Chaste  Release::2018.1
SingleOdeWntCellCycleModel.cpp
1 /*
2 
3 Copyright (c) 2005-2018, University of Oxford.
4 All rights reserved.
5 
6 University of Oxford means the Chancellor, Masters and Scholars of the
7 University of Oxford, having an administrative office at Wellington
8 Square, Oxford OX1 2JD, UK.
9 
10 This file is part of Chaste.
11 
12 Redistribution and use in source and binary forms, with or without
13 modification, are permitted provided that the following conditions are met:
14  * Redistributions of source code must retain the above copyright notice,
15  this list of conditions and the following disclaimer.
16  * Redistributions in binary form must reproduce the above copyright notice,
17  this list of conditions and the following disclaimer in the documentation
18  and/or other materials provided with the distribution.
19  * Neither the name of the University of Oxford nor the names of its
20  contributors may be used to endorse or promote products derived from this
21  software without specific prior written permission.
22 
23 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
25 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
26 ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
27 LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
28 CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
29 GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
30 HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
31 LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
32 OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
33 
34 */
35 
36 #include "UblasIncludes.hpp"
37 #include "SingleOdeWntCellCycleModel.hpp"
38 #include "TransitCellProliferativeType.hpp"
39 #include "DifferentiatedCellProliferativeType.hpp"
40 
41 SingleOdeWntCellCycleModel::SingleOdeWntCellCycleModel(boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
43  mBetaCateninDivisionThreshold(100)// MAGIC NUMBER!
44 {
45  if (mpOdeSolver == boost::shared_ptr<AbstractCellCycleModelOdeSolver>())
46  {
47 #ifdef CHASTE_CVODE
49  mpOdeSolver->Initialise();
50  mpOdeSolver->SetMaxSteps(10000);
51 #else
53  mpOdeSolver->Initialise();
54  SetDt(0.001);
55 #endif //CHASTE_CVODE
56  }
57  assert(mpOdeSolver->IsSetUp());
58 }
59 
61  : SimpleWntCellCycleModel(rModel),
63  mBetaCateninDivisionThreshold(rModel.mBetaCateninDivisionThreshold)
64 {
65  /*
66  * Initialize only those member variables defined in this class.
67  * Create the new cell-cycle model's ODE system and use the current values
68  * of the state variables in mpOdeSystem as an initial condition.
69  *
70  * The member variables mUseCellProliferativeTypeDependentG1Duration,
71  * mWntStemThreshold, mWntTransitThreshold and mWntLabelledThreshold
72  * are initialized in the SimpleWntCellCycleModel constructor.
73  *
74  * The member variables mCurrentCellCyclePhase, mG1Duration,
75  * mMinimumGapDuration, mStemCellG1Duration, mTransitCellG1Duration,
76  * mSDuration, mG2Duration and mMDuration are initialized in the
77  * AbstractPhaseBasedCellCycleModel constructor.
78  *
79  * The member variables mBirthTime, mReadyToDivide and mDimension
80  * are initialized in the AbstractCellCycleModel constructor.
81  */
82 
83  assert(rModel.GetOdeSystem());
84  double wnt_level = rModel.GetWntLevel();
85  SetOdeSystem(new Mirams2010WntOdeSystem(wnt_level, rModel.mpCell->GetMutationState()));
87 }
88 
90 {
91  return new SingleOdeWntCellCycleModel(*this);
92 }
93 
95 {
96  assert(SimulationTime::Instance()->IsStartTimeSetUp());
100 }
101 
103 {
104  assert(mpOdeSystem == nullptr);
105  assert(mpCell != nullptr);
106 
107  double wnt_level = this->GetWntLevel();
108  mpOdeSystem = new Mirams2010WntOdeSystem(wnt_level, mpCell->GetMutationState());
110 
111  // MAGIC NUMBER!
112  //mBetaCateninDivisionThreshold = 100.0;
113 
114  // This call actually sets up the G1 phase to something sensible (random number generated)
116 
118 
120 }
121 
123 {
124  // Pass this time step's Wnt stimulus into the solver as a constant over this timestep.
126 
127  // Use the cell's current mutation status as another input
128  static_cast<Mirams2010WntOdeSystem*>(mpOdeSystem)->SetMutationState(mpCell->GetMutationState());
129 }
130 
132 {
133  assert(mpOdeSystem != nullptr);
134  assert(mpCell != nullptr);
135 
137  {
138  /*
139  * This method is usually called within a CellBasedSimulation, after the CellPopulation
140  * has called CellPropertyRegistry::TakeOwnership(). This means that were we to call
141  * CellPropertyRegistry::Instance() here when setting the CellProliferativeType, we
142  * would be creating a new CellPropertyRegistry. In this case the cell proliferative
143  * type counts, as returned by AbstractCellPopulation::GetCellProliferativeTypeCount(),
144  * would be incorrect. We must therefore access the CellProliferativeType via the cell's
145  * CellPropertyCollection.
146  */
147  boost::shared_ptr<AbstractCellProperty> p_diff_type =
148  mpCell->rGetCellPropertyCollection().GetCellPropertyRegistry()->Get<DifferentiatedCellProliferativeType>();
149  mpCell->SetCellProliferativeType(p_diff_type);
150  }
151  else
152  {
153  boost::shared_ptr<AbstractCellProperty> p_transit_type =
154  mpCell->rGetCellPropertyCollection().GetCellPropertyRegistry()->Get<TransitCellProliferativeType>();
155  mpCell->SetCellProliferativeType(p_transit_type);
156  }
157 }
158 
160 {
162 }
163 
164 void SingleOdeWntCellCycleModel::SetBetaCateninDivisionThreshold(double betaCateninDivisionThreshold)
165 {
166  mBetaCateninDivisionThreshold = betaCateninDivisionThreshold;
167 }
168 
170 {
172 }
173 
175 {
176  // No new parameters to output, so just call method on direct parent class
178 }
179 
180 // Declare identifier for the serializer
183 #include "CellCycleModelOdeSolverExportWrapper.hpp"
184 EXPORT_CELL_CYCLE_MODEL_ODE_SOLVER(SingleOdeWntCellCycleModel)
void SetStateVariables(const std::vector< double > &rStateVariables)
virtual void OutputCellCycleModelParameters(out_stream &rParamsFile)
void SetOdeSystem(AbstractOdeSystem *pOdeSystem)
SingleOdeWntCellCycleModel(const SingleOdeWntCellCycleModel &rModel)
boost::shared_ptr< AbstractCellCycleModelOdeSolver > mpOdeSolver
virtual void AdjustOdeParameters(double currentTime)
void SetBetaCateninDivisionThreshold(double betaCateninDivisionThreshold)
virtual void OutputCellCycleModelParameters(out_stream &rParamsFile)
static SimulationTime * Instance()
void SetStateVariables(const VECTOR &rStateVariables)
static boost::shared_ptr< CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER > > Instance()
const double DOUBLE_UNSET
Definition: Exception.hpp:56
AbstractOdeSystem * GetOdeSystem() const
AbstractCellCycleModel * CreateCellCycleModel()
#define CHASTE_CLASS_EXPORT(T)
bool SolveOdeToTime(double currentTime)