diff --git a/1-Model_construction.R b/1-Model_construction.R
new file mode 100644
index 0000000..0e929b3
--- /dev/null
+++ b/1-Model_construction.R
@@ -0,0 +1,469 @@
+
+
+###################
+# Set environment #
+###################
+
+# load libraries and initialize environment
+source("set_env.R")
+
+
+######################
+# Model construction #
+######################
+
+# Test whether the different models (1-4) fit the data accurately, based on chi2 statistics
+
+# nb_points: number of experimental data points (152)
+# nb_par: number of free parameters
+
+# Go to models directory
+setwd(model_dir)
+
+# Model 1: no inhibition by acetate
+loadModel("Millard2020_Ecoli_glc_ace_model_1.cps")
+res_PE_model1 <- runParameterEstimation(method = "Statistics", model = getCurrentModel())
+res_PE_model1$chi2 <- test_khi2(nb_points=152, k_val=res_PE_model1$main$objective_value, nb_par=8)
+
+print("chi2-test for model 1:")
+print(paste("  p-value = ", res_PE_model1$chi2$`p-value, i.e. P(X^2<=value)`, sep=""))
+print(paste("  conclusion: ", res_PE_model1$chi2$conclusion, sep=""))     
+
+# Model 2: inhibition of glycolysis
+loadModel("Millard2020_Ecoli_glc_ace_model_2.cps")
+res_PE_model2 <- runParameterEstimation(method = "Statistics", model = getCurrentModel())
+res_PE_model2$chi2 <- test_khi2(nb_points=152, k_val=res_PE_model2$main$objective_value, nb_par=9)
+
+print("chi2-test for model 2:")
+print(paste("  p-value = ", res_PE_model2$chi2$`p-value, i.e. P(X^2<=value)`, sep=""))
+print(paste("  conclusion: ", res_PE_model2$chi2$conclusion, sep=""))     
+
+# Model 3: inhibition of TCA cycle
+loadModel("Millard2020_Ecoli_glc_ace_model_3.cps")
+res_PE_model3 <- runParameterEstimation(method = "Statistics", model = getCurrentModel())
+res_PE_model3$chi2 <- test_khi2(nb_points=152, k_val=res_PE_model3$main$objective_value, nb_par=9)
+
+print("chi2-test for model 3:")
+print(paste("  p-value = ", res_PE_model3$chi2$`p-value, i.e. P(X^2<=value)`, sep=""))
+print(paste("  conclusion: ", res_PE_model3$chi2$conclusion, sep=""))     
+
+# Model 4: inhibition of TCA and glycolysis
+loadModel("Millard2020_Ecoli_glc_ace_model_4.cps")
+res_PE_model4 <- runParameterEstimation(method = "Statistics", model = getCurrentModel())
+res_PE_model4$chi2 <- test_khi2(nb_points=152, k_val=res_PE_model4$main$objective_value, nb_par=10)
+
+print("chi2-test for model 4:")
+print(paste("  p-value = ", res_PE_model4$chi2$`p-value, i.e. P(X^2<=value)`, sep=""))
+print(paste("  conclusion: ", res_PE_model4$chi2$conclusion, sep=""))     
+
+# plot model evaluation results
+setwd(results_dir)
+pdf(file="Figure 1B.pdf", width = 5, height = 5)
+
+barplot(c(res_PE_model1$main$objective_value,
+       res_PE_model2$main$objective_value,
+       res_PE_model3$main$objective_value,
+       res_PE_model4$main$objective_value),
+       las=1,
+       ylab="variance-weighted SSR",
+       names.arg=c("model1", "model2", "model3", "model4"))
+chi2_threshold <- 171
+abline(h=chi2_threshold)
+
+dev.off()
+
+
+###########
+# PLOT FIT vs MEASUREMENTS #
+###########
+
+# In current version of CoRc package, custom weights cannot be provided when defining an experiment,
+# hence we cannot define weight according to the experimental standard deviations.
+# To overcome this limitation, we use a copasi model file with weights pre-defined in the
+# Parameter estimation task.
+
+# MODEL 1 #
+###########
+
+setwd(model_dir)
+loadModel("Millard2020_Ecoli_glc_ace_model_1.cps")
+
+# get parameters for the best fit
+res_PE_model <- runParameterEstimation(method = "Statistics", model = getCurrentModel())
+
+# list used to set up global sensitivity analysis and store calculation results
+fit_results_m1 <- list("1" = list("initial_concentrations"= c("Ace0_out"=0.92, "Glc"=12.9, "X"=0.0671),
+                                  "species_idx" = c("[Ace0_out]_0"=1, "[Glc]_0"=1, "[X]_0"=1),
+                                  "data_exp" = read.table("data_1mM.txt", header=TRUE, sep="\t"),
+                                  "sd" = c("Ace"=0.2, "Glc"=0.5, "X"=0.045, "Ace_enr"=0.03),
+                                  "mapping" = c("Ace"="Acet_out", "Glc"="Glc", "X"="X", "Ace_enr"="Values[Ace_enr]")),
+                       "10" = list("initial_concentrations"= c("Ace0_out"=9, "Glc"=14.192, "X"=0.07),
+                                   "species_idx" = c("[Ace0_out]_0"=2, "[Glc]_0"=2, "[X]_0"=2),
+                                   "data_exp" = read.table("data_10mM.txt", header=TRUE, sep="\t"),
+                                   "sd" = c("Ace"=0.2, "Glc"=0.5, "X"=0.045, "Ace_enr"=0.03),
+                                   "mapping" = c("Ace"="Acet_out", "Glc"="Glc", "X"="X", "Ace_enr"="Values[Ace_enr]")),
+                       "30" = list("initial_concentrations"= c("Ace0_out"=30.2448, "Glc"=12.5, "X"=0.07227),
+                                   "species_idx" = c("[Ace0_out]_0"=3, "[Glc]_0"=3, "[X]_0"=3),
+                                   "data_exp" = read.table("data_30mM.txt", header=TRUE, sep="\t"),
+                                   "sd" = c("Ace"=0.2, "Glc"=0.5, "X"=0.045, "Ace_enr"=0.03),
+                                   "mapping" = c("Ace"="Acet_out", "Glc"="Glc", "X"="X", "Ace_enr"="Values[Ace_enr]")),
+                       "res_cost" = c(res_PE_model$main$objective_value),
+                       "res_converged" = c(test_khi2(nb_points=152, k_val=res_PE_model$main$objective_value, nb_par=10)$`p-value, i.e. P(X^2<=value)` < 0.95))
+
+# simulate data for the best fit
+for (i in c("1", "10", "30")){
+  # update initial conditions (Glc, Ace and biomass concentrations)
+  for (j in names(fit_results_m1[[i]][["initial_concentrations"]])){
+    setSpecies(key=j, initial_concentration=fit_results_m1[[i]][["initial_concentrations"]][j])
+  }
+  # apply initial state
+  applyInitialState()
+  # run time course simulation
+  tmp <- as.matrix(runTimeCourse()$result)
+  # get complete simulation results
+  idx_t_max <- (tmp[,"Time"] <= max(fit_results_m1[[i]][["data_exp"]]$time))
+  fit_results_m1[[i]]$simulations <- tmp[idx_t_max,]
+  # get index of simulated data at experimental time points
+  fit_results_m1[[i]]$t_idx <- match(fit_results_m1[[i]][["data_exp"]]$time, fit_results_m1[[i]]$simulations[,"Time"])
+  # get simulated data that match experimental time points
+  sim_data <- fit_results_m1[[i]][["data_exp"]]
+  for (k in names(fit_results_m1[[i]][["mapping"]])){
+    sim_data[,k] <- fit_results_m1[[i]]$simulations[fit_results_m1[[i]]$t_idx,fit_results_m1[[i]][["mapping"]][[k]]]
+  }
+  fit_results_m1[[i]]$sim <- sim_data
+}
+
+# Plot fitting results
+setwd(results_dir)
+pdf(file = "Figure 1-figure supplement 1.pdf", width = 7, height = 9)
+par(mfrow=c(4,3))
+
+plot_no_ci(fit_results_m1, "1", "X", col="#1F4E79", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="[biomass] (gDW/L)", xlab="", main="[acetate]=1mM")
+plot_no_ci(fit_results_m1, "10", "X", col="#2E75B6", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="", xlab="", main="[acetate]=10mM")
+plot_no_ci(fit_results_m1, "30", "X", col="#9DC3E6", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="", xlab="", main="[acetate]=30mM")
+
+plot_no_ci(fit_results_m1, "1", "Glc", col="#548235", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,15), xaxs="i", yaxs="i", ylab="[Glc] (mM)", xlab="", main="")
+plot_no_ci(fit_results_m1, "10", "Glc", col="#70AD47", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,15), xaxs="i", yaxs="i", ylab="", xlab="", main="")
+plot_no_ci(fit_results_m1, "30", "Glc", col="#A9D18E", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,15), xaxs="i", yaxs="i", ylab="", xlab="", main="")
+
+plot_no_ci(fit_results_m1, "1", "Ace", col="#B63A2D", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,5), xaxs="i", yaxs="i", ylab="[Ace] (mM)", xlab="", main="")
+plot_no_ci(fit_results_m1, "10", "Ace", col="#D6685C", lwd=1.0, las=1, xlim=c(0,5), ylim=c(8,11), xaxs="i", yaxs="i", ylab="", xlab="", main="")
+plot_no_ci(fit_results_m1, "30", "Ace", col="#E49890", lwd=1.0, las=1, xlim=c(0,5), ylim=c(25,32), xaxs="i", yaxs="i", ylab="", xlab="", main="")
+
+plot_no_ci(fit_results_m1, "1", "Ace_enr", col="#BF9000", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="[Ace] (mM)", xlab="time (h)", main="")
+plot_no_ci(fit_results_m1, "10", "Ace_enr", col="#FFD966", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,0.7), xaxs="i", yaxs="i", ylab="", xlab="time (h)", main="")
+plot_no_ci(fit_results_m1, "30", "Ace_enr", col="#FFE699", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,0.3), xaxs="i", yaxs="i", ylab="", xlab="time (h)", main="")
+
+dev.off()
+
+# MODEL 2 #
+###########
+
+setwd(model_dir)
+loadModel("Millard2020_Ecoli_glc_ace_model_2.cps")
+
+# get parameters for the best fit
+res_PE_model <- runParameterEstimation(method = "Statistics", model = getCurrentModel())
+
+# list used to set up global sensitivity analysis and store calculation results
+fit_results_m2 <- list("1" = list("initial_concentrations"= c("Ace0_out"=0.92, "Glc"=12.9, "X"=0.0671),
+                                  "species_idx" = c("[Ace0_out]_0"=1, "[Glc]_0"=1, "[X]_0"=1),
+                                  "data_exp" = read.table("data_1mM.txt", header=TRUE, sep="\t"),
+                                  "sd" = c("Ace"=0.2, "Glc"=0.5, "X"=0.045, "Ace_enr"=0.03),
+                                  "mapping" = c("Ace"="Acet_out", "Glc"="Glc", "X"="X", "Ace_enr"="Values[Ace_enr]")),
+                       "10" = list("initial_concentrations"= c("Ace0_out"=9, "Glc"=14.192, "X"=0.07),
