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Fix passing in initial glucose as a parameter value #99

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Merged
allison-li-1016 merged 9 commits into from
Nov 14, 2024
Merged

Fix passing in initial glucose as a parameter value #99

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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
0f35e76
adding volume multiplier to other metabolism classes
allison-li-1016 Nov 14, 2024
cfca8aa
changing intAmts of pyruvate to be based on intAmts glucose
allison-li-1016 Nov 14, 2024
4b43758
changing default initial concentration to be consistent with default …
allison-li-1016 Nov 14, 2024
4f2420c
Merge remote-tracking branch 'origin/develop' into allli/initial-gluc…
allison-li-1016 Nov 14, 2024
21d1741
removing duplicate javadoc lines from merge
allison-li-1016 Nov 14, 2024
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5 changes: 3 additions & 2 deletions src/arcade/patch/agent/process/PatchProcessMetabolismComplex.java
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Expand Up @@ -100,8 +100,9 @@ public PatchProcessMetabolismComplex(PatchCell cell) {

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

@Override
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4 changes: 3 additions & 1 deletion src/arcade/patch/agent/process/PatchProcessMetabolismMedium.java
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Expand Up @@ -61,6 +61,7 @@ public class PatchProcessMetabolismMedium extends PatchProcessMetabolism {
* <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
* <li>{@code INITIAL_GLUCOSE_CONCENTRATION} = initial cell internal glucose concentration
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@jessicasyu jessicasyu Nov 14, 2024

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Remove these duplicates (probably from the merge?)

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

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fixed !

* </ul>
*
* @param cell the {@link PatchCell} the process is associated with
Expand All @@ -83,7 +84,8 @@ public PatchProcessMetabolismMedium(PatchCell cell) {

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

@Override
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4 changes: 3 additions & 1 deletion src/arcade/patch/agent/process/PatchProcessMetabolismRandom.java
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Expand Up @@ -58,6 +58,7 @@ public class PatchProcessMetabolismRandom extends PatchProcessMetabolism {
* <ul>
* <li>{@code CELL_VOLUME} = cell volume
* <li>{@code INITIAL_GLUCOSE_CONCENTRATION} = initial cell internal glucose concentration
* <li>{@code INITIAL_GLUCOSE_CONCENTRATION} = initial cell internal glucose concentration
* </ul>
*
* @param cell the {@link PatchCell} the process is associated with
Expand All @@ -76,7 +77,8 @@ public PatchProcessMetabolismRandom(PatchCell cell) {

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

@Override
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2 changes: 1 addition & 1 deletion src/arcade/patch/parameter.patch.xml
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Expand Up @@ -48,7 +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="0.17" unit="fmol/um^3" description="initial cell internal glucose concentration"/>
<population.process process="metabolism" id="INITIAL_GLUCOSE_CONCENTRATION" value="0.005" unit="fmol/um^3" description="initial cell internal glucose concentration"/>

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