Changed noiseSigma=biomassGrowthRate to Math.sqrt(biomassGrowthRate)*...

07/31/2023 ID

Author: dukovski

Ecoli_core/COMETS_manifest.txt

@@ -1,2 +1,3 @@
-LayoutFileName: C:\Users\ilija\git\comets\Ecoli_core\layout.txt
+LayoutFileName: C:\Users\ilija\git\comets\Ecoli_core\Ecoli_batch_layout.txt
 ModelFileName: C:\Users\ilija\git\comets\Ecoli_core\e_coli_core.txt
+TotalBiomassFileName: ./total_biomass.txt

Ecoli_core/e_coli_core.txt

@@ -1,4 +1,3 @@
-OPTIMIZER GLOP
 SMATRIX  72  95
     1   49   1.000000
     1   75   1.000000
@@ -636,7 +635,7 @@ EXCHANGE_REACTIONS
  20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
 //
 OBJECTIVE_STYLE
-	MAX_OBJECTIVE_FLUX
+	MAX_OBJECTIVE_MIN_TOTAL
 //
 convNonlinDiffZero  0.0
 //

comets_simplified/src/edu/bu/segrelab/comets/fba/FBACell.java

@@ -1314,31 +1314,31 @@ private double addDemographicNoise(double currentBiomass, double biomassGrowthRa
 		double noisyBiomass=currentBiomass;
 		if(biomassGrowthRate>0.0)
 		{	
-			double noiseSigma = biomassGrowthRate*demographicNoiseSigmaZero;
+			double noiseSigma = Math.sqrt(biomassGrowthRate)*demographicNoiseSigmaZero;
 			//System.out.println("sigma  "+noiseSigma);
 			double poissonLambda=2.0*currentBiomass/(cParams.getTimeStep()*noiseSigma*noiseSigma);
 			//System.out.println("poiss  "+poissonLambda);
 			if(poissonLambda>0)
-		{
+		    {
 				//poissonDist=new Poisson(poissonLambda);
 
 				double gammaAlpha=Poisson.random(poissonLambda, new MersenneTwister());
 				//System.out.println("alpha  "+gammaAlpha);
 				if(gammaAlpha>0)
-			{
+			    {
 					//System.out.println(gammaAlpha);
 					//gammaDist=new Gamma(gammaAlpha,1.0);
 					double gammaSample=Gamma.random(gammaAlpha, 1.0, new MersenneTwister());
 					noisyBiomass=0.5*gammaSample*(cParams.getTimeStep()*noiseSigma*noiseSigma);
 					//System.out.println("biomass  "+noisyBiomass);
-			}
+			    }
 				else if(gammaAlpha==0)
 				{
 					noisyBiomass=0.0;
-		}
-	}
+		        }
+	        }
 			else if(poissonLambda==0)
-	{
+	        {
 				noisyBiomass=0.0;
 			}
 		}