WntCellCycleOdeSystem Class Reference

#include <WntCellCycleOdeSystem.hpp>

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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 (2004) [doi:10.1093/bioinformatics/bth110] and a simple Wnt model (unpublished)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, AbstractOdeSystem::SetDefaultInitialCondition(), and AbstractOdeSystem::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().

Dimensionless parameter phi_r.

Definition at line 100 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter phi_i.

Definition at line 102 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter phi_j.

Definition at line 104 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

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().

Dimensionless parameter phi_E2F1.

Definition at line 120 of file WntCellCycleOdeSystem.hpp.

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

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().

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:

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