+                                   "species_idx" = c("[Ace0_out]_0"=2, "[Glc]_0"=2, "[X]_0"=2),
+                                   "data_exp" = read.table("data_10mM.txt", header=TRUE, sep="\t"),
+                                   "sd" = c("Ace"=0.2, "Glc"=0.5, "X"=0.045, "Ace_enr"=0.03),
+                                   "mapping" = c("Ace"="Acet_out", "Glc"="Glc", "X"="X", "Ace_enr"="Values[Ace_enr]")),
+                       "30" = list("initial_concentrations"= c("Ace0_out"=30.2448, "Glc"=12.5, "X"=0.07227),
+                                   "species_idx" = c("[Ace0_out]_0"=3, "[Glc]_0"=3, "[X]_0"=3),
+                                   "data_exp" = read.table("data_30mM.txt", header=TRUE, sep="\t"),
+                                   "sd" = c("Ace"=0.2, "Glc"=0.5, "X"=0.045, "Ace_enr"=0.03),
+                                   "mapping" = c("Ace"="Acet_out", "Glc"="Glc", "X"="X", "Ace_enr"="Values[Ace_enr]")),
+                       "res_cost" = c(res_PE_model$main$objective_value),
+                       "res_converged" = c(test_khi2(nb_points=152, k_val=res_PE_model$main$objective_value, nb_par=10)$`p-value, i.e. P(X^2<=value)` < 0.95))
+
+# simulate data for the best fit
+for (i in c("1", "10", "30")){
+  # update initial conditions (Glc, Ace and biomass concentrations)
+  for (j in names(fit_results_m2[[i]][["initial_concentrations"]])){
+    setSpecies(key=j, initial_concentration=fit_results_m2[[i]][["initial_concentrations"]][j])
+  }
+  # apply initial state
+  applyInitialState()
+  # run time course simulation
+  tmp <- as.matrix(runTimeCourse()$result)
+  # get complete simulation results
+  idx_t_max <- (tmp[,"Time"] <= max(fit_results_m2[[i]][["data_exp"]]$time))
+  fit_results_m2[[i]]$simulations <- tmp[idx_t_max,]
+  # get index of simulated data at experimental time points
+  fit_results_m2[[i]]$t_idx <- match(fit_results_m2[[i]][["data_exp"]]$time, fit_results_m2[[i]]$simulations[,"Time"])
+  # get simulated data that match experimental time points
+  sim_data <- fit_results_m2[[i]][["data_exp"]]
+  for (k in names(fit_results_m2[[i]][["mapping"]])){
+    sim_data[,k] <- fit_results_m2[[i]]$simulations[fit_results_m2[[i]]$t_idx,fit_results_m2[[i]][["mapping"]][[k]]]
+  }
+  fit_results_m2[[i]]$sim <- sim_data
+}
+
+# Plot fitting results
+setwd(results_dir)
+pdf(file = "Figure 1-figure supplement 2.pdf", width = 7, height = 9)
+par(mfrow=c(4,3))
+
+plot_no_ci(fit_results_m2, "1", "X", col="#1F4E79", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="[biomass] (gDW/L)", xlab="", main="[acetate]=1mM")
+plot_no_ci(fit_results_m2, "10", "X", col="#2E75B6", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="", xlab="", main="[acetate]=10mM")
+plot_no_ci(fit_results_m2, "30", "X", col="#9DC3E6", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="", xlab="", main="[acetate]=30mM")
+
+plot_no_ci(fit_results_m2, "1", "Glc", col="#548235", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,15), xaxs="i", yaxs="i", ylab="[Glc] (mM)", xlab="", main="")
+plot_no_ci(fit_results_m2, "10", "Glc", col="#70AD47", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,15), xaxs="i", yaxs="i", ylab="", xlab="", main="")
+plot_no_ci(fit_results_m2, "30", "Glc", col="#A9D18E", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,15), xaxs="i", yaxs="i", ylab="", xlab="", main="")
+
+plot_no_ci(fit_results_m2, "1", "Ace", col="#B63A2D", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,5), xaxs="i", yaxs="i", ylab="[Ace] (mM)", xlab="", main="")
+plot_no_ci(fit_results_m2, "10", "Ace", col="#D6685C", lwd=1.0, las=1, xlim=c(0,5), ylim=c(8,11), xaxs="i", yaxs="i", ylab="", xlab="", main="")
+plot_no_ci(fit_results_m2, "30", "Ace", col="#E49890", lwd=1.0, las=1, xlim=c(0,5), ylim=c(25,32), xaxs="i", yaxs="i", ylab="", xlab="", main="")
+
+plot_no_ci(fit_results_m2, "1", "Ace_enr", col="#BF9000", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="[Ace] (mM)", xlab="time (h)", main="")
+plot_no_ci(fit_results_m2, "10", "Ace_enr", col="#FFD966", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,0.7), xaxs="i", yaxs="i", ylab="", xlab="time (h)", main="")
+plot_no_ci(fit_results_m2, "30", "Ace_enr", col="#FFE699", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,0.3), xaxs="i", yaxs="i", ylab="", xlab="time (h)", main="")
+
+dev.off()
+
+###########
+# MODEL 3 #
+###########
+
+setwd(model_dir)
+loadModel("Millard2020_Ecoli_glc_ace_model_3.cps")
+
+# get parameters for the best fit
+res_PE_model <- runParameterEstimation(method = "Statistics", model = getCurrentModel())
+
+# list used to set up global sensitivity analysis and store calculation results
+fit_results_m3 <- list("1" = list("initial_concentrations"= c("Ace0_out"=0.92, "Glc"=12.9, "X"=0.0671),
+                                  "species_idx" = c("[Ace0_out]_0"=1, "[Glc]_0"=1, "[X]_0"=1),
+                                  "data_exp" = read.table("data_1mM.txt", header=TRUE, sep="\t"),
+                                  "sd" = c("Ace"=0.2, "Glc"=0.5, "X"=0.045, "Ace_enr"=0.03),
+                                  "mapping" = c("Ace"="Acet_out", "Glc"="Glc", "X"="X", "Ace_enr"="Values[Ace_enr]")),
+                       "10" = list("initial_concentrations"= c("Ace0_out"=9, "Glc"=14.192, "X"=0.07),
+                                   "species_idx" = c("[Ace0_out]_0"=2, "[Glc]_0"=2, "[X]_0"=2),
+                                   "data_exp" = read.table("data_10mM.txt", header=TRUE, sep="\t"),
+                                   "sd" = c("Ace"=0.2, "Glc"=0.5, "X"=0.045, "Ace_enr"=0.03),
+                                   "mapping" = c("Ace"="Acet_out", "Glc"="Glc", "X"="X", "Ace_enr"="Values[Ace_enr]")),
+                       "30" = list("initial_concentrations"= c("Ace0_out"=30.2448, "Glc"=12.5, "X"=0.07227),
+                                   "species_idx" = c("[Ace0_out]_0"=3, "[Glc]_0"=3, "[X]_0"=3),
+                                   "data_exp" = read.table("data_30mM.txt", header=TRUE, sep="\t"),
+                                   "sd" = c("Ace"=0.2, "Glc"=0.5, "X"=0.045, "Ace_enr"=0.03),
+                                   "mapping" = c("Ace"="Acet_out", "Glc"="Glc", "X"="X", "Ace_enr"="Values[Ace_enr]")),
+                       "res_cost" = c(res_PE_model$main$objective_value),
+                       "res_converged" = c(test_khi2(nb_points=152, k_val=res_PE_model$main$objective_value, nb_par=10)$`p-value, i.e. P(X^2<=value)` < 0.95))
+
+# simulate data for the best fit
+for (i in c("1", "10", "30")){
+  # update initial conditions (Glc, Ace and biomass concentrations)
+  for (j in names(fit_results_m3[[i]][["initial_concentrations"]])){
+    setSpecies(key=j, initial_concentration=fit_results_m3[[i]][["initial_concentrations"]][j])
+  }
+  # apply initial state
+  applyInitialState()
+  # run time course simulation
+  tmp <- as.matrix(runTimeCourse()$result)
+  # get complete simulation results
+  idx_t_max <- (tmp[,"Time"] <= max(fit_results_m3[[i]][["data_exp"]]$time))
+  fit_results_m3[[i]]$simulations <- tmp[idx_t_max,]
+  # get index of simulated data at experimental time points
+  fit_results_m3[[i]]$t_idx <- match(fit_results_m3[[i]][["data_exp"]]$time, fit_results_m3[[i]]$simulations[,"Time"])
+  # get simulated data that match experimental time points
+  sim_data <- fit_results_m3[[i]][["data_exp"]]
+  for (k in names(fit_results_m3[[i]][["mapping"]])){
+    sim_data[,k] <- fit_results_m3[[i]]$simulations[fit_results_m3[[i]]$t_idx,fit_results_m3[[i]][["mapping"]][[k]]]
+  }
+  fit_results_m3[[i]]$sim <- sim_data
+}
+
+# Plot fitting results
+setwd(results_dir)
+pdf(file = "Figure 1-figure supplement 3.pdf", width = 7, height = 9)
+par(mfrow=c(4,3))
+
+plot_no_ci(fit_results_m3, "1", "X", col="#1F4E79", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="[biomass] (gDW/L)", xlab="", main="[acetate]=1mM")
+plot_no_ci(fit_results_m3, "10", "X", col="#2E75B6", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="", xlab="", main="[acetate]=10mM")
+plot_no_ci(fit_results_m3, "30", "X", col="#9DC3E6", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="", xlab="", main="[acetate]=30mM")
+
+plot_no_ci(fit_results_m3, "1", "Glc", col="#548235", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,15), xaxs="i", yaxs="i", ylab="[Glc] (mM)", xlab="", main="")
+plot_no_ci(fit_results_m3, "10", "Glc", col="#70AD47", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,15), xaxs="i", yaxs="i", ylab="", xlab="", main="")
+plot_no_ci(fit_results_m3, "30", "Glc", col="#A9D18E", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,15), xaxs="i", yaxs="i", ylab="", xlab="", main="")
+
+plot_no_ci(fit_results_m3, "1", "Ace", col="#B63A2D", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,5), xaxs="i", yaxs="i", ylab="[Ace] (mM)", xlab="", main="")
+plot_no_ci(fit_results_m3, "10", "Ace", col="#D6685C", lwd=1.0, las=1, xlim=c(0,5), ylim=c(8,11), xaxs="i", yaxs="i", ylab="", xlab="", main="")
+plot_no_ci(fit_results_m3, "30", "Ace", col="#E49890", lwd=1.0, las=1, xlim=c(0,5), ylim=c(25,32), xaxs="i", yaxs="i", ylab="", xlab="", main="")
+
+plot_no_ci(fit_results_m3, "1", "Ace_enr", col="#BF9000", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="[Ace] (mM)", xlab="time (h)", main="")
+plot_no_ci(fit_results_m3, "10", "Ace_enr", col="#FFD966", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,0.7), xaxs="i", yaxs="i", ylab="", xlab="time (h)", main="")
