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Merged
allison-li-1016 merged 4 commits into from
Nov 14, 2024
Merged

Pass initial glucose concentration as parameter for metabolism modules #96

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22b56a2
adding initial glucose concentration as a parameter in constructor of…
allison-li-1016 Nov 13, 2024
511fe15
making initial glucose assignment in-line
allison-li-1016 Nov 13, 2024
9f1856c
changing default initial glucose concentration to be non-zero, multip…
allison-li-1016 Nov 14, 2024
1eaed0d
fixing linting issues that failed the spotlessCheck
allison-li-1016 Nov 14, 2024
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11 changes: 6 additions & 5 deletions src/arcade/patch/agent/process/PatchProcessMetabolismComplex.java
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Expand Up @@ -74,18 +74,14 @@ public class PatchProcessMetabolismComplex extends PatchProcessMetabolism {
* <li>{@code LACTATE_RATE} = rate of lactate production
* <li>{@code AUTOPHAGY_RATE} = rate of autophagy
* <li>{@code GLUCOSE_UPTAKE_RATE} = rate of glucose uptake
* <li>{@code INITIAL_GLUCOSE_CONCENTRATION} = initial cell internal glucose concentration
* </ul>
*
* @param cell the {@link PatchCell} the process is associated with
*/
public PatchProcessMetabolismComplex(PatchCell cell) {
super(cell);

// Initial internal concentrations.
intAmts = new double[2];
intAmts[GLUCOSE] = extAmts[GLUCOSE];
intAmts[PYRUVATE] = extAmts[GLUCOSE] * PYRU_PER_GLUC;

// Mapping for internal concentration access.
String[] intNames = new String[2];
intNames[GLUCOSE] = "glucose";
Expand All @@ -101,6 +97,11 @@ public PatchProcessMetabolismComplex(PatchCell cell) {
lactateRate = parameters.getDouble("metabolism/LACTATE_RATE");
autophagyRate = parameters.getDouble("metabolism/AUTOPHAGY_RATE");
glucoseUptakeRate = parameters.getDouble("metabolism/GLUCOSE_UPTAKE_RATE");

// Initial internal concentrations.
intAmts = new double[2];
intAmts[GLUCOSE] = parameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION");
intAmts[PYRUVATE] = extAmts[GLUCOSE] * PYRU_PER_GLUC;
}

@Override
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9 changes: 5 additions & 4 deletions src/arcade/patch/agent/process/PatchProcessMetabolismMedium.java
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Expand Up @@ -60,17 +60,14 @@ public class PatchProcessMetabolismMedium extends PatchProcessMetabolism {
* <li>{@code MINIMUM_MASS_FRACTION} = minimum viable cell mass fraction
* <li>{@code AUTOPHAGY_RATE} = rate of autophagy
* <li>{@code ATP_PRODUCTION_RATE} = rate of ATP production
* <li>{@code INITIAL_GLUCOSE_CONCENTRATION} = initial cell internal glucose concentration
* </ul>
*
* @param cell the {@link PatchCell} the process is associated with
*/
public PatchProcessMetabolismMedium(PatchCell cell) {
super(cell);

// Initial internal concentrations.
intAmts = new double[1];
intAmts[GLUCOSE] = extAmts[GLUCOSE];

// Mapping for internal concentration access.
String[] intNames = new String[1];
intNames[GLUCOSE] = "glucose";
Expand All @@ -83,6 +80,10 @@ public PatchProcessMetabolismMedium(PatchCell cell) {
minimumMassFraction = parameters.getDouble("metabolism/MINIMUM_MASS_FRACTION");
autophagyRate = parameters.getDouble("metabolism/AUTOPHAGY_RATE");
atpProductionRate = parameters.getDouble("metabolism/ATP_PRODUCTION_RATE");

// Initial internal concentrations.
intAmts = new double[1];
intAmts[GLUCOSE] = parameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION");
}

@Override
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9 changes: 5 additions & 4 deletions src/arcade/patch/agent/process/PatchProcessMetabolismRandom.java
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Expand Up @@ -57,17 +57,14 @@ public class PatchProcessMetabolismRandom extends PatchProcessMetabolism {
*
* <ul>
* <li>{@code CELL_VOLUME} = cell volume
* <li>{@code INITIAL_GLUCOSE_CONCENTRATION} = initial cell internal glucose concentration
* </ul>
*
* @param cell the {@link PatchCell} the process is associated with
*/
public PatchProcessMetabolismRandom(PatchCell cell) {
super(cell);

