bagherilab · Jannetty · Feb 25, 2026 · Mar 4, 2026 · Mar 6, 2026 · Mar 6, 2026
diff --git a/build.gradle b/build.gradle
@@ -163,6 +163,8 @@ task updateVersion (group: "versioning", description: "Syncs gradle version with
     }
 }
 
+copyJar.mustRunAfter spotlessMisc, spotlessJava, compileTestJava, test, jacocoTestReport
+
 build.dependsOn copyJar
 
 test.finalizedBy jacocoTestReport

diff --git a/input/1.xml b/input/1.xml
@@ -0,0 +1,42 @@
+<set prefix="2026-03-06">
+    <series name="WT_rotation_volume_none_critVolOn" start="1" end="100"
+            ds=".3" margin="0" height="1" length="802" width="802"
+            dt=".083" ticks="576" interval="576">
+        <potts>
+            <potts.term id="volume" />
+            <potts.term id="adhesion" />
+            <potts.term id="surface" />
+            <potts.parameter term="surface" id="LAMBDA" value=".1"/>
+        </potts>
+        <agents>
+            <populations>
+                <population id="fly-stem-mudmut" class="fly-stem-mudmut" init="1" >
+                    <population.link id="fly-gmc" weight="1"/>
+                    <population.parameter id="proliferation/SIZE_TARGET" value="1.2" />
+                    <population.parameter id="CRITICAL_VOLUME" value="170" units="um^3" conversion="DS^-3" />
+                    <population.parameter id="proliferation/CELL_GROWTH_RATE" value="15" units="um^3/hour" conversion="DS^-3DT"/>
+                    <population.parameter id="proliferation/BASAL_APOPTOSIS_RATE" value="0"/>
+                    <population.parameter id="proliferation/VOLUME_BASED_CRITICAL_VOLUME" value="1"/>
+                    <population.parameter id="proliferation/DIV_ROTATION_DISTRIBUTION" value="NORMAL(MU=36,SIGMA=30)"/>
+                    <population.parameter id="proliferation/APICAL_AXIS_RULESET" value="normal" />
+                    <population.parameter id="proliferation/APICAL_AXIS_ROTATION_DISTRIBUTION" value="NORMAL(MU=0,SIGMA=30)" />
+                    <population.parameter id="proliferation/DIFFERENTIATION_RULESET" value="volume" />
+                    <population.parameter id="proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE" value="386" />
+                    <population.parameter id="proliferation/DYNAMIC_GROWTH_RATE_VOLUME" value="0" />
+                    <population.parameter id="proliferation/DYNAMIC_GROWTH_RATE_NB_CONTACT" value="0" />
+                </population>
+                <population id="fly-gmc" class="fly-gmc" init="0">
+                    <population.link id="fly-neuron" weight="1"/>
+                    <population.parameter id="proliferation/BASAL_APOPTOSIS_RATE" value="0"/>
+                    <population.parameter id="proliferation/CELL_GROWTH_RATE" value="5" units="um^2/hour" conversion="DS^-2.DT"/>
+                    <population.parameter id="proliferation/DYNAMIC_GROWTH_RATE_VOLUME" value="0" />
+                </population>
+                <population id="fly-neuron" class="fly-neuron" init="0">
+                    <population.parameter id="proliferation/CELL_GROWTH_RATE" value="0"/>
+                    <population.parameter id="proliferation/BASAL_APOPTOSIS_RATE" value="0"/>
+                    <population.parameter id="CRITICAL_VOLUME" value="11" units="um^3" conversion="DS^-3" />