+plot_no_ci(fit_results_m3, "30", "Ace_enr", col="#FFE699", lwd=1.0, las=1, xlim=c(0,5), ylim=c(0,0.3), xaxs="i", yaxs="i", ylab="", xlab="time (h)", main="")
+
+dev.off()
+
+##############################################
+# MODEL 4 - with global sensitivity analysis #
+##############################################
+
+setwd(model_dir)
+loadModel("Millard2020_Ecoli_glc_ace_model_4_MC.cps")
+
+# create calibration data files for monte carlo simulations
+file.copy("data_1mM.txt", "data_1mM_MC.txt", overwrite=TRUE)
+file.copy("data_10mM.txt", "data_10mM_MC.txt", overwrite=TRUE)
+file.copy("data_30mM.txt", "data_30mM_MC.txt", overwrite=TRUE)
+
+# number of Monte Carlo iterations
+n_iter_mc <- 10
+
+# get parameters for the best fit
+res_PE_model4 <- runParameterEstimation(method = "Statistics", model = getCurrentModel())
+
+# list used to set up global sensitivity analysis and store calculation results
+fit_results <- list("1" = list("initial_concentrations"= c("Ace0_out"=0.92, "Glc"=12.9, "X"=0.0671),
+                               "species_idx" = c("[Ace0_out]_0"=1, "[Glc]_0"=1, "[X]_0"=1),
+                               "data_exp" = read.table("data_1mM.txt", header=TRUE, sep="\t"),
+                               "sd" = c("Ace"=0.2, "Glc"=0.5, "X"=0.045, "Ace_enr"=0.03),
+                               "mapping" = c("Ace"="Acet_out", "Glc"="Glc", "X"="X", "Ace_enr"="Values[Ace_enr]")),
+                    "10" = list("initial_concentrations"= c("Ace0_out"=9, "Glc"=14.192, "X"=0.07),
+                                "species_idx" = c("[Ace0_out]_0"=2, "[Glc]_0"=2, "[X]_0"=2),
+                                "data_exp" = read.table("data_10mM.txt", header=TRUE, sep="\t"),
+                                "sd" = c("Ace"=0.2, "Glc"=0.5, "X"=0.045, "Ace_enr"=0.03),
+                                "mapping" = c("Ace"="Acet_out", "Glc"="Glc", "X"="X", "Ace_enr"="Values[Ace_enr]")),
+                    "30" = list("initial_concentrations"= c("Ace0_out"=30.2448, "Glc"=12.5, "X"=0.07227),
+                                "species_idx" = c("[Ace0_out]_0"=3, "[Glc]_0"=3, "[X]_0"=3),
+                                "data_exp" = read.table("data_30mM.txt", header=TRUE, sep="\t"),
+                                "sd" = c("Ace"=0.2, "Glc"=0.5, "X"=0.045, "Ace_enr"=0.03),
+                                "mapping" = c("Ace"="Acet_out", "Glc"="Glc", "X"="X", "Ace_enr"="Values[Ace_enr]")),
+                    "res_par" = res_PE_model4$parameters[, c("parameter", "value")],
+                    "res_cost" = c(res_PE_model4$main$objective_value),
+                    "res_converged" = c(test_khi2(nb_points=152, k_val=res_PE_model4$main$objective_value, nb_par=10)$`p-value, i.e. P(X^2<=value)` < 0.95))
+
+# simulate data for the best fit
+for (i in c("1", "10", "30")){
+  # update initial conditions (Glc, Ace and biomass concentrations)
+  for (j in names(fit_results[[i]][["initial_concentrations"]])){
+    setSpecies(key=j, initial_concentration=fit_results[[i]][["initial_concentrations"]][j])
+  }
+  # apply initial state
+  applyInitialState()
+  # run time course simulation
+  tmp <- as.matrix(runTimeCourse()$result)
+  # get complete simulation results
+  idx_t_max <- (tmp[,"Time"] <= max(fit_results[[i]][["data_exp"]]$time))
+  fit_results[[i]]$simulations <- array(NA, dim=c(n_iter_mc+1, sum(idx_t_max), ncol(tmp)), dimnames=list(iter=NULL, time=NULL, specie=colnames(tmp)))
+  fit_results[[i]]$simulations[1,,] <- tmp[idx_t_max,]
+  # get index of simulated data at experimental time points
+  fit_results[[i]]$t_idx <- match(fit_results[[i]][["data_exp"]]$time, fit_results[[i]]$simulations[1,,"Time"])
+  # get simulated data that match experimental time points
+  sim_data <- fit_results[[i]][["data_exp"]]
+  for (k in names(fit_results[[i]][["mapping"]])){
+    sim_data[,k] <- fit_results[[i]]$simulations[1,fit_results[[i]]$t_idx,fit_results[[i]][["mapping"]][[k]]]
+  }
+  fit_results[[i]]$sim_mc <- sim_data
+}
+
+# create progress bar
+pb <- txtProgressBar(min=0, max=n_iter_mc, style=3)
+
+# run global sensitivity analysis
+j <- 0
+while (j < n_iter_mc){
+  
+  # generate noisy datasets according to the experimental standard deviation
+  for (i in c("1", "10", "30")){
+    # initialize dataset with simulations of the best fit
+    data_noise <- fit_results[[i]]$sim_mc
+    nr <- nrow(data_noise)
+    # add noise
+    for (k in names(fit_results[[i]]$sd)){
+      data_noise[,k] <- rnorm(nr, mean=data_noise[,k], sd=fit_results[[i]]$sd[[k]])
+    }
+    # set negative concentrations to 0
+    data_noise[data_noise < 0] <- 0
+    # save the noisy dataset
+    write.table(data_noise, paste("data_", i, "mM_MC.txt", sep=""), sep="\t", row.names = FALSE, quote = FALSE)
+  }
+  
+  # run parameter estimation (SRES followed by Hooke and Jeeves and Levenberg-Marquadt methods to refine convergence)
+  # note: this protocol ensures faster convergence in comparison to PSO, which is necessary for monte carlo analysis
+  res_PE_tmp <- runParameterEstimation(method = "SRES", randomize_start_values=TRUE, update_model=TRUE)
+  res_PE_tmp <- runParameterEstimation(method = "HookeJeeves", randomize_start_values=FALSE, update_model=TRUE)
+  res_PE_tmp <- runParameterEstimation(method = "LevenbergMarquardt", randomize_start_values=FALSE, update_model=TRUE)
+  
+  # check if optimization has converged, reiterate if not
+  p_val_chi2 <- test_khi2(nb_points=152, k_val=res_PE_tmp$main$objective_value, nb_par=10)$`p-value, i.e. P(X^2<=value)`
+  if (p_val_chi2 < 0.95){
+    j = j+1
+  }else{
+    next
+  }
+  
+  # update the progress bar
+  setTxtProgressBar(pb, j)
+  
+  # save parameter estimation results
+  fit_results$res_par <- cbind(fit_results$res_par, res_PE_tmp$parameters[, "value"])
+  fit_results$res_cost <- c(fit_results$res_cost, res_PE_tmp$main$objective_value)
+  fit_results$res_converged <- c(fit_results$res_converged, p_val_chi2 < 0.95)
+  
+  # simulate all experiments
+  for (i in c("1", "10", "30")){
+    # update experiment-dependent parameters
+    for (l in names(fit_results[[i]]$species_idx)){
+      idx <- which(res_PE_tmp$parameters$parameter==l)[fit_results[[i]]$species_idx[l]]
+      k <- sub(".*\\[(.*)\\].*", "\\1", l, perl=TRUE)
+      setSpecies(key=k, initial_concentration=as.numeric(res_PE_tmp$parameters[idx,"value"]))
+    }
+    # apply initial state
+    applyInitialState()
+    # run time course simulations
+    tmp <- as.matrix(runTimeCourse()$result)
+    # get complete simulation results
+    fit_results[[i]]$simulations[j+1,,] <- tmp[tmp[,"Time"] <= max(fit_results[[i]][["data_exp"]]$time),]
+  }
+}
+
+# close progress bar
+close(pb)
+
+# save global sensitivity analysis results for further use
+setwd(results_dir)
+save(fit_results, file = "mc_results_10.RData")
+
+# load global sensitivity analysis results
+# (here we use results obtained with 100 iterations)
+load("mc_results_100.RData")
+
+# Calculate statistics on parameters (mean, sd, rsd)
+res_stats_params <- get_parameters_stats(fit_results)
+print(res_stats_params)
+write.table(res_stats_params, "parameters_stats.txt", sep="\t", quote = FALSE)
+
+# Plot fitting results
+pdf(file = "Figure 1C.pdf", width = 7, height = 9)
+par(mfrow=c(4,3))
+
+plot_with_ci(fit_results, "1", "X", col="#1F4E79", lwd=1.2, las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="[biomass] (gDW/L)", xlab="", main="[acetate]=1mM")
+plot_with_ci(fit_results, "10", "X", col="#2E75B6", lwd=1.2, las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="", xlab="", main="[acetate]=10mM")
+plot_with_ci(fit_results, "30", "X", col="#9DC3E6", lwd=1.2, las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="", xlab="", main="[acetate]=30mM")
+
+plot_with_ci(fit_results, "1", "Glc", col="#548235", lwd=1.2, las=1, xlim=c(0,5), ylim=c(0,15), xaxs="i", yaxs="i", ylab="[Glc] (mM)", xlab="", main="")
+plot_with_ci(fit_results, "10", "Glc", col="#70AD47", lwd=1.2, las=1, xlim=c(0,5), ylim=c(0,15), xaxs="i", yaxs="i", ylab="", xlab="", main="")
+plot_with_ci(fit_results, "30", "Glc", col="#A9D18E", lwd=1.2, las=1, xlim=c(0,5), ylim=c(0,15), xaxs="i", yaxs="i", ylab="", xlab="", main="")
+
+plot_with_ci(fit_results, "1", "Ace", col="#B63A2D", lwd=1.2, las=1, xlim=c(0,5), ylim=c(0,5), xaxs="i", yaxs="i", ylab="[Ace] (mM)", xlab="", main="")
+plot_with_ci(fit_results, "10", "Ace", col="#D6685C", lwd=1.2, las=1, xlim=c(0,5), ylim=c(8,11), xaxs="i", yaxs="i", ylab="", xlab="", main="")
+plot_with_ci(fit_results, "30", "Ace", col="#E49890", lwd=1.2, las=1, xlim=c(0,5), ylim=c(27,32), xaxs="i", yaxs="i", ylab="", xlab="", main="")
+
+plot_with_ci(fit_results, "1", "Ace_enr", col="#BF9000", lwd=1.2, las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="[Ace] (mM)", xlab="time (h)", main="")
+plot_with_ci(fit_results, "10", "Ace_enr", col="#FFD966", lwd=1.2, las=1, xlim=c(0,5), ylim=c(0,0.7), xaxs="i", yaxs="i", ylab="", xlab="time (h)", main="")
+plot_with_ci(fit_results, "30", "Ace_enr", col="#FFE699", lwd=1.2, las=1, xlim=c(0,5), ylim=c(0,0.3), xaxs="i", yaxs="i", ylab="", xlab="time (h)", main="")
+
+dev.off()
+
+
diff --git a/2-Model_validation.R b/2-Model_validation.R
new file mode 100644
index 0000000..ef6b6f4
--- /dev/null
+++ b/2-Model_validation.R
@@ -0,0 +1,1049 @@
+
+
+###################
+# Set environment #
+###################
+
+# load libraries and initialize environment
+source("set_env.R")
+
+
+############################################
+# Load global sensitivity analysis results #
+############################################
+
+# This file is generated by script "1-Model_construction.R".
