added inverted division stem cell types

bagherilab · Aug 5, 2024 · 3bc39be · 3bc39be
1 parent c73c759
commit 3bc39be
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Showing 12 changed files with 529 additions and 15 deletions.
diff --git a/setup/setupInvertOneStemDaughterStemDaughterBasal.xml b/setup/setupInvertOneStemDaughterStemDaughterBasal.xml
@@ -0,0 +1,21 @@
+<set prefix="20240730">
+    <series name="testing" start="0" end="0"
+            ds="1" margin="0" height="1" length="100" width="100"
+            dt="1" ticks="200" interval="50">
+        <potts>
+            <potts.term id="volume" />
+            <potts.term id="adhesion" />
+            <potts.parameter term="adhesion" id="ADHESION" value="150" target="invert" />
+        </potts>
+        <agents>
+            <populations>
+                <population id="invert" class="flystem-invert-onestemdaughter-stemdaughterbasal" init="1" >
+                    <population.parameter id="CRITICAL_VOLUME_MEAN" value="30" units="um^3" conversion="DS^-3" />
+                    <population.parameter id="CRITICAL_VOLUME_STDEV" value="5" units="um^3" conversion="DS^-3" />
+                </population>
+                <population id="neuron" init="0">
+                </population>
+            </populations>
+        </agents>
+    </series>
+</set>
diff --git a/setup/setupInvertTwoStemDaughtersStemDaughterBasalOrBoth.xml b/setup/setupInvertTwoStemDaughtersStemDaughterBasalOrBoth.xml
@@ -0,0 +1,25 @@
+<set prefix="20240730">
+    <series name="testing" start="0" end="0"
+            ds="1" margin="0" height="1" length="100" width="100"
+            dt="1" ticks="200" interval="50">
+        <potts>
+            <potts.term id="volume" />
+            <potts.term id="adhesion" />
+            <potts.parameter term="adhesion" id="ADHESION" value="150" target="invert2" />
+        </potts>
+        <agents>
+            <populations>
+                <population id="invert2" class="flystem-invert-twostemdaughters-stemdaughterbasalorboth" init="1" >
+                    <population.parameter id="CRITICAL_VOLUME_MEAN" value="30" units="um^3" conversion="DS^-3" />
+                    <population.parameter id="CRITICAL_VOLUME_STDEV" value="5" units="um^3" conversion="DS^-3" />
+                </population>
+                <population id="neuron" init="0">
+                </population>
+                <population id="wt" class="flystem-wt" init="1" >
+                    <population.parameter id="CRITICAL_VOLUME_MEAN" value="30" units="um^3" conversion="DS^-3" />
+                    <population.parameter id="CRITICAL_VOLUME_STDEV" value="5" units="um^3" conversion="DS^-3" />
+                </population>
+            </populations>
+        </agents>
+    </series>
+</set>
diff --git a/setup/setupMUDmutOneStemDaughterStemDaughterLeft.xml b/setup/setupMUDmutOneStemDaughterStemDaughterLeft.xml
@@ -13,7 +13,7 @@
                     <population.parameter id="CRITICAL_VOLUME_MEAN" value="30" units="um^3" conversion="DS^-3" />
                     <population.parameter id="CRITICAL_VOLUME_STDEV" value="5" units="um^3" conversion="DS^-3" />
                 </population>
-                <population id="neuron" class="flyneuronwt" init="0">
+                <population id="neuron" init="0">
                 </population>
             </populations>
         </agents>

diff --git a/setup/setupMUDmutOneStemDaughterStemDaughterRandom.xml b/setup/setupMUDmutOneStemDaughterStemDaughterRandom.xml
@@ -13,7 +13,7 @@
                     <population.parameter id="CRITICAL_VOLUME_MEAN" value="30" units="um^3" conversion="DS^-3" />
                     <population.parameter id="CRITICAL_VOLUME_STDEV" value="5" units="um^3" conversion="DS^-3" />
                 </population>
-                <population id="neuron" class="flyneuronwt" init="0">
+                <population id="neuron" init="0">
                 </population>
             </populations>
         </agents>

