chemotherapy scheduling

bagherilab · Nov 12, 2024 · fb122da · fb122da
1 parent 137f99e
commit fb122da
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Showing 4 changed files with 33 additions and 25 deletions.
diff --git a/src/arcade/patch/agent/process/PatchProcessChemotherapy.java b/src/arcade/patch/agent/process/PatchProcessChemotherapy.java
@@ -91,7 +91,6 @@ public abstract class PatchProcessChemotherapy extends PatchProcess {
     private void updateExternal(Simulation sim) {
         extAmt = sim.getLattice("DRUG").getAverageValue(location) * location.getVolume();
         extAmt *= (1.0 - drugDecayRate);
-        System.out.println("extAmt: " + extAmt);
     }
 
     @Override

diff --git a/src/arcade/patch/env/component/PatchComponentDose.java b/src/arcade/patch/env/component/PatchComponentDose.java
@@ -24,8 +24,10 @@ public class PatchComponentDose implements Component {
     private final double mediaVolume;
     private final double latticePatchVolume;
     private final double latticePatchArea;
-    private final double doseDelay;
+    private final double doseStart;
     private final double doseDuration;
+    private final double doseInterval;
+    private final double doseEnd;
 
     public PatchComponentDose(Series series, MiniBox parameters) {
         layers = new ArrayList<>();
@@ -36,8 +38,10 @@ public PatchComponentDose(Series series, MiniBox parameters) {
 
         // Set loaded parameters.
         mediaAmount = parameters.getDouble("MEDIA_AMOUNT");
-        doseDelay = parameters.getDouble("DOSE_DELAY");
+        doseStart = parameters.getDouble("DOSE_START");
         doseDuration = parameters.getDouble("DOSE_DURATION");
+        doseInterval = parameters.getDouble("DOSE_INTERVAL");
+        doseEnd = parameters.getDouble("DOSE_END");
 
         // Set patch parameters.
         MiniBox patch = ((PatchSeries) series).patch;
@@ -65,7 +69,7 @@ protected static class DoseLayer {
 
     @Override
     public void schedule(Schedule schedule) {
-        schedule.scheduleOnce(doseDelay, Ordering.FIRST_COMPONENT.ordinal() - 1, this);
+        schedule.scheduleRepeating(doseStart, Ordering.FIRST_COMPONENT.ordinal(), this);
     }
 
     @Override
@@ -95,27 +99,24 @@ public void register(Simulation sim, String layer) {
 
     @Override
     public void step(SimState simstate) {
+        double tick = simstate.schedule.getTime();
+
+        double doseAmount = 400000;
         for (DoseLayer layer : layers) {
-            double delta = 0;
-            for (int k = 0; k < latticeHeight; k++) {
-                for (int i = 0; i < latticeLength; i++) {
-                    for (int j = 0; j < latticeWidth; j++) {
-                        delta +=
-                                latticePatchVolume
-                                        * (layer.current[k][i][j] - layer.siteLayer.concentration);
-                    }
-                }
+            if (tick > doseEnd) {
+                layer.currentAmount = 0;
+                layer.siteLayer.concentration = 0;
+                return;
+            }
+
+            if (tick >= doseStart && (tick - doseStart) % doseInterval < doseDuration) {
+            layer.currentAmount += doseAmount;
+            } else {
+                layer.currentAmount = 0;
             }
-            layer.currentAmount = Math.max(0, layer.currentAmount - delta);
+
             layer.siteLayer.concentration = layer.currentAmount / mediaVolume;
 
-            // System.out.print(simstate.schedule.getTime());
-            // System.out.print((doseDelay + doseDuration));
-            // if (simstate.schedule.getTime() >= (doseDelay + doseDuration)) {
-            //     System.out.println("Dose Ends");
-            //     layer.currentAmount = layer.initialConcentration * mediaVolume;
-            //     layer.siteLayer.concentration = layer.initialConcentration;
-            // }
         }
     }
 }
diff --git a/src/arcade/patch/env/component/PatchComponentPulse.java b/src/arcade/patch/env/component/PatchComponentPulse.java
@@ -173,10 +173,15 @@ public void step(SimState simstate) {
                 }
             }
 
+            System.out.println(delta);
+            System.out.println(layer.currentAmount);
             // Update available concentrations.
             layer.currentAmount = Math.max(0, layer.currentAmount - delta);
-            layer.siteLayer.concentration = layer.currentAmount / mediaVolume;
+            System.out.println(layer.currentAmount);
 
+            System.out.println(layer.siteLayer.concentration);
+            layer.siteLayer.concentration = layer.currentAmount / mediaVolume;
+            System.out.println(layer.siteLayer.concentration);
             // Pulse returns concentration to initial value.
             if (tick % pulseInterval == 0) {
                 layer.currentAmount = layer.initialConcentration * mediaVolume;

diff --git a/src/arcade/patch/parameter.patch.xml b/src/arcade/patch/parameter.patch.xml
@@ -58,7 +58,7 @@
     <!-- chemotherapy process parameters -->
     <population.process process="chemotherapy" id="CHEMOTHERAPY_THRESHOLD" value="1.5" unit="fmol" description="chemotherapy threshold before apoptosis" />
     <population.process process="chemotherapy" id="CONSTANT_DRUG_UPTAKE_RATE" value="1" unit="fmol drug/um^2 cell/min/M drug" />
-    <population.process process="chemotherapy" id="DRUG_REMOVAL_RATE" value="0.001" unit="/min" description="removal rate of drug in cell" />
+    <population.process process="chemotherapy" id="DRUG_REMOVAL_RATE" value="0.1" unit="/min" description="removal rate of drug in cell" />
     <population.process process="chemotherapy" id="DRUG_DECAY_RATE" value="0.1" unit="/min" description="degradation rate of drug in environment" />
 
 
@@ -114,8 +114,11 @@
     <component class="pulse" id="MEDIA_AMOUNT" value="2000" unit="um^3/um^2" description="media volume per area" />
 
     <!-- dose component parameters -->
-    <component class="dose" id="DOSE_DELAY" value="20" unit="min" description="Amount of simulation time before does is introduced" />
-    <component class="dose" id="DOSE_DURATION" value="60" unit="min" description="Length of drug exposure" />
+    <component class="dose" id="DOSE_START" value="10080" unit="min" description="Amount of simulation time before does is introduced" />
+    <component class="dose" id="DOSE_END" value="20160" unit="min" description="Simulation time where drug treatments end" />
+    <component class="dose" id="DOSE_DURATION" value="120" unit="min" description="Length of drug exposure" />
+    <component class="dose" id="DOSE_INTERVAL" value="1440" unit="min" description="Time between drug doses" />
+    <component class="dose" id="MEDIA_AMOUNT" value="2000" unit="um^3/um^2" description="media volume per area" />
 
     <!-- degrade component parameters -->
     <component class="degrade" id="DEGRADATION_INTERVAL" value="1" units="min" description="interval between degradation steps" />