+setwd(results_dir)
+load("mc_results_100.RData")
+
+
+###################
+# Testing model 4 #
+###################
+
+setwd(results_dir)
+pdf(file="Figure 3.pdf", width = 7, height = 9)
+par(mfrow=c(4,3))
+
+# Pulse experiment (Enjalbert et al., 2017)
+###########################################
+
+setwd(model_dir)
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model.cps")
+setwd(results_dir)
+
+# set biomass concentration at which the pulse is performed
+setGlobalQuantities(key = "_X_conc_pulse", initial_value = 0.9)
+# simulate response to acetate pulse
+res_pulse <- runTimeCourse()
+# get simulation results
+id_start <- which(res_pulse$result$Ace_out >= 30)[1]+1
+id_end <- which(res_pulse$result$Time >= (res_pulse$result$Time[id_start]+8/60))[1]+1
+t_pulse <- (res_pulse$result$Time[seq(id_start, id_end)] - res_pulse$result$Time[id_start])
+ace_conc_pulse <- res_pulse$result$Ace_out[seq(id_start, id_end)] - res_pulse$result$Ace_out[id_start]
+glc_conc_pulse <- res_pulse$result$Glc[seq(id_start, id_end)] - res_pulse$result$Glc[id_start]
+
+# set biomass concentration at which the pulse is performed
+setGlobalQuantities(key = "_X_conc_pulse", initial_value = 1000)
+res_nopulse <- runTimeCourse()
+# get simulation results
+ace_conc_nopulse <- res_nopulse$result$Ace_out[seq(id_start, id_end)] - res_nopulse$result$Ace_out[id_start]
+glc_conc_nopulse <- res_nopulse$result$Glc[seq(id_start, id_end)] - res_nopulse$result$Glc[id_start]
+
+run_sa <- function(){
+  # set biomass concentration at which the pulse is performed
+  setGlobalQuantities(key = "_X_conc_pulse", initial_value = 0.9)
+
+  # simulate response to acetate pulse
+  res_pulse <- runTimeCourse()
+  
+  # get simulation results
+  id_start <- which(res_pulse$result$Ace_out >= 30)[1]+1
+  id_end <- which(res_pulse$result$Time >= (res_pulse$result$Time[id_start]+8/60))[1]+1
+  
+  t_pulse <- (res_pulse$result$Time[seq(id_start, id_end)] - res_pulse$result$Time[id_start])
+  ace_conc_pulse <- res_pulse$result$Ace_out[seq(id_start, id_end)] - res_pulse$result$Ace_out[id_start]
+  glc_conc_pulse <- res_pulse$result$Glc[seq(id_start, id_end)] - res_pulse$result$Glc[id_start]
+  
+  # set biomass concentration at which the pulse is performed
+  setGlobalQuantities(key = "_X_conc_pulse", initial_value = 1000)
+  
+  # simulate response to water pulse (control experiment)
+  res_nopulse <- runTimeCourse()
+  
+  # get simulation results
+  ace_conc_nopulse <- res_nopulse$result$Ace_out[seq(id_start, id_end)] - res_nopulse$result$Ace_out[id_start]
+  glc_conc_nopulse <- res_nopulse$result$Glc[seq(id_start, id_end)] - res_nopulse$result$Glc[id_start]
+  
+  return(list(ace_conc_pulse=ace_conc_pulse, glc_conc_pulse=glc_conc_pulse, ace_conc_nopulse=ace_conc_nopulse, glc_conc_nopulse=glc_conc_nopulse, t_pulse=t_pulse))
+}
+
+# create progress bar
+pb <- txtProgressBar(min=0, max=ncol(fit_results$res_par)-1, style=3)
+
+# sensitivity analysis
+# run simulations for all sets of parameters
+res <- array(NA, dim=c(ncol(fit_results$res_par)-1, 4, length(t_pulse)), dimnames=list(iter=NULL, var=c("ace_conc_pulse", "glc_conc_pulse", "ace_conc_nopulse", "glc_conc_nopulse"), time=NULL))
+for (i in seq(ncol(fit_results$res_par)-1)){
+  rp <- c(fit_results$res_par[,i+1])
+  names(rp) <- fit_results$res_par[,"parameter"]
+  model <- update_params(getCurrentModel(), rp)
+  rsa <- run_sa()
+  for (j in names(rsa)){
+    if (j != "t_pulse"){
+      res[i,j,] <- rsa[[j]]
+    }
+  }
+  # update the progress bar
+  setTxtProgressBar(pb, i)
+}
+
+# close progress bar
+close(pb)
+
+# measurements
+# sampling time
+time_meas <- seq(0,8)/60
+# acetate pulse experiment
+glc <- c(0, -0.06931183, -0.151415145, -0.189227994, -0.269451057, -0.290764495, -0.230785281, -0.464084162, -0.551878527)
+sd_glc <- c(0, 0.032476344, 0.073133915, 0.113018846, 0.049485284, 0.005325541, 0.163377704, 0.034786419, 0.048477157)
+ace <- c(0, -0.027907926, -0.078000853, -0.155334163, -0.165031608, -0.111098424, -0.182877548, -0.237262298, -0.276903255)
+sd_ace <- c(0, 0.002740145, 0.025693594, 0.053641876, 0.089975321, 0.005875669, 0.085604161, 0.061930626, 0.099140975)
+# control experiment (pulse without acetate)
+glc_nopulse <- c(0, -0.195637774, -0.325512845, -0.433785334, -0.628518958, -0.726913548, -0.892908748, -1.071230579, -1.16285575)
+sd_glc_nopulse <- c(0, 0.058023617, 0.109115511, 0.047090371, 0.052331837, 0.065619906, 0.133896355, 0.16828754, 0.03515465)
+ace_nopulse <- c(0, 0.01012067, 0.05974009, 0.086787283, 0.086690257, 0.104329693, 0.128507087, 0.130026354, 0.187336965)
+sd_ace_nopulse <- c(0, 0.005117257, 0.022507218, 0.040319045, 0.037548873, 0.037235285, 0.044494365, 0.045029023, 0.023982374)
+
+# plot simulations vs measurements
+plot_with_ci_2(t_pulse, ace_conc_pulse, res[,"ace_conc_pulse",], time_meas, ace, sd_ace, col="#D6685C", h=0, ylim=c(-0.4,0.3), las=1, main="Enjalbert_2017 (pulse 30mM ace)", ylab="change of [Ace]", xlab="time (h)", lwd=1.2)
+plot_with_ci_2(t_pulse, glc_conc_pulse, res[,"glc_conc_pulse",], time_meas, glc, sd_glc, col="#70AD47", h=NULL, ylim=c(-1.4,0), las=1, main="Enjalbert_2017 (pulse 30mM ace)", ylab="change of [Glc]", xlab="time (h)", lwd=1.2)
+plot_with_ci_2(t_pulse, ace_conc_nopulse, res[,"ace_conc_nopulse",], time_meas, ace_nopulse, sd_ace_nopulse, col="#D6685C", h=0, ylim=c(-0.4,0.3), las=1, main="Enjalbert_2017 (control)", ylab="change of [Ace]", xlab="time (h)", lwd=1.2)
+plot_with_ci_2(t_pulse, glc_conc_nopulse, res[,"glc_conc_nopulse",], time_meas, glc_nopulse, sd_glc_nopulse, col="#70AD47", h=NULL, ylim=c(-1.4,0), las=1, main="Enjalbert_2017 (control)", ylab="change of [Glc]", xlab="time (h)", lwd=1.2)
+
+# Chemostat experiment (Renilla et al., 2012)
+#############################################
+
+setwd(model_dir)
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model.cps")
+setwd(results_dir)
+
+# delete events and set glc feed to 1
+deleteEvent(getEvents()$key)
+setGlobalQuantities(key = "_feed", initial_value = 1)
+
+n_step <- 50
+dilution_rates <- seq(0.1, 0.5, length.out = n_step)
+fluxes <- c("Values[v_growth_rate]", "Values[v_glc_uptake]", "Values[v_ace_net]")
+  
+# sensitivity analysis
+
+# create progress bar
+pb <- txtProgressBar(min=0, max=ncol(fit_results$res_par)-1, style=3)
+
+# run simulations for all sets of parameters
+res <- array(NA, dim=c(ncol(fit_results$res_par)-1, n_step, length(fluxes)+1), dimnames=list(iter=NULL, dilution_rate=NULL, specie=c("dilution_rate", "Values[v_growth_rate]", "Values[v_glc_uptake]", "Values[v_ace_net]")))
+for (i in seq(ncol(fit_results$res_par)-1)){
+  rp <- c(fit_results$res_par[,i+1])
+  names(rp) <- fit_results$res_par[,"parameter"]
+  model <- update_params(getCurrentModel(), rp)
+  res_chemostat <- matrix(NA, nrow=n_step, ncol=length(fluxes)+1, dimnames=list(r=NULL, c=c("dilution_rate", fluxes)))
+  for (j in seq(n_step)){
+    setGlobalQuantities(key = "_dilution_rate", initial_value = dilution_rates[j], model=model)
+    res_ss <- runSteadyState(model=model)
+    res_chemostat[j,] <- c(dilution_rates[j], unlist(res_ss$global_quantities[res_ss$global_quantities$key %in% fluxes, "value"]))
+  }
+  res[i,,] <- res_chemostat
+  # update the progress bar
+  setTxtProgressBar(pb, i)
+}
+
+# close progress bar
+close(pb)
+
+# acetate flux as function of dilution rate
+dilution_rate <- c(0.09586056644880175, 0.20043572984749464, 0.2997821350762528, 0.3468409586056645, 0.39912854030501094, 0.44618736383442276, 0.5002178649237474)
+q_ace <- c(0.40472342596168076, 0.7396156614846294, 1.477019302736899, 1.2154669794005626, 1.96934635755591, 2.0929143843289824, 2.006569318707304)
+q_ace_sd <- c(0.120440687823878, 0.15316333195082, 0.04595662724122, 0.0274214232252601, 0.28885933172199, 0.0777639526513201, 0.28664731148963)
+
+plot_with_ci_3(res, "dilution_rate", "Values[v_ace_net]", "#D6685C", las=1, xlim=c(0,0.6), ylim=c(0,4), main="Renilla_2012", lwd=1.2, xlab="dilution rate (h-1)", ylab="ace flux (mmol/gDW/h)")
+plot_points(dilution_rate, q_ace, q_ace_sd, offset=0.01, col="#D6685C")
+
+# acetate flux as function of glc uptake
+q_glc <- c(1.43478260869565, 2.7391304347826, 4.59130434782608, 4.69565217391304, 5.7391304347826, 5.92173913043478, 6.10434782608695, 7.12173913043477, 8.34782608695652)
+q_ace <- c(0.381358340437624, 0.762906128635029, 1.40509614473808, 1.17836506583309, 1.99602159704461, 2.08290233967983, 2.01292033721701, 2.44717249218528, 2.5848252344416)
+q_ace_sd <- c(0.139547219854126, 0.139471440750213, 0.15697641375391, 0.1045751633987, 0.19179691200152, 0.0174291938997801, 0.24397082504499, 0.52295159609737, 0.33130624230368)
+q_glc_sd <- c(0.20234760540444, 0.58899555210581, 0.36827270271402, 0.14607356337583, 0.630432119199, 0.13069807968161, 0.47630364392495, 0.99361847036576, 0.66185122193432)
+
+plot_with_ci_3(res, "Values[v_glc_uptake]", "Values[v_ace_net]", col="#D6685C", las=1, xlim=c(0,10), ylim=c(0,4), main="Renilla_2012", lwd=1.2, xlab="glc uptake (mmol/gDW/h)", ylab="ace flux (mmol/gDW/h)")
+plot_points(q_glc, q_ace, q_ace_sd, offset=0.2, col="#D6685C")
+plot_points(q_glc, q_ace, q_glc_sd, offset=0.08, mode="h", col="#D6685C")
+
+# Steady-state fluxes for acetate concentration between 0.1 and 100mM (Enjalbert et al., 2017; Pinhal et al., 2019)
+###################################################################################################################
+
+setwd(model_dir)
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model.cps")