diff --git a/setup/setupMudmutTwoStemDaughtersStemDaughterRandom.xml b/setup/setupMudmutTwoStemDaughtersStemDaughterRandom.xml
@@ -5,15 +5,19 @@
         <potts>
             <potts.term id="volume" />
             <potts.term id="adhesion" />
-            <potts.parameter term="adhesion" id="ADHESION" value="150" target="mudmut" />
+            <potts.parameter term="adhesion" id="ADHESION" value="150" target="mudmut2" />
         </potts>
         <agents>
             <populations>
-                <population id="mudmut" class="flystem-mudmut-twostemdaughters-stemdaughterrandom" init="1" >
+                <population id="mudmut2" class="flystem-mudmut-twostemdaughters-stemdaughterrandom" init="1" >
                     <population.parameter id="CRITICAL_VOLUME_MEAN" value="30" units="um^3" conversion="DS^-3" />
                     <population.parameter id="CRITICAL_VOLUME_STDEV" value="5" units="um^3" conversion="DS^-3" />
                 </population>
-                <population id="neuron" class="flyneuronwt" init="0">
+                <population id="neuron" init="0">
+                </population>
+                <population id="mudmut1" class="flystem-mudmut-onestemdaughter-stemdaughterrandom" init="0" >
+                    <population.parameter id="CRITICAL_VOLUME_MEAN" value="30" units="um^3" conversion="DS^-3" />
+                    <population.parameter id="CRITICAL_VOLUME_STDEV" value="5" units="um^3" conversion="DS^-3" />
                 </population>
             </populations>
         </agents>

diff --git a/setup/setupWT.xml b/setup/setupWT.xml
@@ -9,11 +9,11 @@
         </potts>
         <agents>
             <populations>
-                <population id="flystem" class="flystemwt" init="1" >
+                <population id="flystem" class="flystem-wt" init="1" >
                     <population.parameter id="CRITICAL_VOLUME_MEAN" value="30" units="um^3" conversion="DS^-3" />
                     <population.parameter id="CRITICAL_VOLUME_STDEV" value="5" units="um^3" conversion="DS^-3" />
                 </population>
-                <population id="neuron" class="flyneuronwt" init="0">
+                <population id="neuron" init="0">
                 </population>
             </populations>
         </agents>

diff --git a/src/arcade/potts/agent/cell/PottsCellContainer.java b/src/arcade/potts/agent/cell/PottsCellContainer.java
@@ -189,7 +189,29 @@ private Cell convert(PottsCellFactory factory, Location location) {
                             null, null);
                 }
                 break;
-            case "flystemwt":
+            case "flystem-invert-onestemdaughter-stemdaughterbasal":
+                if (factory.popToRegions.get(pop)) {
+                    cell = new PottsCellFlyStemInvert1StemBasal(id, parent, pop, state, age, divisions,
+                            location, true, parameters, criticalVolume, criticalHeight,
+                            criticalRegionVolumes, criticalRegionHeights);
+                } else {
+                    cell = new PottsCellFlyStemInvert1StemBasal(id, parent, pop, state, age, divisions,
+                            location, false, parameters, criticalVolume, criticalHeight,
+                            null, null);
+                }
+                break;
+            case "flystem-invert-twostemdaughters-stemdaughterbasalorboth":
+                if (factory.popToRegions.get(pop)) {
+                    cell = new PottsCellFlyStemInvert2StemBasalOrBoth(id, parent, pop, state, age, divisions,
+                            location, true, parameters, criticalVolume, criticalHeight,
+                            criticalRegionVolumes, criticalRegionHeights);
+                } else {
+                    cell = new PottsCellFlyStemInvert2StemBasalOrBoth(id, parent, pop, state, age, divisions,
+                            location, false, parameters, criticalVolume, criticalHeight,
+                            null, null);
+                }
+                break;
+            case "flystem-wt":
                 if (factory.popToRegions.get(pop)) {
                     cell = new PottsCellFlyStemWT(id, parent, pop, state, age, divisions,
                             location, true, parameters, criticalVolume, criticalHeight,

