WntCellCycleOdeSystem Class Reference

#include <WntCellCycleOdeSystem.hpp>

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List of all members.

Public Member Functions

 WntCellCycleOdeSystem (double WntStimulus=0.0, const CellMutationState &rMutationState=HEALTHY)
 ~WntCellCycleOdeSystem ()
void Init ()
void SetMutationState (const CellMutationState &rMutationState)
CellMutationState & rGetMutationState ()
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)

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
CellMutationState mMutationState

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 (2004) [doi:10.1093/bioinformatics/bth110] and a simple Wnt model (unpublished)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 54 of file WntCellCycleOdeSystem.hpp.

Constructor & Destructor Documentation

WntCellCycleOdeSystem::WntCellCycleOdeSystem ( double  WntStimulus = 0.0,
const CellMutationState &  rMutationState = HEALTHY 
)

Constructor.

Parameters:
WntStimulus is a non-dimensional Wnt value between 0 and 1. This sets up the Wnt pathway in its steady state.
rMutationState affects the ODE system and is given by CellMutationStates.hpp

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 31 of file WntCellCycleOdeSystem.cpp.

References Init(), ma2d, ma3d, ma4d, ma5d, mMutationState, AbstractOdeSystem::mpSystemInfo, and AbstractOdeSystem::SetInitialConditionsComponent().

WntCellCycleOdeSystem::~WntCellCycleOdeSystem (  ) 

Destructor.

Definition at line 97 of file WntCellCycleOdeSystem.cpp.

Member Function Documentation

void WntCellCycleOdeSystem::Init (  ) 

Initialise parameter values.

Definition at line 102 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 ( const CellMutationState &  rMutationState  ) 

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:
rMutationState the mutation state.

Definition at line 92 of file WntCellCycleOdeSystem.cpp.

References mMutationState.

CellMutationState & WntCellCycleOdeSystem::rGetMutationState (  ) 

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

Returns:
mMutationState the mutation state of the cell defined by CellMutationStates.hpp

Definition at line 262 of file WntCellCycleOdeSystem.cpp.

References mMutationState.

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 169 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, mMutationState, mphi_i, mphi_j, mphi_p, mphi_r, and mPhiE2F1.

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 267 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 281 of file WntCellCycleOdeSystem.cpp.

Member Data Documentation

double WntCellCycleOdeSystem::mk2d [private]

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

Definition at line 63 of file WntCellCycleOdeSystem.hpp.

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

double WntCellCycleOdeSystem::mk3d [private]

Dimensional parameter k_3.

Definition at line 65 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mk34d [private]

Dimensional parameter k_34.

Definition at line 67 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mk43d [private]

Dimensional parameter k_2.

Definition at line 69 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mk23d [private]

Dimensional parameter k_23.

Definition at line 71 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mad [private]

Dimensional parameter a.

Definition at line 73 of file WntCellCycleOdeSystem.hpp.

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

double WntCellCycleOdeSystem::mJ11d [private]

Dimensional parameter J_11.

Definition at line 75 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mJ12d [private]

Dimensional parameter J_12.

Definition at line 77 of file WntCellCycleOdeSystem.hpp.

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

double WntCellCycleOdeSystem::mJ13d [private]

Dimensional parameter J_13.

Definition at line 79 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mJ61d [private]

Dimensional parameter J_13.

Definition at line 81 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mJ62d [private]

Dimensional parameter J_62.

Definition at line 83 of file WntCellCycleOdeSystem.hpp.

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

double WntCellCycleOdeSystem::mJ63d [private]

Dimensional parameter J_63.

Definition at line 85 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mKm1d [private]

Dimensional parameter K_m1.

Definition at line 87 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mkpd [private]

Dimensional parameter k_p.

Definition at line 89 of file WntCellCycleOdeSystem.hpp.

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

double WntCellCycleOdeSystem::mphi_r [private]

Dimensionless parameter phi_r.

Definition at line 91 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mphi_i [private]

Dimensionless parameter phi_i.

Definition at line 93 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mphi_j [private]

Dimensionless parameter phi_j.

Definition at line 95 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mphi_p [private]

Dimensionless parameter phi_p.

Definition at line 97 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::ma2d [private]

Dimensional parameter a_2.

Definition at line 99 of file WntCellCycleOdeSystem.hpp.

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

double WntCellCycleOdeSystem::ma3d [private]

Dimensional parameter a_3.

Definition at line 101 of file WntCellCycleOdeSystem.hpp.

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

double WntCellCycleOdeSystem::ma4d [private]

Dimensional parameter a_4.

Definition at line 103 of file WntCellCycleOdeSystem.hpp.

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

double WntCellCycleOdeSystem::ma5d [private]

Dimensional parameter a_5.

Definition at line 105 of file WntCellCycleOdeSystem.hpp.

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

double WntCellCycleOdeSystem::mk16d [private]

Dimensional parameter k_16.

Definition at line 107 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mk61d [private]

Dimensional parameter k_61.

Definition at line 109 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mPhiE2F1 [private]

Dimensionless parameter phi_E2F1.

Definition at line 111 of file WntCellCycleOdeSystem.hpp.

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

CellMutationState WntCellCycleOdeSystem::mMutationState [private]

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

Definition at line 114 of file WntCellCycleOdeSystem.hpp.

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

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