+setwd(results_dir)
+
+# remove events and fix concentrations of actate, glucose and biomass
+deleteEvent(getEvents()$key)
+setSpecies(key="Ace_out", type="fixed")
+setSpecies(key="Glc", type="fixed")
+setSpecies(key="X", type="fixed")
+
+# run simulations
+n_step <- 50
+ace_concentration <- 10**seq(-1, 2, length.out = n_step)
+fluxes <- c("Values[v_growth_rate]", "Values[v_glc_uptake]", "Values[v_ace_net]")
+
+# sensitivity analysis
+# run simulations for all sets of parameters
+res_e2 <- array(NA, dim=c(ncol(fit_results$res_par)-1, n_step, length(fluxes)+1), dimnames=list(iter=NULL, ace_concentration=NULL, specie=c("ace_concentration", fluxes)))
+
+# create progress bar
+pb <- txtProgressBar(min=0, max=ncol(fit_results$res_par)-1, style=3)
+
+for (i in seq(ncol(fit_results$res_par)-1)){
+  rp <- c(fit_results$res_par[,i+1])
+  names(rp) <- fit_results$res_par[,"parameter"]
+  model <- update_params(getCurrentModel(), rp)
+  
+  res_ace_range <- matrix(NA, nrow=n_step, ncol=length(fluxes)+1, dimnames=list(r=NULL, c=c("ace_concentration", fluxes)))
+  for (j in seq(n_step)){
+    setSpecies(key="Ace_out", initial_concentration=ace_concentration[j])
+    applyInitialState()
+    res_ss <- runSteadyState()
+    res_ace_range[j,] <- c(ace_concentration[j], unlist(res_ss$global_quantities[res_ss$global_quantities$key %in% fluxes, "value"]))
+  }
+  res_e2[i,,] <- res_ace_range
+  # update the progress bar
+  setTxtProgressBar(pb, i)
+}
+
+# close progress bar
+close(pb)
+
+xlab_main <- c(0.1, 1, 10, 100)
+xlab_sec <- c(seq(0.2, 0.9, by=0.1), seq(2, 9, by=1), seq(20, 90, by=10))
+
+# growth rate as function of acetate concentration
+growth_rates <- c(0.521128511, 0.611148842625582, 0.613161998174498, 0.502533817, 0.496290415, 0.488201506, 0.547635665, 0.499830448, 0.474554197, 0.425356578, 0.377534684, 0.645724326, 0.618475601, 0.554887936, 0.564811523, 0.527571192, 0.434972836, 0.3824734, 0.583623355, 0.620905534, 0.564259247, 0.532148135, 0.483885215, 0.557074418, 0.630654409249223)
+sd_growth_rates <- c(0.001793104, 0.00204807928657914, 0.00219396182484705, 0.001709207, 0.001846205, 0.001757403, 0.001821375, 0.001025702, 0.001940912, 0.001204707, 0.001999188, 0.001418374, 0.001932601, 0.001455791, 0.001574234, 0.001206265, 0.001292476, 0.001068259, 0.001804648, 0.001643459, 0.001598405, 0.001121218, 0.000912408, 0.00194896, 0.00203369597574686)
+ace_conc <- c(0.451964624, 1.11600286648471, 2.04718732931708, 2.86252145, 5.285907977, 9.106164204, 16.67476528, 16.76626787, 17.00218707, 30.8667961, 57.92292091, 0.478352574, 4.55673229, 8.10163028, 8.22100734, 7.829591756, 33.53244905, 66.20361403, 0.436956014, 1.28468189, 1.555875222, 12.02564968, 30.24566673, 0.548011282, 2.29562227069566)
+sd_ace_conc <- c(0.262318006, 0.281361538208953, 0.289527601555302, 0.302351163, 0.327705513, 0.330782201, 0.277259011, 0.233956798, 0.31883929, 0.300578057, 0.313371784, 0.231202155, 0.264687437, 0.243480317, 0.289821733, 0.263808862, 0.289478134, 0.264861034, 0.22461248, 0.229031308, 0.241718918, 0.254111384, 0.187394292, 0.011107606, 0.290519090995892)
+
+plot_with_ci_3(res_e2, "ace_concentration", "Values[v_growth_rate]", col="#2E75B6", xaxt='n', las=1, lwd=1.2, xlim=c(0.1,100), ylim=c(0,0.8), log="x", main="Enjalbert_2017", xlab="[acetate] (mM)", ylab="growth rate (h-1)")
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+plot_points(ace_conc, growth_rates, sd_growth_rates, offset=0.01, col="#2E75B6")
+plot_points(ace_conc, growth_rates, sd_ace_conc, offset=0.02, mode="h", col="#2E75B6")
+
+# glc uptake as function of acetate concentration
+glc_upt <- c(8.654860167, 8.36127542981722, 7.98010111285252, 9.236935826, 8.274418986, 7.560431219, 7.339194455, 5.775312502, 6.423391263, 5.1544758, 3.938631573, 8.115447647, 9.28067031, 6.737153424, 7.172748804, 5.884186033, 5.684201497, 4.811576974, 9.632702365, 8.055042777, 9.708342814, 7.100081588, 5.505759496, 9.242859752, 8.18621623190759)
+sd_glc_upt <- c(0.337812425, 0.38531328268303, 0.373770045721031, 0.356787032, 0.334672954, 0.317509322, 0.288025925, 0.16053276, 0.375934255, 0.293148172, 0.359225607, 0.197331684, 0.360984112, 0.229372278, 0.241820396, 0.20450532, 0.260869273, 0.216134352, 0.34289286, 0.350305744, 0.293144783, 0.220135755, 0.153471508, 0.25245346, 0.396815184905029)
+ace_conc <- c(0.451964624, 1.11600286648471, 2.04718732931708, 2.86252145, 5.285907977, 9.106164204, 16.67476528, 16.76626787, 17.00218707, 30.8667961, 57.92292091, 0.478352574, 4.55673229, 8.10163028, 8.22100734, 7.829591756, 33.53244905, 66.20361403, 0.436956014, 1.28468189, 1.555875222, 12.02564968, 30.24566673, 0.548011282, 2.29562227069566)
+sd_ace_conc <- c(0.262318006, 0.281361538208953, 0.289527601555302, 0.302351163, 0.327705513, 0.330782201, 0.277259011, 0.233956798, 0.31883929, 0.300578057, 0.313371784, 0.231202155, 0.264687437, 0.243480317, 0.289821733, 0.263808862, 0.289478134, 0.264861034, 0.22461248, 0.229031308, 0.241718918, 0.254111384, 0.187394292, 0.011107606, 0.290519090995892)
+
+plot_with_ci_3(res_e2, "ace_concentration", "Values[v_glc_uptake]", col="#70AD47", xaxt='n', las=1, lwd=1.2, xlim=c(0.1,100), ylim=c(0,10), log="x", main="Enjalbert_2017", xlab="[acetate] (mM)", ylab="glc uptake (mmol/gDW/h)")
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+plot_points(ace_conc, glc_upt, sd_glc_upt, offset=0.02, col="#70AD47")
+plot_points(ace_conc, glc_upt, sd_ace_conc, offset=0.2, mode="h", col="#70AD47")
+
+# ace flux as function of acetate concentration
+ace_flx <- c(3.5, -2.7, 1.516999356, 1.26845123082679, 0.775821380507016, 0.678877137, 0.017366464, -0.991478151, -1.286687213, -2.078474994, -1.530841439, -1.525342269, -1.253581266, 1.984679487, 0.546462624, -0.136780389, -0.393883917, -0.610240984, -1.120767885, -1.277455315, 2.574285211, 2.051935093, 1.828415596, -1.262442483, -1.317987733, 2.333568565, 1.85234639824858)
+sd_ace_flx <- c(0.35, 0.27, 0.316118066, 0.388752117258161, 0.40715278851436, 0.33357638, 0.37333751, 0.347029894, 0.280501612, 0.195031303, 0.376252463, 0.226182385, 0.303661317, 0.253610517, 0.385450715, 0.243880325, 0.30665695, 0.257983739, 0.23844407, 0.198458448, 0.299832036, 0.334956504, 0.317134334, 0.263807154, 0.195219648, 0.016120887, 0.386174129654754)
+ace_conc <- c(0.2, 100, 0.451964624, 1.11600286648471, 2.04718732931708, 2.86252145, 5.285907977, 9.106164204, 16.67476528, 16.76626787, 17.00218707, 30.8667961, 57.92292091, 0.478352574, 4.55673229, 8.10163028, 8.22100734, 7.829591756, 33.53244905, 66.20361403, 0.436956014, 1.28468189, 1.555875222, 12.02564968, 30.24566673, 0.548011282, 2.29562227069566)
+sd_ace_conc <- c(0.05, 10, 0.262318006, 0.281361538208953, 0.289527601555302, 0.302351163, 0.327705513, 0.330782201, 0.277259011, 0.233956798, 0.31883929, 0.300578057, 0.313371784, 0.231202155, 0.264687437, 0.243480317, 0.289821733, 0.263808862, 0.289478134, 0.264861034, 0.22461248, 0.229031308, 0.241718918, 0.254111384, 0.187394292, 0.011107606, 0.290519090995892)
+plot_with_ci_3(res_e2, "ace_concentration", "Values[v_ace_net]", col="#D6685C", xaxt='n', las=1, lwd=1.2, xlim=c(0.1,100), ylim=c(-4,4), log="x", main="Enjalbert_2017", xlab="[acetate] (mM)", ylab="ace flux (mmol/gDW/h)")
+abline(h=0)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+plot_points(ace_conc, ace_flx, sd_ace_flx, offset=0.04, col="#D6685C")
+plot_points(ace_conc, ace_flx, sd_ace_conc, offset=0.2, mode="h", col="#D6685C")
+
+dev.off()
+
+
+##############################
+# Testing alternative models #
+##############################
+
+###########
+# Model 1 #
+###########
+
+setwd(results_dir)
+pdf(file="Figure 3-figure supplement 1.pdf", width = 7, height = 9)
+par(mfrow=c(4,3))
+
+# Pulse experiment (Enjalbert et al., 2017)
+###########################################
+
+setwd(model_dir)
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_1.cps")
+
+# set biomass concentration at which the pulse is performed
+setGlobalQuantities(key = "_X_conc_pulse", initial_value = 0.9)
+
+# simulate response to acetate pulse
+res_pulse <- runTimeCourse()
+
+# get simulation results
+id_start <- which(res_pulse$result$Ace_out >= 30)[1]+1
+id_end <- which(res_pulse$result$Time >= (res_pulse$result$Time[id_start]+8/60))[1]+1
+
+t_pulse <- (res_pulse$result$Time[seq(id_start, id_end)] - res_pulse$result$Time[id_start])
+ace_conc_pulse <- res_pulse$result$Ace_out[seq(id_start, id_end)] - res_pulse$result$Ace_out[id_start]
+glc_conc_pulse <- res_pulse$result$Glc[seq(id_start, id_end)] - res_pulse$result$Glc[id_start]
+
+# measurements
+time_meas <- seq(0,8)/60
+glc <- c(0, -0.06931183, -0.151415145, -0.189227994, -0.269451057, -0.290764495, -0.230785281, -0.464084162, -0.551878527)
+sd_glc <- c(0, 0.032476344, 0.073133915, 0.113018846, 0.049485284, 0.005325541, 0.163377704, 0.034786419, 0.048477157)
+ace <- c(0, -0.027907926, -0.078000853, -0.155334163, -0.165031608, -0.111098424, -0.182877548, -0.237262298, -0.276903255)
+sd_ace <- c(0, 0.002740145, 0.025693594, 0.053641876, 0.089975321, 0.005875669, 0.085604161, 0.061930626, 0.099140975)
+
+# plot simulations vs measurements
+plot(t_pulse, ace_conc_pulse, type="l", ylim=c(-0.4,0), las=1, main="Enjalbert_2017 (pulse 30mM ace)", ylab="change of [Ace]", xlab="time (h)", col="#D6685C", lwd=2)
+plot_points(time_meas, ace, sd_ace, offset=0.002, col="#D6685C")
+plot(t_pulse, glc_conc_pulse, type="l", main="Enjalbert_2017 (pulse 30mM ace)", las=1, ylab="change of [Glc]", xlab="time (h)", col="#70AD47", lwd=2)