+                </population>
+            </populations>
+        </agents>
+    </series>
+</set>
diff --git a/setup/1.xml b/setup/1.xml
@@ -0,0 +1,42 @@
+<set prefix="2025-01-01">
+    <series name="WT_rotation_volume_none_critVolOn" start="1" end="100"
+            ds=".3" margin="0" height="1" length="802" width="802"
+            dt=".083" ticks="576" interval="576">
+        <potts>
+            <potts.term id="volume" />
+            <potts.term id="adhesion" />
+            <potts.term id="surface" />
+            <potts.parameter term="surface" id="LAMBDA" value=".1"/>
+        </potts>
+        <agents>
+            <populations>
+                <population id="fly-stem-wt" class="fly-stem-wt" init="1" >
+                    <population.link id="fly-gmc" weight="1"/>
+                    <population.parameter id="proliferation/SIZE_TARGET" value="1.2" />
+                    <population.parameter id="CRITICAL_VOLUME" value="170" units="um^3" conversion="DS^-3" />
+                    <population.parameter id="proliferation/CELL_GROWTH_RATE" value="15" units="um^3/hour" conversion="DS^-3DT"/>
+                    <population.parameter id="proliferation/BASAL_APOPTOSIS_RATE" value="0"/>
+                    <population.parameter id="proliferation/VOLUME_BASED_CRITICAL_VOLUME" value="1"/>
+                    <population.parameter id="proliferation/DIV_ROTATION_DISTRIBUTION" value="NORMAL(MU=36,SIGMA=30)"/>
+                    <population.parameter id="proliferation/APICAL_AXIS_RULESET" value="rotation" />
+                    <population.parameter id="proliferation/APICAL_AXIS_ROTATION_DISTRIBUTION" value="NORMAL(MU=0,SIGMA=30)" />
+                    <population.parameter id="proliferation/DIFFERENTIATION_RULESET" value="volume" />
+                    <population.parameter id="proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE" value="386" />
+                    <population.parameter id="proliferation/DYNAMIC_GROWTH_RATE_VOLUME" value="0" />
+                    <population.parameter id="proliferation/DYNAMIC_GROWTH_RATE_NB_CONTACT" value="0" />
+                </population>
+                <population id="fly-gmc" class="fly-gmc" init="0">
+                    <population.link id="fly-neuron" weight="1"/>
+                    <population.parameter id="proliferation/BASAL_APOPTOSIS_RATE" value="0"/>
+                    <population.parameter id="proliferation/CELL_GROWTH_RATE" value="5" units="um^2/hour" conversion="DS^-2.DT"/>
+                    <population.parameter id="proliferation/DYNAMIC_GROWTH_RATE_VOLUME" value="0" />
+                </population>
+                <population id="fly-neuron" class="fly-neuron" init="0">
+                    <population.parameter id="proliferation/CELL_GROWTH_RATE" value="0"/>
+                    <population.parameter id="proliferation/BASAL_APOPTOSIS_RATE" value="0"/>
+                    <population.parameter id="CRITICAL_VOLUME" value="11" units="um^3" conversion="DS^-3" />
+                </population>
+            </populations>
+        </agents>
+    </series>
+</set>
diff --git a/src/arcade/potts/PottsARCADE.java b/src/arcade/potts/PottsARCADE.java
@@ -31,6 +31,8 @@ public OutputLoader getLoader(Series series) {
 
