Adding simple OS monolayer Reference Model

src/Test02aMonolayerGrowth/FixedDurationCellCycleModel.cpp

@@ -0,0 +1,106 @@
+/*
+
+Copyright (c) 2005-2022, University of Oxford.
+All rights reserved.
+
+University of Oxford means the Chancellor, Masters and Scholars of the
+University of Oxford, having an administrative office at Wellington
+Square, Oxford OX1 2JD, UK.
+
+This file is part of Chaste.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+ * Neither the name of the University of Oxford nor the names of its
+   contributors may be used to endorse or promote products derived from this
+   software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+*/
+
+#include "AbstractSimplePhaseBasedCellCycleModel.hpp"
+#include "DifferentiatedCellProliferativeType.hpp"
+
+#include "FixedDurationCellCycleModel.hpp"
+
+template<class Archive>
+void FixedDurationCellCycleModel::serialize(Archive & archive, const unsigned int version)
+{
+    // Archive cell-cycle model using serialization code from AbstractSimplePhaseBasedCellCycleModel
+    archive & boost::serialization::base_object<AbstractSimplePhaseBasedCellCycleModel>(*this);
+}
+
+FixedDurationCellCycleModel::FixedDurationCellCycleModel()
+    : AbstractSimplePhaseBasedCellCycleModel()
+{
+  SetPhaseDurations();
+}
+
+void FixedDurationCellCycleModel::SetPhaseDurations()
+{
+    SetStemCellG1Duration(7.0);
+    SetTransitCellG1Duration(7.0);
+    SetSDuration(6.0);
+    SetG2Duration(3.0);
+    SetMDuration(2.0);
+    SetMinimumGapDuration(3.0);
+}
+
+void FixedDurationCellCycleModel::SetG1Duration()
+{
+    assert(mpCell != NULL);  // Make sure cell exists
+
+    mG1Duration = 7.0;
+}
+
+AbstractCellCycleModel* FixedDurationCellCycleModel::CreateCellCycleModel()
+{
+    // Create a new cell-cycle model
+    FixedDurationCellCycleModel* pCellCycleModel = new FixedDurationCellCycleModel();
+    return pCellCycleModel;
+}
+
+void FixedDurationCellCycleModel::UpdateCellCyclePhase()
+{
+    double timeSinceBirth = GetAge();
+    assert(timeSinceBirth >= 0);
+
+    if (mpCell->GetCellProliferativeType()->IsType<DifferentiatedCellProliferativeType>())
+    {
+        mCurrentCellCyclePhase = G_ZERO_PHASE;
+    }
+    else if (timeSinceBirth < GetG1Duration())
+    {
+        mCurrentCellCyclePhase = G_ONE_PHASE;
+    }
+    else if (timeSinceBirth <  GetG1Duration() + GetSDuration())
+    {
+        mCurrentCellCyclePhase = S_PHASE;
+    }
+    else if (timeSinceBirth < GetG1Duration() + GetSDuration() + GetG2Duration())
+    {
+        mCurrentCellCyclePhase = G_TWO_PHASE;
+    }
+    else if (timeSinceBirth < GetG1Duration() + GetSDuration() + GetG2Duration() + GetMDuration())
+    {
+        mCurrentCellCyclePhase = M_PHASE;
+    }
+}
+
+#include "SerializationExportWrapperForCpp.hpp"
+CHASTE_CLASS_EXPORT(FixedDurationCellCycleModel)

src/Test02aMonolayerGrowth/FixedDurationCellCycleModel.hpp

@@ -0,0 +1,69 @@
+/*
+
+Copyright (c) 2005-2022, University of Oxford.
+All rights reserved.
+
+University of Oxford means the Chancellor, Masters and Scholars of the
+University of Oxford, having an administrative office at Wellington
+Square, Oxford OX1 2JD, UK.
+
+This file is part of Chaste.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+ * Neither the name of the University of Oxford nor the names of its
+   contributors may be used to endorse or promote products derived from this
+   software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+*/
+
+#ifndef FIXEDDURATIONCELLCYCLEMODEL_HPP_
+#define FIXEDDURATIONCELLCYCLEMODEL_HPP_
+
+#include "AbstractSimplePhaseBasedCellCycleModel.hpp"
+
+// "Simple" cell-cycle model: phase durations are set when the model is created.
+class FixedDurationCellCycleModel : public AbstractSimplePhaseBasedCellCycleModel
+{
+private:
+    // For archiving (saving or loading) the cell-cycle model object in a cell-based simulation. 
+    friend class boost::serialization::access;
+    template<class Archive>
+    void serialize(Archive & archive, const unsigned int version);
+
+    void SetPhaseDurations();
+    void SetG1Duration() override;
+
+public:
+    FixedDurationCellCycleModel();
+
+    // Override builder method for new copies of the cell-cycle model.
+    AbstractCellCycleModel* CreateCellCycleModel() override;
+
+    // Override to start phase from G1
+    void UpdateCellCyclePhase() override;
+};
+
+// Provides a unique identifier for the custom cell-cycle model.
+// Needed for archiving and for writing out parameters file.
+// Simulations will throw errors if missing.
+#include "SerializationExportWrapper.hpp"
+CHASTE_CLASS_EXPORT(FixedDurationCellCycleModel)
+
+#endif // FIXEDDURATIONCELLCYCLEMODEL_HPP_