+plot_points(time_meas, glc, sd_glc, offset=0.002, col="#70AD47")
+
+# simulate control experiment (i.e. no acetate pulse)
+deleteEvent(getEvents()$key)
+
+res_nopulse <- runTimeCourse()
+
+# get simulation results
+ace_conc_nopulse <- res_nopulse$result$Ace_out[seq(id_start, id_end)] - res_nopulse$result$Ace_out[id_start]
+glc_conc_nopulse <- res_nopulse$result$Glc[seq(id_start, id_end)] - res_nopulse$result$Glc[id_start]
+
+# measurements
+glc_nopulse <- c(0, -0.195637774, -0.325512845, -0.433785334, -0.628518958, -0.726913548, -0.892908748, -1.071230579, -1.16285575)
+sd_glc_nopulse <- c(0, 0.058023617, 0.109115511, 0.047090371, 0.052331837, 0.065619906, 0.133896355, 0.16828754, 0.03515465)
+ace_nopulse <- c(0, 0.01012067, 0.05974009, 0.086787283, 0.086690257, 0.104329693, 0.128507087, 0.130026354, 0.187336965)
+sd_ace_nopulse <- c(0, 0.005117257, 0.022507218, 0.040319045, 0.037548873, 0.037235285, 0.044494365, 0.045029023, 0.023982374)
+
+# plot simulations vs measurements
+plot(t_pulse, ace_conc_nopulse, type="l", ylim=c(0,0.3), main="Enjalbert_2017 (control)", las=1, ylab="change of [Ace]", xlab="time (h)", col="#D6685C", lwd=2)
+plot_points(time_meas, ace_nopulse, sd_ace_nopulse, offset=0.002, col="#D6685C")
+plot(t_pulse, glc_conc_nopulse, type="l", ylim=c(-1.4,0), main="Enjalbert_2017 (control)", las=1, ylab="change of [Glc]", xlab="time (h)", col="#70AD47", lwd=2)
+plot_points(time_meas, glc_nopulse, sd_glc_nopulse, offset=0.002, col="#70AD47")
+
+# Chemostat experiment (Renilla et al., 2012)
+#############################################
+
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_1.cps")
+
+# delete events and set glc feed to 1
+deleteEvent(getEvents()$key)
+setGlobalQuantities(key = "_feed", initial_value = 1)
+
+n_step <- 50
+dilution_rates <- seq(0.1, 0.5, length.out = n_step)
+fluxes <- c("Values[v_growth_rate]", "Values[v_glc_uptake]", "Values[v_ace_net]")
+res_chemostat <- matrix(NA, nrow=n_step, ncol=length(fluxes)+1, dimnames=list(r=NULL, c=c("dilution_rate", fluxes)))
+for (i in seq(n_step)){
+  setGlobalQuantities(key = "_dilution_rate", initial_value = dilution_rates[i])
+  res_ss <- runSteadyState()
+  res_chemostat[i,] <- c(dilution_rates[i], unlist(res_ss$global_quantities[res_ss$global_quantities$key %in% fluxes, "value"]))
+}
+
+# acetate flux as function of dilution rate
+dilution_rate <- c(0.09586056644880175, 0.20043572984749464, 0.2997821350762528, 0.3468409586056645, 0.39912854030501094, 0.44618736383442276, 0.5002178649237474)
+q_ace <- c(0.40472342596168076, 0.7396156614846294, 1.477019302736899, 1.2154669794005626, 1.96934635755591, 2.0929143843289824, 2.006569318707304)
+q_ace_sd <- c(0.120440687823878, 0.15316333195082, 0.04595662724122, 0.0274214232252601, 0.28885933172199, 0.0777639526513201, 0.28664731148963)
+
+plot(res_chemostat[,"dilution_rate"], res_chemostat[,"Values[v_ace_net]"], type="l", las=1, xlim=c(0,0.6), ylim=c(0,4), main="Renilla_2012", lwd=2, xlab="dilution rate (h-1)", ylab="ace flux (mmol/gDW/h)", col="#D6685C")
+plot_points(dilution_rate, q_ace, q_ace_sd, offset=0.01, col="#D6685C")
+
+# acetate flux as function of glc uptake
+q_glc <- c(1.43478260869565, 2.7391304347826, 4.59130434782608, 4.69565217391304, 5.7391304347826, 5.92173913043478, 6.10434782608695, 7.12173913043477, 8.34782608695652)
+q_ace <- c(0.381358340437624, 0.762906128635029, 1.40509614473808, 1.17836506583309, 1.99602159704461, 2.08290233967983, 2.01292033721701, 2.44717249218528, 2.5848252344416)
+q_ace_sd <- c(0.139547219854126, 0.139471440750213, 0.15697641375391, 0.1045751633987, 0.19179691200152, 0.0174291938997801, 0.24397082504499, 0.52295159609737, 0.33130624230368)
+q_glc_sd <- c(0.20234760540444, 0.58899555210581, 0.36827270271402, 0.14607356337583, 0.630432119199, 0.13069807968161, 0.47630364392495, 0.99361847036576, 0.66185122193432)
+
+plot(res_chemostat[,"Values[v_glc_uptake]"], res_chemostat[,"Values[v_ace_net]"], type="l", las=1, xlim=c(0,10), ylim=c(0,4), main="Renilla_2012", lwd=2, xlab="glc uptake (mmol/gDW/h)", ylab="ace flux (mmol/gDW/h)", col="#D6685C")
+plot_points(q_glc, q_ace, q_ace_sd, offset=0.2, col="#D6685C")
+plot_points(q_glc, q_ace, q_glc_sd, offset=0.08, mode="h", col="#D6685C")
+
+# Steady-state fluxes for acetate concentration between 0.1 and 100mM (Enjalbert et al., 2017; Pinhal et al., 2019)
+##############################################################################################
+
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_1.cps")
+
+# remove events and fix concentrations of actate, glucose and biomass
+deleteEvent(getEvents()$key)
+setSpecies(key="Ace_out", type="fixed")
+setSpecies(key="Glc", type="fixed")
+setSpecies(key="X", type="fixed")
+
+# run simulations
+n_step <- 50
+ace_concentration <- 10**seq(-1, 2, length.out = n_step)
+fluxes <- c("Values[v_growth_rate]", "Values[v_glc_uptake]", "Values[v_ace_net]")
+res_ace_range <- matrix(NA, nrow=n_step, ncol=length(fluxes)+1, dimnames=list(r=NULL, c=c("ace_concentration", fluxes)))
+for (i in seq(n_step)){
+  setSpecies(key="Ace_out", initial_concentration=ace_concentration[i])
+  applyInitialState()
+  res_ss <- runSteadyState()
+  res_ace_range[i,] <- c(ace_concentration[i], unlist(res_ss$global_quantities[res_ss$global_quantities$key %in% fluxes, "value"]))
+}
+
+xlab_main <- c(0.1, 1, 10, 100)
+xlab_sec <- c(seq(0.2, 0.9, by=0.1), seq(2, 9, by=1), seq(20, 90, by=10))
+
+# growth rate as function of acetate concentration
+growth_rates <- c(0.521128511, 0.611148842625582, 0.613161998174498, 0.502533817, 0.496290415, 0.488201506, 0.547635665, 0.499830448, 0.474554197, 0.425356578, 0.377534684, 0.645724326, 0.618475601, 0.554887936, 0.564811523, 0.527571192, 0.434972836, 0.3824734, 0.583623355, 0.620905534, 0.564259247, 0.532148135, 0.483885215, 0.557074418, 0.630654409249223)
+sd_growth_rates <- c(0.001793104, 0.00204807928657914, 0.00219396182484705, 0.001709207, 0.001846205, 0.001757403, 0.001821375, 0.001025702, 0.001940912, 0.001204707, 0.001999188, 0.001418374, 0.001932601, 0.001455791, 0.001574234, 0.001206265, 0.001292476, 0.001068259, 0.001804648, 0.001643459, 0.001598405, 0.001121218, 0.000912408, 0.00194896, 0.00203369597574686)
+ace_conc <- c(0.451964624, 1.11600286648471, 2.04718732931708, 2.86252145, 5.285907977, 9.106164204, 16.67476528, 16.76626787, 17.00218707, 30.8667961, 57.92292091, 0.478352574, 4.55673229, 8.10163028, 8.22100734, 7.829591756, 33.53244905, 66.20361403, 0.436956014, 1.28468189, 1.555875222, 12.02564968, 30.24566673, 0.548011282, 2.29562227069566)
+sd_ace_conc <- c(0.262318006, 0.281361538208953, 0.289527601555302, 0.302351163, 0.327705513, 0.330782201, 0.277259011, 0.233956798, 0.31883929, 0.300578057, 0.313371784, 0.231202155, 0.264687437, 0.243480317, 0.289821733, 0.263808862, 0.289478134, 0.264861034, 0.22461248, 0.229031308, 0.241718918, 0.254111384, 0.187394292, 0.011107606, 0.290519090995892)
+plot(res_ace_range[,"ace_concentration"], xaxt='n', res_ace_range[,"Values[v_growth_rate]"], las=1, col="#2E75B6", lwd=2, type="l", xlim=c(0.1,100), ylim=c(0,0.8), log="x", main="Enjalbert_2017", xlab="[acetate] (mM)", ylab="growth rate (h-1)")
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+plot_points(ace_conc, growth_rates, sd_growth_rates, offset=0.01, col="#2E75B6")
+plot_points(ace_conc, growth_rates, sd_ace_conc, offset=0.02, mode="h", col="#2E75B6")
+
+# glc uptake as function of acetate concentration
+glc_upt <- c(8.654860167, 8.36127542981722, 7.98010111285252, 9.236935826, 8.274418986, 7.560431219, 7.339194455, 5.775312502, 6.423391263, 5.1544758, 3.938631573, 8.115447647, 9.28067031, 6.737153424, 7.172748804, 5.884186033, 5.684201497, 4.811576974, 9.632702365, 8.055042777, 9.708342814, 7.100081588, 5.505759496, 9.242859752, 8.18621623190759)
+sd_glc_upt <- c(0.337812425, 0.38531328268303, 0.373770045721031, 0.356787032, 0.334672954, 0.317509322, 0.288025925, 0.16053276, 0.375934255, 0.293148172, 0.359225607, 0.197331684, 0.360984112, 0.229372278, 0.241820396, 0.20450532, 0.260869273, 0.216134352, 0.34289286, 0.350305744, 0.293144783, 0.220135755, 0.153471508, 0.25245346, 0.396815184905029)
+ace_conc <- c(0.451964624, 1.11600286648471, 2.04718732931708, 2.86252145, 5.285907977, 9.106164204, 16.67476528, 16.76626787, 17.00218707, 30.8667961, 57.92292091, 0.478352574, 4.55673229, 8.10163028, 8.22100734, 7.829591756, 33.53244905, 66.20361403, 0.436956014, 1.28468189, 1.555875222, 12.02564968, 30.24566673, 0.548011282, 2.29562227069566)
+sd_ace_conc <- c(0.262318006, 0.281361538208953, 0.289527601555302, 0.302351163, 0.327705513, 0.330782201, 0.277259011, 0.233956798, 0.31883929, 0.300578057, 0.313371784, 0.231202155, 0.264687437, 0.243480317, 0.289821733, 0.263808862, 0.289478134, 0.264861034, 0.22461248, 0.229031308, 0.241718918, 0.254111384, 0.187394292, 0.011107606, 0.290519090995892)
+plot(res_ace_range[,"ace_concentration"], res_ace_range[,"Values[v_glc_uptake]"], xaxt='n', las=1, type="l", lwd=2, xlim=c(0.1,100), col="#70AD47", ylim=c(0,10), log="x", main="Enjalbert_2017", xlab="[acetate] (mM)", ylab="glc uptake (mmol/gDW/h)")
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+plot_points(ace_conc, glc_upt, sd_glc_upt, offset=0.02, col="#70AD47")
+plot_points(ace_conc, glc_upt, sd_ace_conc, offset=0.2, mode="h", col="#70AD47")
+
+# ace flux as function of acetate concentration