     @Override
     public OutputSaver getSaver(Series series) {
-        return new PottsOutputSaver(series);
+        PottsOutputSaver saver = new PottsOutputSaver(series);
+        saver.saveProspero = settings.contains("SAVE_PROSPERO");
+        return saver;
     }
 }
diff --git a/src/arcade/potts/agent/cell/PottsCellContainer.java b/src/arcade/potts/agent/cell/PottsCellContainer.java
@@ -105,6 +105,8 @@ public PottsCellContainer(
     /**
      * Creates a {@code PottsCellContainer} instance.
      *
+     * <p>The container does not have prospero.
+     *
      * @param id the cell ID
      * @param parent the parent ID
      * @param pop the cell population index

diff --git a/src/arcade/potts/agent/cell/PottsCellFly.java b/src/arcade/potts/agent/cell/PottsCellFly.java
@@ -0,0 +1,42 @@
+package arcade.potts.agent.cell;
+
+import arcade.core.env.location.Location;
+import arcade.core.util.GrabBag;
+import arcade.core.util.Parameters;
+
+/**
+ * Implementation of {@link PottsCell} for Potts Fly models.
+ *
+ * <p>Cells follow {@link PottsCell} rules, but additionally keep track of the amount of prospero.
+ *
+ * <p>[TODO: fix class comment]
+ */
+public abstract class PottsCellFly extends PottsCell {
+
+    /** Amount of prospero in cell. */
+    private double prospero;
+
+    public PottsCellFly(
+            PottsCellContainer container, Location location, Parameters parameters, GrabBag links) {
+        super(container, location, parameters, links);
+        this.prospero = 0;
+    }
+
+    /**
+     * Gets the amount of prospero in the cell.
+     *
+     * @return the amount of prospero in the cell.
+     */
+    public double getProspero() {
+        return prospero;
+    }
+
+    /**
+     * Sets the amount of prospero for the cell.
+     *
+     * @param prospero the amount of prospero in the cell.
+     */
+    public void setProspero(double prospero) {
+        this.prospero = prospero;
+    }
+}
diff --git a/src/arcade/potts/agent/cell/PottsCellFlyGMC.java b/src/arcade/potts/agent/cell/PottsCellFlyGMC.java
@@ -16,7 +16,7 @@
  * PottsModuleProliferationVolumeBasedDivision} module. The basal apoptosis rate of this cell should
  * be set to 0 in the setup file.
  */
-public class PottsCellFlyGMC extends PottsCell {
+public class PottsCellFlyGMC extends PottsCellFly {
 
     /**
      * Creates a fly GMC {@code PottsCell} agent.

diff --git a/src/arcade/potts/agent/cell/PottsCellFlyNeuron.java b/src/arcade/potts/agent/cell/PottsCellFlyNeuron.java
@@ -9,7 +9,7 @@
 import static arcade.potts.util.PottsEnums.State;
 
 /** Represents a fly neuron cell in the Potts model. This cell is quiescent. */
-public final class PottsCellFlyNeuron extends PottsCell {
+public final class PottsCellFlyNeuron extends PottsCellFly {
 
     /**
      * Creates a {@code PottsCellFlyNeuron} {@code PottsCell} agent.

diff --git a/src/arcade/potts/agent/cell/PottsCellFlyStem.java b/src/arcade/potts/agent/cell/PottsCellFlyStem.java
@@ -11,7 +11,7 @@
 import arcade.potts.util.PottsEnums.Phase;
 import static arcade.potts.util.PottsEnums.State;
 
-public class PottsCellFlyStem extends PottsCell {
+public class PottsCellFlyStem extends PottsCellFly {
     /** Enum outlining parameters for each cell type. */
     public enum StemType {
         /** Wild type stem cell. */
@@ -59,7 +59,7 @@
    /** The type of stem cell. */
    public final StemType stemType;

    private Vector apicalAxis;

    /**
     * Constructor for PottsCellFlyStem.
@@ -91,7 +91,7 @@
        }
    }

    public void setApicalAxis(Vector apicalAxis) {
        this.apicalAxis = apicalAxis;
    }

@@ -112,10 +112,10 @@
    @Override
    public PottsCellContainer make(int newID, CellState newState, MersenneTwisterFast random) {
        throw new UnsupportedOperationException(
                "make(int, CellState, MersenneTwisterFast) not supported. Please use make(int, CellState, MersenneTwisterFast, int, double) instead.");
    }

    public PottsCellContainer make(
            int newID,
            CellState newState,
            MersenneTwisterFast random,

diff --git a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java
@@ -4,10 +4,7 @@
 import arcade.core.agent.cell.CellContainer;
 import arcade.core.env.location.Location;
 import arcade.core.sim.Simulation;
-import arcade.potts.agent.cell.PottsCell;
-import arcade.potts.agent.cell.PottsCellContainer;
-import arcade.potts.agent.cell.PottsCellFlyGMC;
-import arcade.potts.agent.cell.PottsCellFlyNeuron;
+import arcade.potts.agent.cell.*;
 import arcade.potts.env.location.PottsLocation2D;
 import arcade.potts.sim.Potts;
 import arcade.potts.sim.PottsSimulation;
@@ -20,8 +17,11 @@
 */
 public class PottsModuleFlyGMCDifferentiation extends PottsModuleProliferationVolumeBasedDivision {
 