// Initial internal concentrations.
intAmts = new double[1];
intAmts[GLUCOSE] = extAmts[GLUCOSE];

// Mapping for internal concentration access.
String[] intNames = new String[1];
intNames[GLUCOSE] = "glucose";
Expand All @@ -76,6 +73,10 @@ public PatchProcessMetabolismRandom(PatchCell cell) {
// Set loaded parameters.
Parameters parameters = cell.getParameters();
averageCellVolume = parameters.getDouble("CELL_VOLUME");

// Initial internal concentrations.
intAmts = new double[1];
intAmts[GLUCOSE] = parameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION");
}

@Override
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9 changes: 5 additions & 4 deletions src/arcade/patch/agent/process/PatchProcessMetabolismSimple.java
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Expand Up @@ -46,17 +46,14 @@ public class PatchProcessMetabolismSimple extends PatchProcessMetabolism {
* <li>{@code CONSTANT_GLUCOSE_UPTAKE_RATE} = constant glucose uptake rate
* <li>{@code CONSTANT_ATP_PRODUCTION_RATE} = constant ATP production rate
* <li>{@code CONSTANT_VOLUME_GROWTH_RATE} = constant volume growth rate
* <li>{@code INITIAL_GLUCOSE_CONCENTRATION} = initial cell internal glucose concentration
* </ul>
*
* @param cell the {@link PatchCell} the process is associated with
*/
public PatchProcessMetabolismSimple(PatchCell cell) {
super(cell);

// Initial internal concentrations.
intAmts = new double[1];
intAmts[GLUCOSE] = extAmts[GLUCOSE];

// Mapping for internal concentration access.
String[] intNames = new String[1];
intNames[GLUCOSE] = "glucose";
Expand All @@ -69,6 +66,10 @@ public PatchProcessMetabolismSimple(PatchCell cell) {
glucoseUptakeRate = parameters.getDouble("metabolism/CONSTANT_GLUCOSE_UPTAKE_RATE");
atpProductionRate = parameters.getDouble("metabolism/CONSTANT_ATP_PRODUCTION_RATE");
volumeGrowthRate = parameters.getDouble("metabolism/CONSTANT_VOLUME_GROWTH_RATE");

// Initial internal concentrations.
intAmts = new double[1];
intAmts[GLUCOSE] = parameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION");
}

@Override
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1 change: 1 addition & 0 deletions src/arcade/patch/parameter.patch.xml
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Expand Up @@ -48,6 +48,7 @@
<population.process process="metabolism" id="CONSTANT_GLUCOSE_UPTAKE_RATE" value="929.88" unit="fmol glucose/min/M glucose" description="constant glucose uptake rate" />
<population.process process="metabolism" id="CONSTANT_ATP_PRODUCTION_RATE" value="4.9817" unit="fmol ATP/cell/min" description="constant ATP production rate" />
<population.process process="metabolism" id="CONSTANT_VOLUME_GROWTH_RATE" value="2.819" unit="um^3/min" description="constant volume growth rate"/>
<population.process process="metabolism" id="INITIAL_GLUCOSE_CONCENTRATION" value="0" unit="fmol" description="initial cell internal glucose concentration"/>
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@cainja cainja Nov 13, 2024

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Don't love this being 0 by default

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@allison-li-1016 allison-li-1016 Nov 14, 2024

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What default values would you suggest?

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@cainja cainja Nov 14, 2024

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Isn't this value being 0 the source of the bug that you had identified before?

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@allison-li-1016 allison-li-1016 Nov 14, 2024

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Yeah - it probably makes sense to set it to the average(?) internal glucose amt of engineered cells, Im just not sure what that is.

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@allison-li-1016 allison-li-1016 Nov 14, 2024

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For now Ill set it as 30fmol since thats what CARCADE seems to be giving me, but we can revisit this value

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@jessicasyu jessicasyu Nov 14, 2024

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@allison-li-1016 @cainja Possible alternative: keep the parameter as a concentration that matches the glucose concentration and do the conversion to mass in the constructor by multiplying by cell volume?


<!-- signaling process parameters -->
<population.process process="signaling" id="MIGRATORY_THRESHOLD" value="10" description="threshold fold change in PLCg for migration" />
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