+ace_flx <- c(3.5, -2.7, 1.516999356, 1.26845123082679, 0.775821380507016, 0.678877137, 0.017366464, -0.991478151, -1.286687213, -2.078474994, -1.530841439, -1.525342269, -1.253581266, 1.984679487, 0.546462624, -0.136780389, -0.393883917, -0.610240984, -1.120767885, -1.277455315, 2.574285211, 2.051935093, 1.828415596, -1.262442483, -1.317987733, 2.333568565, 1.85234639824858)
+sd_ace_flx <- c(0.35, 0.27, 0.316118066, 0.388752117258161, 0.40715278851436, 0.33357638, 0.37333751, 0.347029894, 0.280501612, 0.195031303, 0.376252463, 0.226182385, 0.303661317, 0.253610517, 0.385450715, 0.243880325, 0.30665695, 0.257983739, 0.23844407, 0.198458448, 0.299832036, 0.334956504, 0.317134334, 0.263807154, 0.195219648, 0.016120887, 0.386174129654754)
+ace_conc <- c(0.2, 100, 0.451964624, 1.11600286648471, 2.04718732931708, 2.86252145, 5.285907977, 9.106164204, 16.67476528, 16.76626787, 17.00218707, 30.8667961, 57.92292091, 0.478352574, 4.55673229, 8.10163028, 8.22100734, 7.829591756, 33.53244905, 66.20361403, 0.436956014, 1.28468189, 1.555875222, 12.02564968, 30.24566673, 0.548011282, 2.29562227069566)
+sd_ace_conc <- c(0.05, 10, 0.262318006, 0.281361538208953, 0.289527601555302, 0.302351163, 0.327705513, 0.330782201, 0.277259011, 0.233956798, 0.31883929, 0.300578057, 0.313371784, 0.231202155, 0.264687437, 0.243480317, 0.289821733, 0.263808862, 0.289478134, 0.264861034, 0.22461248, 0.229031308, 0.241718918, 0.254111384, 0.187394292, 0.011107606, 0.290519090995892)
+plot(res_ace_range[,"ace_concentration"], res_ace_range[,"Values[v_ace_net]"], xaxt='n', las=1, type="l", lwd=2, xlim=c(0.1,100), ylim=c(-4,4), log="x", main="Enjalbert_2017, Pinhal_2019", col="#D6685C", xlab="[acetate] (mM)", ylab="ace flux (mmol/gDW/h)")
+abline(h=0)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+plot_points(ace_conc, ace_flx, sd_ace_flx, offset=0.04, col="#D6685C")
+plot_points(ace_conc, ace_flx, sd_ace_conc, offset=0.2, mode="h", col="#D6685C")
+
+dev.off()
+
+###########
+# Model 2 #
+###########
+
+setwd(results_dir)
+pdf(file="Figure 3-figure supplement 2.pdf", width = 7, height = 9)
+par(mfrow=c(4,3))
+
+# Pulse experiment (Enjalbert et al., 2017)
+###########################################
+
+setwd(model_dir)
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_2.cps")
+
+# set biomass concentration at which the pulse is performed
+setGlobalQuantities(key = "_X_conc_pulse", initial_value = 0.9)
+
+# simulate response to acetate pulse
+res_pulse <- runTimeCourse()
+
+# get simulation results
+id_start <- which(res_pulse$result$Ace_out >= 30)[1]+1
+id_end <- which(res_pulse$result$Time >= (res_pulse$result$Time[id_start]+8/60))[1]+1
+
+t_pulse <- (res_pulse$result$Time[seq(id_start, id_end)] - res_pulse$result$Time[id_start])
+ace_conc_pulse <- res_pulse$result$Ace_out[seq(id_start, id_end)] - res_pulse$result$Ace_out[id_start]
+glc_conc_pulse <- res_pulse$result$Glc[seq(id_start, id_end)] - res_pulse$result$Glc[id_start]
+
+# measurements
+time_meas <- seq(0,8)/60
+glc <- c(0, -0.06931183, -0.151415145, -0.189227994, -0.269451057, -0.290764495, -0.230785281, -0.464084162, -0.551878527)
+sd_glc <- c(0, 0.032476344, 0.073133915, 0.113018846, 0.049485284, 0.005325541, 0.163377704, 0.034786419, 0.048477157)
+ace <- c(0, -0.027907926, -0.078000853, -0.155334163, -0.165031608, -0.111098424, -0.182877548, -0.237262298, -0.276903255)
+sd_ace <- c(0, 0.002740145, 0.025693594, 0.053641876, 0.089975321, 0.005875669, 0.085604161, 0.061930626, 0.099140975)
+
+# plot simulations vs measurements
+plot(t_pulse, ace_conc_pulse, type="l", ylim=c(-0.4,0), las=1, main="Enjalbert_2017 (pulse 30mM ace)", ylab="change of [Ace]", xlab="time (h)", col="#D6685C", lwd=2)
+plot_points(time_meas, ace, sd_ace, offset=0.002, col="#D6685C")
+plot(t_pulse, glc_conc_pulse, type="l", main="Enjalbert_2017 (pulse 30mM ace)", las=1, ylab="change of [Glc]", xlab="time (h)", col="#70AD47", lwd=2)
+plot_points(time_meas, glc, sd_glc, offset=0.002, col="#70AD47")
+
+# simulate control experiment (i.e. no acetate pulse)
+deleteEvent(getEvents()$key)
+
+res_nopulse <- runTimeCourse()
+
+# get simulation results
+ace_conc_nopulse <- res_nopulse$result$Ace_out[seq(id_start, id_end)] - res_nopulse$result$Ace_out[id_start]
+glc_conc_nopulse <- res_nopulse$result$Glc[seq(id_start, id_end)] - res_nopulse$result$Glc[id_start]
+
+# measurements
+glc_nopulse <- c(0, -0.195637774, -0.325512845, -0.433785334, -0.628518958, -0.726913548, -0.892908748, -1.071230579, -1.16285575)
+sd_glc_nopulse <- c(0, 0.058023617, 0.109115511, 0.047090371, 0.052331837, 0.065619906, 0.133896355, 0.16828754, 0.03515465)
+ace_nopulse <- c(0, 0.01012067, 0.05974009, 0.086787283, 0.086690257, 0.104329693, 0.128507087, 0.130026354, 0.187336965)
+sd_ace_nopulse <- c(0, 0.005117257, 0.022507218, 0.040319045, 0.037548873, 0.037235285, 0.044494365, 0.045029023, 0.023982374)
+
+# plot simulations vs measurements
+plot(t_pulse, ace_conc_nopulse, type="l", ylim=c(0,0.3), main="Enjalbert_2017 (control)", las=1, ylab="change of [Ace]", xlab="time (h)", col="#D6685C", lwd=2)
+plot_points(time_meas, ace_nopulse, sd_ace_nopulse, offset=0.002, col="#D6685C")
+plot(t_pulse, glc_conc_nopulse, type="l", ylim=c(-1.4,0), main="Enjalbert_2017 (control)", las=1, ylab="change of [Glc]", xlab="time (h)", col="#70AD47", lwd=2)
+plot_points(time_meas, glc_nopulse, sd_glc_nopulse, offset=0.002, col="#70AD47")
+
+# Chemostat experiment (Renilla et al., 2012)
+#############################################
+
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_2.cps")
+
+# delete events and set glc feed to 1
+deleteEvent(getEvents()$key)
+setGlobalQuantities(key = "_feed", initial_value = 1)
+
+n_step <- 50
+dilution_rates <- seq(0.1, 0.5, length.out = n_step)
+fluxes <- c("Values[v_growth_rate]", "Values[v_glc_uptake]", "Values[v_ace_net]")
+res_chemostat <- matrix(NA, nrow=n_step, ncol=length(fluxes)+1, dimnames=list(r=NULL, c=c("dilution_rate", fluxes)))
+for (i in seq(n_step)){
+  setGlobalQuantities(key = "_dilution_rate", initial_value = dilution_rates[i])
+  res_ss <- runSteadyState()
+  res_chemostat[i,] <- c(dilution_rates[i], unlist(res_ss$global_quantities[res_ss$global_quantities$key %in% fluxes, "value"]))
+}
+
+# acetate flux as function of dilution rate
+dilution_rate <- c(0.09586056644880175, 0.20043572984749464, 0.2997821350762528, 0.3468409586056645, 0.39912854030501094, 0.44618736383442276, 0.5002178649237474)
+q_ace <- c(0.40472342596168076, 0.7396156614846294, 1.477019302736899, 1.2154669794005626, 1.96934635755591, 2.0929143843289824, 2.006569318707304)
+q_ace_sd <- c(0.120440687823878, 0.15316333195082, 0.04595662724122, 0.0274214232252601, 0.28885933172199, 0.0777639526513201, 0.28664731148963)
+
+plot(res_chemostat[,"dilution_rate"], res_chemostat[,"Values[v_ace_net]"], type="l", las=1, xlim=c(0,0.6), ylim=c(0,4), main="Renilla_2012", lwd=2, xlab="dilution rate (h-1)", ylab="ace flux (mmol/gDW/h)", col="#D6685C")
+plot_points(dilution_rate, q_ace, q_ace_sd, offset=0.01, col="#D6685C")
+
+# acetate flux as function of glc uptake
+q_glc <- c(1.43478260869565, 2.7391304347826, 4.59130434782608, 4.69565217391304, 5.7391304347826, 5.92173913043478, 6.10434782608695, 7.12173913043477, 8.34782608695652)
+q_ace <- c(0.381358340437624, 0.762906128635029, 1.40509614473808, 1.17836506583309, 1.99602159704461, 2.08290233967983, 2.01292033721701, 2.44717249218528, 2.5848252344416)
+q_ace_sd <- c(0.139547219854126, 0.139471440750213, 0.15697641375391, 0.1045751633987, 0.19179691200152, 0.0174291938997801, 0.24397082504499, 0.52295159609737, 0.33130624230368)
+q_glc_sd <- c(0.20234760540444, 0.58899555210581, 0.36827270271402, 0.14607356337583, 0.630432119199, 0.13069807968161, 0.47630364392495, 0.99361847036576, 0.66185122193432)
+
+plot(res_chemostat[,"Values[v_glc_uptake]"], res_chemostat[,"Values[v_ace_net]"], type="l", las=1, xlim=c(0,10), ylim=c(0,4), main="Renilla_2012", lwd=2, xlab="glc uptake (mmol/gDW/h)", ylab="ace flux (mmol/gDW/h)", col="#D6685C")
+plot_points(q_glc, q_ace, q_ace_sd, offset=0.2, col="#D6685C")
+plot_points(q_glc, q_ace, q_glc_sd, offset=0.08, mode="h", col="#D6685C")
+
+# Steady-state fluxes for acetate concentration between 0.1 and 100mM (Enjalbert et al., 2017; Pinhal et al., 2019)
+##############################################################################################
+
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_2.cps")
+
+# remove events and fix concentrations of actate, glucose and biomass
+deleteEvent(getEvents()$key)
+setSpecies(key="Ace_out", type="fixed")
+setSpecies(key="Glc", type="fixed")
+setSpecies(key="X", type="fixed")
+
+# run simulations
+n_step <- 50
+ace_concentration <- 10**seq(-1, 2, length.out = n_step)
+fluxes <- c("Values[v_growth_rate]", "Values[v_glc_uptake]", "Values[v_ace_net]")
+res_ace_range <- matrix(NA, nrow=n_step, ncol=length(fluxes)+1, dimnames=list(r=NULL, c=c("ace_concentration", fluxes)))
+for (i in seq(n_step)){
+  setSpecies(key="Ace_out", initial_concentration=ace_concentration[i])
+  applyInitialState()
+  res_ss <- runSteadyState()
+  res_ace_range[i,] <- c(ace_concentration[i], unlist(res_ss$global_quantities[res_ss$global_quantities$key %in% fluxes, "value"]))
+}
+
+xlab_main <- c(0.1, 1, 10, 100)
+xlab_sec <- c(seq(0.2, 0.9, by=0.1), seq(2, 9, by=1), seq(20, 90, by=10))
+
+# growth rate as function of acetate concentration
+growth_rates <- c(0.521128511, 0.611148842625582, 0.613161998174498, 0.502533817, 0.496290415, 0.488201506, 0.547635665, 0.499830448, 0.474554197, 0.425356578, 0.377534684, 0.645724326, 0.618475601, 0.554887936, 0.564811523, 0.527571192, 0.434972836, 0.3824734, 0.583623355, 0.620905534, 0.564259247, 0.532148135, 0.483885215, 0.557074418, 0.630654409249223)
