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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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15 changes: 10 additions & 5 deletions src/arcade/patch/agent/process/PatchProcessMetabolismComplex.java
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Expand Up @@ -59,6 +59,9 @@ public class PatchProcessMetabolismComplex extends PatchProcessMetabolism {
/** Rate of glucose uptake [fmol glucose/um<sup>2</sup> cell/min/M glucose]. */
private final double glucoseUptakeRate;

/** Initial cell internal glucose concentration [fmol]. */
private final double initGluc;

/**
* Creates a complex metabolism {@code Process} for the given {@link PatchCell}.
*
Expand All @@ -74,18 +77,14 @@ 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 +100,12 @@ public PatchProcessMetabolismComplex(PatchCell cell) {
lactateRate = parameters.getDouble("metabolism/LACTATE_RATE");
autophagyRate = parameters.getDouble("metabolism/AUTOPHAGY_RATE");
glucoseUptakeRate = parameters.getDouble("metabolism/GLUCOSE_UPTAKE_RATE");
initGluc = parameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION");

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

@Override
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13 changes: 9 additions & 4 deletions src/arcade/patch/agent/process/PatchProcessMetabolismMedium.java
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Expand Up @@ -47,6 +47,9 @@ public class PatchProcessMetabolismMedium extends PatchProcessMetabolism {
/** Rate of ATP production [fmol ATP/um<sup>3</sup>/min/M glucose]. */
private final double atpProductionRate;

/** Initial cell internal glucose concentration [fmol]. */
private final double initGluc;
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@jessicasyu jessicasyu Nov 13, 2024

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Since initGluc is only used in the constructor, I think you can just inline the variable

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@allison-li-1016 allison-li-1016 Nov 13, 2024

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fixed !


/**
* Creates a medium metabolism {@code Process} for the given {@link PatchCell}.
*
Expand All @@ -60,17 +63,14 @@ 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 +83,11 @@ public PatchProcessMetabolismMedium(PatchCell cell) {
minimumMassFraction = parameters.getDouble("metabolism/MINIMUM_MASS_FRACTION");
autophagyRate = parameters.getDouble("metabolism/AUTOPHAGY_RATE");
atpProductionRate = parameters.getDouble("metabolism/ATP_PRODUCTION_RATE");
initGluc = parameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION");

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

@Override
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13 changes: 9 additions & 4 deletions src/arcade/patch/agent/process/PatchProcessMetabolismRandom.java
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Expand Up @@ -48,6 +48,9 @@ public class PatchProcessMetabolismRandom extends PatchProcessMetabolism {
/** Average cell volume [um<sup>3</sup>]. */
private final double averageCellVolume;

/** Initial cell internal glucose concentration [fmol]. */
private final double initGluc;

/**
* Creates a random metabolism {@code Process} for the given {@link PatchCell}.
*
Expand All @@ -57,17 +60,14 @@ 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 +76,11 @@ public PatchProcessMetabolismRandom(PatchCell cell) {
// Set loaded parameters.
Parameters parameters = cell.getParameters();
averageCellVolume = parameters.getDouble("CELL_VOLUME");
initGluc = parameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION");

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

@Override
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13 changes: 9 additions & 4 deletions src/arcade/patch/agent/process/PatchProcessMetabolismSimple.java
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Expand Up @@ -33,6 +33,9 @@ public class PatchProcessMetabolismSimple extends PatchProcessMetabolism {
/** Constant volume growth rate [um<sup>3</sup>/min]. */
private final double volumeGrowthRate;

/** Initial cell internal glucose concentration [fmol]. */
private final double initGluc;

/**
* Creates a simple metabolism {@code Process} for the given {@link PatchCell}.
*
Expand All @@ -46,17 +49,14 @@ 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 +69,11 @@ 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");
initGluc = parameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION");

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

@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" />
Expand Down