     Boolean pdeLike;
 
+    /* Rate of Prospero degradation (ticks^-1). */
+    final double prosperoDegradationRate;
+
     /**
      * Creates a fly GMC proliferation module.
      *
@@ -30,6 +30,21 @@
     public PottsModuleFlyGMCDifferentiation(PottsCellFlyGMC cell) {
         super(cell);
         pdeLike = (cell.getParameters().getInt("proliferation/PDELIKE") != 0);
+        prosperoDegradationRate =
+                cell.getParameters().getDouble("proliferation/PROSPERO_DEGRADATION_RATE");
+        if (prosperoDegradationRate < 0) {
+            throw new IllegalArgumentException("Prospero degradation rate should not be negative");
+        }
+    }
+
+    @Override
+    public void step(MersenneTwisterFast random, Simulation sim) {
+        super.step(random, sim);
+        ((PottsCellFly) cell)
+                .setProspero(
+                        Math.max(0, ((PottsCellFly) cell).getProspero() - prosperoDegradationRate));
+        System.out.println(
+                "GMC ID " + cell.getID() + " prospero: " + ((PottsCellFly) cell).getProspero());
     }
 
     /**
@@ -95,7 +110,7 @@
        differentiatedGMC.schedule(sim.getSchedule());
    }

    public void updateGrowthRate(Simulation sim) {
        if (!dynamicGrowthRateVolume) {
            cellGrowthRate = cellGrowthRateBase;
        } else {
@@ -112,10 +127,10 @@

                for (int i = 0; i < objs.numObjs; i++) {
                    Object o = objs.objs[i];
                    if (!(o instanceof arcade.potts.agent.cell.PottsCell)) continue;

                    arcade.potts.agent.cell.PottsCell c = (arcade.potts.agent.cell.PottsCell) o;
                    if (c.getPop() != cell.getPop()) continue; // keep to same population

                    if (o instanceof arcade.potts.agent.cell.PottsCellFlyGMC) {
                        arcade.potts.agent.cell.PottsCellFlyGMC gmc =

diff --git a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java
@@ -16,6 +16,7 @@
 import arcade.core.util.distributions.UniformDistribution;
 import arcade.potts.agent.cell.PottsCell;
 import arcade.potts.agent.cell.PottsCellContainer;
+import arcade.potts.agent.cell.PottsCellFly;
 import arcade.potts.agent.cell.PottsCellFlyStem;
 import arcade.potts.agent.cell.PottsCellFlyStem.StemType;
 import arcade.potts.env.location.PottsLocation;
@@ -30,7 +31,7 @@
 import static arcade.potts.util.PottsEnums.Phase;
 import static arcade.potts.util.PottsEnums.State;

 public class PottsModuleFlyStemProliferation extends PottsModuleProliferationVolumeBasedDivision {

    /** Threshold for critical volume size checkpoint. */
    static final double SIZE_CHECKPOINT = 0.95;
@@ -38,6 +39,9 @@
     /** Basal rate of apoptosis (ticks^-1). */
     final double basalApoptosisRate;
 
+    /** Rate of Prospero synthesis (ticks^-1). */
+    final double prosperoSynthesisRate;
+
     /** Distribution that determines rotational offset of cell's division plane. */
     final NormalDistribution splitDirectionDistribution;
 
@@ -65,7 +69,7 @@
    /** Boolean flag indicating whether growth rate should be regulated by NB-NB contact. */
    final boolean dynamicGrowthRateNBSelfRepression;

    final double volumeBasedCriticalVolumeMultiplier;

    /**
     * Range of values considered equal when determining daughter cell identity. ex. if ruleset is
@@ -88,11 +92,11 @@
    /*
     * Boolean flag for whether the daughter cell's differentiation is determined deterministically.
     */
    final boolean hasDeterministicDifferentiation;

    final double initialSize;

    public static final double EPSILON = 1e-8;