src/Test02aMonolayerGrowth/FixedDurationCellCycleModelWithGrowthInhibition.cpp

@@ -0,0 +1,161 @@
+/*
+
+Copyright (c) 2005-2022, University of Oxford.
+All rights reserved.
+
+University of Oxford means the Chancellor, Masters and Scholars of the
+University of Oxford, having an administrative office at Wellington
+Square, Oxford OX1 2JD, UK.
+
+This file is part of Chaste.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+ * Neither the name of the University of Oxford nor the names of its
+   contributors may be used to endorse or promote products derived from this
+   software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+*/
+
+#include "AbstractSimplePhaseBasedCellCycleModel.hpp"
+#include "DifferentiatedCellProliferativeType.hpp"
+
+#include "FixedDurationCellCycleModelWithGrowthInhibition.hpp"
+
+#include <iostream>
+
+#include "RandomNumberGenerator.hpp"
+
+template<class Archive>
+void FixedDurationCellCycleModelWithGrowthInhibition::serialize(Archive & archive, const unsigned int version)
+{
+    // Archive cell-cycle model using serialization code from AbstractSimplePhaseBasedCellCycleModel
+    archive & boost::serialization::base_object<AbstractSimplePhaseBasedCellCycleModel>(*this);
+}
+
+FixedDurationCellCycleModelWithGrowthInhibition::FixedDurationCellCycleModelWithGrowthInhibition()
+    : AbstractSimplePhaseBasedCellCycleModel()
+{
+  SetPhaseDurations();
+  mPhaseTimer = 0.0;
+  mLastCellAge = 0.0;
+}
+
+void FixedDurationCellCycleModelWithGrowthInhibition::ResetForDivision()
+{
+    AbstractCellCycleModel::ResetForDivision();
+    mCurrentCellCyclePhase = G_ONE_PHASE;
+    mPhaseTimer = 0.0;
+    mLastCellAge = 0.0;
+}
+
+void FixedDurationCellCycleModelWithGrowthInhibition::SetPhaseDurations()
+{
+    SetStemCellG1Duration(7.0);  
+    SetTransitCellG1Duration(7.0);
+    SetSDuration(6.0);
+    SetG2Duration(3.0);
+    SetMDuration(2.0);
+    SetMinimumGapDuration(3.0);
+}
+
+void FixedDurationCellCycleModelWithGrowthInhibition::SetG1Duration()
+{
+    assert(mpCell != NULL);  // Make sure cell exists
+
+    mG1Duration = 7.0;
+}
+
+AbstractCellCycleModel* FixedDurationCellCycleModelWithGrowthInhibition::CreateCellCycleModel()
+{
+    // Create a new cell-cycle model
+    FixedDurationCellCycleModelWithGrowthInhibition* pCellCycleModel = new FixedDurationCellCycleModelWithGrowthInhibition();
+    return pCellCycleModel;
+}
+
+
+void FixedDurationCellCycleModelWithGrowthInhibition::SetPhaseTimer(const double value) {
+    mPhaseTimer = value;
+}
+
+bool FixedDurationCellCycleModelWithGrowthInhibition::ReadyToDivide() {
+    assert(mpCell != nullptr);
+
+    if (!mReadyToDivide)
+    {
+        UpdateCellCyclePhase();
+        if ((mCurrentCellCyclePhase != G_ZERO_PHASE) &&
+            (mPhaseTimer >= GetMDuration() + GetG1Duration() + GetSDuration() + GetG2Duration()) &&
+            (mCurrentCellCyclePhase == M_PHASE)) 
+        {
+            mReadyToDivide = true;
+        }
+    }
+
+    mpCell->GetCellData()->SetItem("growth inhibited", 0.0);
+    return mReadyToDivide;
+}
+
+void FixedDurationCellCycleModelWithGrowthInhibition::UpdateCellCyclePhase()
+{
+    double timeSinceBirth = GetAge();
+    assert(timeSinceBirth >= 0);
+
+    // Update cell growth phase timer
+    double change_in_cell_age = timeSinceBirth - mLastCellAge;
+    mPhaseTimer += change_in_cell_age;
+    mLastCellAge = timeSinceBirth;
+
+    // Select the correct phase
+    if (mpCell->GetCellProliferativeType()->IsType<DifferentiatedCellProliferativeType>())
+    {
+        mCurrentCellCyclePhase = G_ZERO_PHASE;
+    }
+    else if (mPhaseTimer < GetG1Duration())
+    {
+        if (mpCell->GetCellData()->GetItem("growth inhibited") != 0.0) {
+            //std::cout << "Cell inhibited\n";
+            mPhaseTimer -= change_in_cell_age;
+            return;
+        }
+        mCurrentCellCyclePhase = G_ONE_PHASE;
+    }
+    else if (mPhaseTimer <  GetG1Duration() + GetSDuration())
+    {
+        mCurrentCellCyclePhase = S_PHASE;
+    }
+    else if (mPhaseTimer < GetG1Duration() + GetSDuration() + GetG2Duration())
+    {
+        if (mpCell->GetCellData()->GetItem("growth inhibited") != 0.0) {
+            //std::cout << "Cell inhibited\n";
+            mPhaseTimer -= change_in_cell_age;
+            return;
+        }
+        mCurrentCellCyclePhase = G_TWO_PHASE;
+    }
+    else if (mPhaseTimer < GetG1Duration() + GetSDuration() + GetG2Duration() + GetMDuration())
+    {
+        mCurrentCellCyclePhase = M_PHASE;
+    }
+
+    mpCell->GetCellData()->SetItem("cell age", mPhaseTimer);
+}
+
+#include "SerializationExportWrapperForCpp.hpp"
+CHASTE_CLASS_EXPORT(FixedDurationCellCycleModelWithGrowthInhibition)