diff --git a/src/arcade/potts/agent/cell/PottsCellFlyStemInvert1StemBasal.java b/src/arcade/potts/agent/cell/PottsCellFlyStemInvert1StemBasal.java
@@ -0,0 +1,67 @@
+package arcade.potts.agent.cell;
+
+import java.util.EnumMap;
+import arcade.core.agent.cell.CellState;
+import arcade.core.env.location.Location;
+import arcade.core.util.MiniBox;
+import arcade.potts.agent.module.PottsModuleApoptosisSimple;
+import arcade.potts.agent.module.PottsModuleAutosis;
+import arcade.potts.agent.module.PottsModuleNecrosis;
+import arcade.potts.agent.module.PottsModuleProliferationFlyStemOneThirdSplitBasalReturn;
+import arcade.potts.agent.module.PottsModuleQuiescence;
+import arcade.potts.util.PottsEnums.Region;
+import arcade.potts.util.PottsEnums.State;
+import ec.util.MersenneTwisterFast;
+
+public final class PottsCellFlyStemInvert1StemBasal extends PottsCell{
+
+    public static final int POTTS_CELL_FLY_NEURON_WT_POP = 2;
+
+    public PottsCellFlyStemInvert1StemBasal(int id, int parent, int pop, CellState state, int age, int divisions,
+                         Location location, boolean hasRegions, MiniBox parameters,
+                         double criticalVolume, double criticalHeight,
+                         EnumMap<Region, Double> criticalRegionVolumes,
+                         EnumMap<Region, Double> criticalRegionHeights) {
+        super(id, parent, pop, state, age, divisions, location, hasRegions, parameters,
+                criticalVolume, criticalHeight, criticalRegionVolumes, criticalRegionHeights);
+    }
+
+    @Override
+    public PottsCell make(int newID, CellState newState, Location newLocation,
+                          MersenneTwisterFast random) {
+        divisions++;
+        MiniBox newParameters = new MiniBox();
+        for (String key : this.getParameters().getKeys()) {
+            newParameters.put(key, this.getParameters().get(key));
+        }
+        newParameters.put("proliferation/CELL_GROWTH_RATE", "0");
+        return new PottsCellFlyNeuronWT(newID, id, POTTS_CELL_FLY_NEURON_WT_POP, newState, age, divisions, newLocation,
+                hasRegions, newParameters, criticalVolume, criticalHeight,
+                criticalRegionVolumes, criticalRegionHeights);
+    }
+
+    @Override
+    void setStateModule(CellState newState) {
+        switch ((State) newState) {
+            case QUIESCENT:
+                module = new PottsModuleQuiescence(this);
+                break;
+            case PROLIFERATIVE:
+                module = new PottsModuleProliferationFlyStemOneThirdSplitBasalReturn(this);
+                break;
+            case APOPTOTIC:
+                module = new PottsModuleApoptosisSimple(this);
+                break;
+            case NECROTIC:
+                module = new PottsModuleNecrosis(this);
+                break;
+            case AUTOTIC:
+                module = new PottsModuleAutosis(this);
+                break;
+            default:
+                // State must be one of the above cases.
+                module = null;
+                break;
+        }
+    }
+}
diff --git a/src/arcade/potts/agent/cell/PottsCellFlyStemInvert2StemBasalOrBoth.java b/src/arcade/potts/agent/cell/PottsCellFlyStemInvert2StemBasalOrBoth.java
@@ -0,0 +1,85 @@
+package arcade.potts.agent.cell;
+
+import java.util.EnumMap;
+import arcade.core.agent.cell.CellState;
+import arcade.core.env.location.Location;
+import arcade.core.util.MiniBox;
+import arcade.potts.agent.module.PottsModuleApoptosisSimple;
+import arcade.potts.agent.module.PottsModuleAutosis;
+import arcade.potts.agent.module.PottsModuleNecrosis;
+import arcade.potts.agent.module.PottsModuleProliferationFlyStemOneThirdSplitBasalReturn;
+import arcade.potts.agent.module.PottsModuleQuiescence;
+import arcade.potts.util.PottsEnums.Region;
+import arcade.potts.util.PottsEnums.State;
+import ec.util.MersenneTwisterFast;
+
+public final class PottsCellFlyStemInvert2StemBasalOrBoth extends PottsCell{
+
+    public static final int POTTS_STEM_INVERT_2_POP = 1;
+    public static final int POTTS_CELL_FLY_NEURON_WT_POP = 2;
+    public static final int POTTS_STEM_WT_POP = 3;
+
+    public PottsCellFlyStemInvert2StemBasalOrBoth(int id, int parent, int pop, CellState state, int age, int divisions,
+                         Location location, boolean hasRegions, MiniBox parameters,
+                         double criticalVolume, double criticalHeight,
+                         EnumMap<Region, Double> criticalRegionVolumes,