    /**
     * Boolean determining whether growth and division rates are universal across all NBs. If true
@@ -116,6 +120,7 @@
         Parameters parameters = cell.getParameters();
 
         basalApoptosisRate = parameters.getDouble("proliferation/BASAL_APOPTOSIS_RATE");
+        prosperoSynthesisRate = parameters.getDouble("proliferation/PROSPERO_SYNTHESIS_RATE");
         splitDirectionDistribution =
                 (NormalDistribution)
                         parameters.getDistribution("proliferation/DIV_ROTATION_DISTRIBUTION");
@@ -135,7 +140,7 @@

        if (dynamicGrowthRateVolume && dynamicGrowthRateNBSelfRepression) {
            throw new InvalidParameterException(
                    "Dynamic growth rate can be either volume-based or NB-contact-based, not both.");
        }

        volumeBasedCriticalVolumeMultiplier =
@@ -160,6 +165,15 @@
         setPhase(Phase.UNDEFINED);
     }
 
+    @Override
+    public void step(MersenneTwisterFast random, Simulation sim) {
+        super.step(random, sim);
+        ((PottsCellFly) cell)
+                .setProspero(((PottsCellFly) cell).getProspero() + prosperoSynthesisRate);
+        System.out.println(
+                "Stem ID " + cell.getID() + " prospero: " + ((PottsCellFly) cell).getProspero());
+    }
+
     @Override
     public void addCell(MersenneTwisterFast random, Simulation sim) {
         Potts potts = ((PottsSimulation) sim).getPotts();
@@ -190,17 +204,17 @@
     * @param sim the simulation
     */
    public void updateGrowthRate(Simulation sim) {
        if (dynamicGrowthRateVolume == true) {
            updateVolumeBasedGrowthRate(sim);
        } else if (dynamicGrowthRateNBSelfRepression == true) {
            updateGrowthRateBasedOnOtherNBs(sim);
        } else {
            cellGrowthRate = cellGrowthRateBase;
        }
    }

    public void updateVolumeBasedGrowthRate(Simulation sim) {
        if (pdeLike == false) {
            updateCellVolumeBasedGrowthRate(
                    cell.getLocation().getVolume(), cell.getCriticalVolume());
        } else {
@@ -245,7 +259,7 @@
        return stemNeighbors;
    }

    protected void updateGrowthRateBasedOnOtherNBs(Simulation sim) {
        int nbsInContact;
        if (pdeLike) {
            int nbsInSim = getNBsInSimulation(sim).size();
@@ -255,8 +269,8 @@
        }
        double np = Math.max(0.0, (double) nbsInContact);

        double Kn = Math.pow(nbContactHalfMax, nbContactHillN);
        double Npn = Math.pow(np, nbContactHillN);

        double hillRepression;
        if (Kn == 0.0) {
@@ -305,7 +319,7 @@
     */
    public Plane getWTDivisionPlaneWithRotationalVariance(
            PottsCellFlyStem cell, double rotationOffset) {
        Vector apical_axis = cell.getApicalAxis();
        Vector rotatedNormalVector =
                Vector.rotateVectorAroundAxis(
                        apical_axis, Direction.XY_PLANE.vector, rotationOffset);
@@ -347,7 +361,7 @@
     * @return the voxel location where the cell will split
     */
    public static Voxel getCellSplitVoxel(
            StemType stemType, PottsCellFlyStem cell, Vector rotatedNormalVector) {
        ArrayList<Integer> splitOffsetPercent = new ArrayList<>();
        splitOffsetPercent.add(stemType.splitOffsetPercentX);
        splitOffsetPercent.add(stemType.splitOffsetPercentY);
@@ -371,7 +385,7 @@
            if (differentiationRuleset.equals("volume")) {
                double vol1 = loc1.getVolume();
                double vol2 = loc2.getVolume();
                if (Math.abs(vol1 - vol2) < range) {
                    return true;
                } else {
                    return false;
@@ -388,13 +402,13 @@
    }

