88 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mJ61d [private]

Dimensional parameter J_13.

Definition at line 90 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mJ62d [private]

Dimensional parameter J_62.

Definition at line 92 of file WntCellCycleOdeSystem.hpp.

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

double WntCellCycleOdeSystem::mJ63d [private]

Dimensional parameter J_63.

Definition at line 94 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mKm1d [private]

Dimensional parameter K_m1.

Definition at line 96 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mkpd [private]

Dimensional parameter k_p.

Definition at line 98 of file WntCellCycleOdeSystem.hpp.

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

double WntCellCycleOdeSystem::mphi_r [private]

Dimensionless parameter phi_r.

Definition at line 100 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mphi_i [private]

Dimensionless parameter phi_i.

Definition at line 102 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mphi_j [private]

Dimensionless parameter phi_j.

Definition at line 104 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mphi_p [private]

Dimensionless parameter phi_p.

Definition at line 106 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::ma2d [private]

Dimensional parameter a_2.

Definition at line 108 of file WntCellCycleOdeSystem.hpp.

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

double WntCellCycleOdeSystem::ma3d [private]

Dimensional parameter a_3.

Definition at line 110 of file WntCellCycleOdeSystem.hpp.

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

double WntCellCycleOdeSystem::ma4d [private]

Dimensional parameter a_4.

Definition at line 112 of file WntCellCycleOdeSystem.hpp.

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

double WntCellCycleOdeSystem::ma5d [private]

Dimensional parameter a_5.

Definition at line 114 of file WntCellCycleOdeSystem.hpp.

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

double WntCellCycleOdeSystem::mk16d [private]

Dimensional parameter k_16.

Definition at line 116 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mk61d [private]

Dimensional parameter k_61.

Definition at line 118 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mPhiE2F1 [private]

Dimensionless parameter phi_E2F1.

Definition at line 120 of file WntCellCycleOdeSystem.hpp.

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

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 123 of file WntCellCycleOdeSystem.hpp.

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

double WntCellCycleOdeSystem::mWntLevel [private]

The Wnt level (this affects the ODE system).

Definition at line 126 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
	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
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