+                         EnumMap<Region, Double> criticalRegionHeights) {
+        super(id, parent, pop, state, age, divisions, location, hasRegions, parameters,
+                criticalVolume, criticalHeight, criticalRegionVolumes, criticalRegionHeights);
+    }
+
+    @Override
+    public PottsCell make(int newID, CellState newState, Location newLocation,
+                          MersenneTwisterFast random) {
+        divisions++;
+        // 25% chance of making PottsCellFlyStemWT, 25% chance of making PottsCellFlyStemInvert2StemRandom 50% chance of making FlyNeuronWT
+        if (random.nextDouble() < 0.25) {
+            System.out.println("Making new PottsCellFlyStemWT");
+            System.out.println("Inside make method, growth rate is " + this.getParameters().get("proliferation/CELL_GROWTH_RATE"));
+            return new PottsCellFlyStemWT(newID, id, POTTS_STEM_WT_POP, newState, age, divisions, newLocation,
+                    hasRegions, this.getParameters(), criticalVolume, criticalHeight,
+                    criticalRegionVolumes, criticalRegionHeights);
+        } else if (random.nextDouble() < 0.5) {
+            System.out.println("Making new PottsCellFlyStemInvert2StemRandom");
+            System.out.println("Inside make method, growth rate is " + this.getParameters().get("proliferation/CELL_GROWTH_RATE"));
+            return new PottsCellFlyStemInvert2StemBasalOrBoth(newID, id, POTTS_STEM_INVERT_2_POP, newState, age, divisions, newLocation,
+                    hasRegions, this.getParameters(), criticalVolume, criticalHeight,
+                    criticalRegionVolumes, criticalRegionHeights);
+        } else {
+            System.out.println("Making new FlyNeuronWT");
+            MiniBox newParameters = new MiniBox();
+            for (String key : this.getParameters().getKeys()) {
+                newParameters.put(key, this.getParameters().get(key));
+            }
+            newParameters.put("proliferation/CELL_GROWTH_RATE", "0");
+            return new PottsCellFlyNeuronWT(newID, id, POTTS_CELL_FLY_NEURON_WT_POP, newState, age, divisions, newLocation,
+                    hasRegions, newParameters, criticalVolume, criticalHeight,
+                    criticalRegionVolumes, criticalRegionHeights);
+        }
+    }
+
+    @Override
+    void setStateModule(CellState newState) {
+        switch ((State) newState) {
+            case QUIESCENT:
+                module = new PottsModuleQuiescence(this);
+                break;
+            case PROLIFERATIVE:
+                module = new PottsModuleProliferationFlyStemOneThirdSplitBasalReturn(this);
+                break;
+            case APOPTOTIC:
+                module = new PottsModuleApoptosisSimple(this);
+                break;
+            case NECROTIC:
+                module = new PottsModuleNecrosis(this);
+                break;
+            case AUTOTIC:
+                module = new PottsModuleAutosis(this);
+                break;
+            default:
+                // State must be one of the above cases.
+                module = null;
+                break;
+        }
+    }
+}
diff --git a/src/arcade/potts/agent/cell/PottsCellFlyStemMUDMut2StemRandom.java b/src/arcade/potts/agent/cell/PottsCellFlyStemMUDMut2StemRandom.java
@@ -16,7 +16,7 @@
 public final class PottsCellFlyStemMUDMut2StemRandom extends PottsCell{
 
     public static final int POTTS_CELL_FLY_NEURON_WT_POP = 2;
-    public static final int POTTS_STEM_POP = 1;
+    public static final int POTTS_STEM_1_POP = 3;;
 
     public PottsCellFlyStemMUDMut2StemRandom(int id, int parent, int pop, CellState state, int age, int divisions,
                          Location location, boolean hasRegions, MiniBox parameters,
@@ -42,7 +42,7 @@ public PottsCell make(int newID, CellState newState, Location newLocation,
         } else if (random.nextDouble() < 0.5) {
             System.out.println("Making new MUDMut1StemRandom");
             System.out.println("Inside make method, growth rate is " + this.getParameters().get("proliferation/CELL_GROWTH_RATE"));
-            return new PottsCellFlyStemMUDMut1StemRandom(newID, id, pop, newState, age, divisions, newLocation,
+            return new PottsCellFlyStemMUDMut1StemRandom(newID, id, POTTS_STEM_1_POP, newState, age, divisions, newLocation,
                     hasRegions, this.getParameters(), criticalVolume, criticalHeight,
                     criticalRegionVolumes, criticalRegionHeights);
         } else {