    /*
     * Determines whether the daughter cell should be a neuroblast or a GMC according to the orientation.
     * This is deterministic.
     *
     * @param divisionPlane
     * @return {@code true} if the daughter should be a stem cell. {@code false} if the daughter should be a GMC.
     */
    private boolean daughterStemDeterministic(Plane divisionPlane) {

        Vector normalVector = divisionPlane.getUnitNormalVector();

@@ -453,7 +467,7 @@
        return distanceAlongAxis - range <= EPSILON;
    }

    /**
     * Makes a daughter NB cell
     *
     * @param daughterLoc the location of the daughter NB cell
@@ -478,10 +492,13 @@
         PottsCellContainer container =
                 ((PottsCellFlyStem) cell)
                         .make(newID, State.PROLIFERATIVE, random, cell.getPop(), criticalVol);
-        scheduleNewCell(container, daughterLoc, sim, potts, random);
+
+        double daughterProspero = splitStemProspero(((PottsCellFly) cell).getProspero(), random);
+        System.out.print("Creating daughter stem cell with prospero " + daughterProspero + " and ");
+        scheduleNewCell(container, daughterLoc, sim, potts, random, daughterProspero);
     }
 
     /**
     * Makes a daughter GMC cell
     *
     * @param parentLoc the location of the parent NB cell
@@ -510,7 +527,39 @@
         PottsCellContainer container =
                 ((PottsCellFlyStem) cell)
                         .make(newID, State.PROLIFERATIVE, random, newPop, criticalVolume);
-        scheduleNewCell(container, daughterLoc, sim, potts, random);
+        PottsCellFlyStem flyStemCell = (PottsCellFlyStem) cell;
+
+        System.out.print(
+                "Creating daughter GMC with prospero "
+                        + ((PottsCellFly) cell).getProspero()
+                        + " and ");
+        scheduleNewCell(
+                container, daughterLoc, sim, potts, random, ((PottsCellFly) cell).getProspero());
+    }
+
+    /**
+     * Determines how prospero is split between the parent and daughter cell. Can be edited to
+     * change behavior. Current prototype behavior divides the prospero evenly 50% of the time, and
+     * randomly selects which cell gets all prospero the other 50% of the time.
+     *
+     * @param parentProspero the parent cell's prospero to be divided
+     * @param random the random number generator
+     * @return double with daughter prospero amount
+     */
+    static double splitStemProspero(double parentProspero, MersenneTwisterFast random) {
+        if (parentProspero <= 0) {
+            return 0;
+        }
+
+        if (random.nextBoolean()) { // 50% of the time, split prospero evenly
+            return parentProspero / 2;
+        } else { // 50% of the time, randomly choose which cell gets all the prospero
+            if (random.nextBoolean()) {
+                return parentProspero;
+            } else {
+                return 0;
+            }
+        }
     }
 
     /**
@@ -527,7 +576,8 @@
             PottsLocation daughterLoc,
             Simulation sim,
             Potts potts,
-            MersenneTwisterFast random) {
+            MersenneTwisterFast random,
+            double daughterProspero) {
         PottsCell newCell =
                 (PottsCell) container.convert(sim.getCellFactory(), daughterLoc, random);
         if (newCell.getClass() == PottsCellFlyStem.class) {
@@ -537,6 +587,10 @@
         potts.register(newCell);
         newCell.reset(potts.ids, potts.regions);
         newCell.schedule(sim.getSchedule());
+        System.out.println("ID " + newCell.getID());
+
+        ((PottsCellFly) newCell).setProspero(daughterProspero);
+        ((PottsCellFly) cell).setProspero(((PottsCellFly) cell).getProspero() - daughterProspero);
     }
 
