Pass initial glucose concentration as parameter for metabolism modules #96
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… metabolism classes, adding default parameter value to parameters.xml
| private final double atpProductionRate; | ||
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| /** Initial cell internal glucose concentration [fmol]. */ | ||
| private final double initGluc; |
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Since initGluc is only used in the constructor, I think you can just inline the variable
cainja
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cainja
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I don't think that this value represents a concentration...
src/arcade/patch/parameter.patch.xml
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| <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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Don't love this being 0 by default
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What default values would you suggest?
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Isn't this value being 0 the source of the bug that you had identified before?
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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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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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@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?
…lying concentration by volume to get glucose mass
jessicasyu
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type: feature
jessicasyu
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closes #93
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Summary
Allows for initial internal glucose concentrations to be passed in as a parameter. By default, this value is set to 0.
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