     /**
@@ -551,7 +605,7 @@
            case "uniform":
                if (!(apicalAxisRotationDistribution instanceof UniformDistribution)) {
                    throw new IllegalArgumentException(
                            "apicalAxisRotationDistribution must be a UniformDistribution under the uniform apical axis ruleset.");
                }
                Vector newRandomApicalAxis =
                        Vector.rotateVectorAroundAxis(
@@ -564,7 +618,7 @@
            case "normal":
                if (!(apicalAxisRotationDistribution instanceof NormalDistribution)) {
                    throw new IllegalArgumentException(
                            "apicalAxisRotationDistribution must be a NormalDistribution under the rotation apical axis ruleset.");
                }
                Vector newRotatedApicalAxis =
                        Vector.rotateVectorAroundAxis(
@@ -600,7 +654,7 @@
        }
    }

    /**
     * Calculates the critical volume of a GMC daughter cell
     *
     * @param gmcLoc the location of the GMC daughter cell
@@ -655,12 +709,12 @@
        return (proj1 < proj2) ? loc2 : loc1; // higher projection = more basal
    }

    public HashSet<PottsCellFlyStem> getNBsInSimulation(Simulation sim) {
        HashSet<PottsCellFlyStem> nbsInSimulation = new HashSet<>();
        Bag simObjects = sim.getGrid().getAllObjects();
        for (int i = 0; i < simObjects.numObjs; i++) {
            Object o = simObjects.objs[i];
            if (!(o instanceof PottsCell)) continue; // skip non-cell objects
            PottsCell cellInSim = (PottsCell) o;
            if (cell.getPop() == cellInSim.getPop() && o instanceof PottsCellFlyStem) {
                nbsInSimulation.add((PottsCellFlyStem) o);

diff --git a/src/arcade/potts/command.potts.xml b/src/arcade/potts/command.potts.xml
@@ -1,2 +1,3 @@
 <commands>
+    <switch id="SAVE_PROSPERO" short="p" long="prospero" help="Save the PROSPERO output files" />
 </commands>
diff --git a/src/arcade/potts/parameter.potts.xml b/src/arcade/potts/parameter.potts.xml
@@ -86,6 +86,9 @@
     <population.module module="proliferation" id="VOLUME_BASED_CRITICAL_VOLUME_MULTIPLIER" value="1" description="if enabled, GMC critical volume = daughter_volume × multiplier" />
     <!-- Deterministic Differentiation-->
     <population.module module="proliferation" id="HAS_DETERMINISTIC_DIFFERENTIATION" value="TRUE" description="if TRUE, differentiation is determined deterministically" />
+    <!-- Prospero synthesis and degradation rates -->
+    <population.module module="proliferation" id="PROSPERO_SYNTHESIS_RATE" value="1" units="Prospero/hour" conversion="DT" description="synthesis rate of Prospero" />
+    <population.module module="proliferation" id="PROSPERO_DEGRADATION_RATE" value="-1" units="Prospero/hour" conversion="DT" description="degradation rate of Prospero" />
 
     <!-- apoptosis module parameters -->
     <population.module module="apoptosis" id="RATE_EARLY" value="4" units="steps/hour" conversion="DT" description="rate of events in early apoptosis phase" />
@@ -96,4 +99,5 @@
     <population.module module="apoptosis" id="CYTOPLASMIC_BLEBBING_RATE" value="175" units="um^3/hour" conversion="DS^-3.DT" description="basal rate of cytoplasmic blebbing" />
     <population.module module="apoptosis" id="NUCLEUS_PYKNOSIS_RATE" value="100" units="um^3/hour" conversion="DS^-3.DT" description="basal rate of nuclear pyknosis" />
     <population.module module="apoptosis" id="NUCLEUS_FRAGMENTATION_RATE" value="75" units="um^3/hour" conversion="DS^-3.DT" description="basal rate of nuclear fragmentation" />
+
 </parameters>
-Original file line number
+Diff line change
@@ Expand Up @@
         }
     }
+    copyJar.mustRunAfter spotlessMisc, spotlessJava, compileTestJava, test, jacocoTestReport
     build.dependsOn copyJar
     test.finalizedBy jacocoTestReport
@@ Expand Down @@