+sd_growth_rates <- c(0.001793104, 0.00204807928657914, 0.00219396182484705, 0.001709207, 0.001846205, 0.001757403, 0.001821375, 0.001025702, 0.001940912, 0.001204707, 0.001999188, 0.001418374, 0.001932601, 0.001455791, 0.001574234, 0.001206265, 0.001292476, 0.001068259, 0.001804648, 0.001643459, 0.001598405, 0.001121218, 0.000912408, 0.00194896, 0.00203369597574686)
+ace_conc <- c(0.451964624, 1.11600286648471, 2.04718732931708, 2.86252145, 5.285907977, 9.106164204, 16.67476528, 16.76626787, 17.00218707, 30.8667961, 57.92292091, 0.478352574, 4.55673229, 8.10163028, 8.22100734, 7.829591756, 33.53244905, 66.20361403, 0.436956014, 1.28468189, 1.555875222, 12.02564968, 30.24566673, 0.548011282, 2.29562227069566)
+sd_ace_conc <- c(0.262318006, 0.281361538208953, 0.289527601555302, 0.302351163, 0.327705513, 0.330782201, 0.277259011, 0.233956798, 0.31883929, 0.300578057, 0.313371784, 0.231202155, 0.264687437, 0.243480317, 0.289821733, 0.263808862, 0.289478134, 0.264861034, 0.22461248, 0.229031308, 0.241718918, 0.254111384, 0.187394292, 0.011107606, 0.290519090995892)
+plot(res_ace_range[,"ace_concentration"], xaxt='n', res_ace_range[,"Values[v_growth_rate]"], las=1, col="#2E75B6", lwd=2, type="l", xlim=c(0.1,100), ylim=c(0,0.8), log="x", main="Enjalbert_2017", xlab="[acetate] (mM)", ylab="growth rate (h-1)")
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+plot_points(ace_conc, growth_rates, sd_growth_rates, offset=0.01, col="#2E75B6")
+plot_points(ace_conc, growth_rates, sd_ace_conc, offset=0.02, mode="h", col="#2E75B6")
+
+# glc uptake as function of acetate concentration
+glc_upt <- c(8.654860167, 8.36127542981722, 7.98010111285252, 9.236935826, 8.274418986, 7.560431219, 7.339194455, 5.775312502, 6.423391263, 5.1544758, 3.938631573, 8.115447647, 9.28067031, 6.737153424, 7.172748804, 5.884186033, 5.684201497, 4.811576974, 9.632702365, 8.055042777, 9.708342814, 7.100081588, 5.505759496, 9.242859752, 8.18621623190759)
+sd_glc_upt <- c(0.337812425, 0.38531328268303, 0.373770045721031, 0.356787032, 0.334672954, 0.317509322, 0.288025925, 0.16053276, 0.375934255, 0.293148172, 0.359225607, 0.197331684, 0.360984112, 0.229372278, 0.241820396, 0.20450532, 0.260869273, 0.216134352, 0.34289286, 0.350305744, 0.293144783, 0.220135755, 0.153471508, 0.25245346, 0.396815184905029)
+ace_conc <- c(0.451964624, 1.11600286648471, 2.04718732931708, 2.86252145, 5.285907977, 9.106164204, 16.67476528, 16.76626787, 17.00218707, 30.8667961, 57.92292091, 0.478352574, 4.55673229, 8.10163028, 8.22100734, 7.829591756, 33.53244905, 66.20361403, 0.436956014, 1.28468189, 1.555875222, 12.02564968, 30.24566673, 0.548011282, 2.29562227069566)
+sd_ace_conc <- c(0.262318006, 0.281361538208953, 0.289527601555302, 0.302351163, 0.327705513, 0.330782201, 0.277259011, 0.233956798, 0.31883929, 0.300578057, 0.313371784, 0.231202155, 0.264687437, 0.243480317, 0.289821733, 0.263808862, 0.289478134, 0.264861034, 0.22461248, 0.229031308, 0.241718918, 0.254111384, 0.187394292, 0.011107606, 0.290519090995892)
+plot(res_ace_range[,"ace_concentration"], res_ace_range[,"Values[v_glc_uptake]"], xaxt='n', las=1, type="l", lwd=2, xlim=c(0.1,100), col="#70AD47", ylim=c(0,10), log="x", main="Enjalbert_2017", xlab="[acetate] (mM)", ylab="glc uptake (mmol/gDW/h)")
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+plot_points(ace_conc, glc_upt, sd_glc_upt, offset=0.02, col="#70AD47")
+plot_points(ace_conc, glc_upt, sd_ace_conc, offset=0.2, mode="h", col="#70AD47")
+
+# ace flux as function of acetate concentration
+ace_flx <- c(3.5, -2.7, 1.516999356, 1.26845123082679, 0.775821380507016, 0.678877137, 0.017366464, -0.991478151, -1.286687213, -2.078474994, -1.530841439, -1.525342269, -1.253581266, 1.984679487, 0.546462624, -0.136780389, -0.393883917, -0.610240984, -1.120767885, -1.277455315, 2.574285211, 2.051935093, 1.828415596, -1.262442483, -1.317987733, 2.333568565, 1.85234639824858)
+sd_ace_flx <- c(0.35, 0.27, 0.316118066, 0.388752117258161, 0.40715278851436, 0.33357638, 0.37333751, 0.347029894, 0.280501612, 0.195031303, 0.376252463, 0.226182385, 0.303661317, 0.253610517, 0.385450715, 0.243880325, 0.30665695, 0.257983739, 0.23844407, 0.198458448, 0.299832036, 0.334956504, 0.317134334, 0.263807154, 0.195219648, 0.016120887, 0.386174129654754)
+ace_conc <- c(0.2, 100, 0.451964624, 1.11600286648471, 2.04718732931708, 2.86252145, 5.285907977, 9.106164204, 16.67476528, 16.76626787, 17.00218707, 30.8667961, 57.92292091, 0.478352574, 4.55673229, 8.10163028, 8.22100734, 7.829591756, 33.53244905, 66.20361403, 0.436956014, 1.28468189, 1.555875222, 12.02564968, 30.24566673, 0.548011282, 2.29562227069566)
+sd_ace_conc <- c(0.05, 10, 0.262318006, 0.281361538208953, 0.289527601555302, 0.302351163, 0.327705513, 0.330782201, 0.277259011, 0.233956798, 0.31883929, 0.300578057, 0.313371784, 0.231202155, 0.264687437, 0.243480317, 0.289821733, 0.263808862, 0.289478134, 0.264861034, 0.22461248, 0.229031308, 0.241718918, 0.254111384, 0.187394292, 0.011107606, 0.290519090995892)
+plot(res_ace_range[,"ace_concentration"], res_ace_range[,"Values[v_ace_net]"], xaxt='n', las=1, type="l", lwd=2, xlim=c(0.1,100), ylim=c(-4,4), log="x", main="Enjalbert_2017, Pinhal_2019", col="#D6685C", xlab="[acetate] (mM)", ylab="ace flux (mmol/gDW/h)")
+abline(h=0)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+plot_points(ace_conc, ace_flx, sd_ace_flx, offset=0.04, col="#D6685C")
+plot_points(ace_conc, ace_flx, sd_ace_conc, offset=0.2, mode="h", col="#D6685C")
+
+dev.off()
+
+###########
+# Model 3 #
+###########
+
+setwd(results_dir)
+pdf(file="Figure 3-figure supplement 3.pdf", width = 7, height = 9)
+par(mfrow=c(4,3))
+
+# Pulse experiment (Enjalbert et al., 2017)
+###########################################
+
+setwd(model_dir)
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_3.cps")
+
+# set biomass concentration at which the pulse is performed
+setGlobalQuantities(key = "_X_conc_pulse", initial_value = 0.9)
+
+# simulate response to acetate pulse
+res_pulse <- runTimeCourse()
+
+# get simulation results
+id_start <- which(res_pulse$result$Ace_out >= 30)[1]+1
+id_end <- which(res_pulse$result$Time >= (res_pulse$result$Time[id_start]+8/60))[1]+1
+
+t_pulse <- (res_pulse$result$Time[seq(id_start, id_end)] - res_pulse$result$Time[id_start])
+ace_conc_pulse <- res_pulse$result$Ace_out[seq(id_start, id_end)] - res_pulse$result$Ace_out[id_start]
+glc_conc_pulse <- res_pulse$result$Glc[seq(id_start, id_end)] - res_pulse$result$Glc[id_start]
+
+# measurements
+time_meas <- seq(0,8)/60
+glc <- c(0, -0.06931183, -0.151415145, -0.189227994, -0.269451057, -0.290764495, -0.230785281, -0.464084162, -0.551878527)
+sd_glc <- c(0, 0.032476344, 0.073133915, 0.113018846, 0.049485284, 0.005325541, 0.163377704, 0.034786419, 0.048477157)
+ace <- c(0, -0.027907926, -0.078000853, -0.155334163, -0.165031608, -0.111098424, -0.182877548, -0.237262298, -0.276903255)
+sd_ace <- c(0, 0.002740145, 0.025693594, 0.053641876, 0.089975321, 0.005875669, 0.085604161, 0.061930626, 0.099140975)
+
+# plot simulations vs measurements
+plot(t_pulse, ace_conc_pulse, type="l", ylim=c(-0.4,0), las=1, main="Enjalbert_2017 (pulse 30mM ace)", ylab="change of [Ace]", xlab="time (h)", col="#D6685C", lwd=2)
+plot_points(time_meas, ace, sd_ace, offset=0.002, col="#D6685C")
+plot(t_pulse, glc_conc_pulse, type="l", main="Enjalbert_2017 (pulse 30mM ace)", las=1, ylab="change of [Glc]", xlab="time (h)", col="#70AD47", lwd=2)
+plot_points(time_meas, glc, sd_glc, offset=0.002, col="#70AD47")
+
+# simulate control experiment (i.e. no acetate pulse)
+deleteEvent(getEvents()$key)
+
+res_nopulse <- runTimeCourse()
+
+# get simulation results
+ace_conc_nopulse <- res_nopulse$result$Ace_out[seq(id_start, id_end)] - res_nopulse$result$Ace_out[id_start]
+glc_conc_nopulse <- res_nopulse$result$Glc[seq(id_start, id_end)] - res_nopulse$result$Glc[id_start]
+
+# measurements
+glc_nopulse <- c(0, -0.195637774, -0.325512845, -0.433785334, -0.628518958, -0.726913548, -0.892908748, -1.071230579, -1.16285575)
+sd_glc_nopulse <- c(0, 0.058023617, 0.109115511, 0.047090371, 0.052331837, 0.065619906, 0.133896355, 0.16828754, 0.03515465)
+ace_nopulse <- c(0, 0.01012067, 0.05974009, 0.086787283, 0.086690257, 0.104329693, 0.128507087, 0.130026354, 0.187336965)
+sd_ace_nopulse <- c(0, 0.005117257, 0.022507218, 0.040319045, 0.037548873, 0.037235285, 0.044494365, 0.045029023, 0.023982374)
+
+# plot simulations vs measurements
+plot(t_pulse, ace_conc_nopulse, type="l", ylim=c(0,0.3), main="Enjalbert_2017 (control)", las=1, ylab="change of [Ace]", xlab="time (h)", col="#D6685C", lwd=2)
+plot_points(time_meas, ace_nopulse, sd_ace_nopulse, offset=0.002, col="#D6685C")
+plot(t_pulse, glc_conc_nopulse, type="l", ylim=c(-1.4,0), main="Enjalbert_2017 (control)", las=1, ylab="change of [Glc]", xlab="time (h)", col="#70AD47", lwd=2)
+plot_points(time_meas, glc_nopulse, sd_glc_nopulse, offset=0.002, col="#70AD47")
+
+# Chemostat experiment (Renilla et al., 2012)
+#############################################
+
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_3.cps")
+
+# delete events and set glc feed to 1
+deleteEvent(getEvents()$key)
+setGlobalQuantities(key = "_feed", initial_value = 1)
+
+n_step <- 50
+dilution_rates <- seq(0.1, 0.5, length.out = n_step)
+fluxes <- c("Values[v_growth_rate]", "Values[v_glc_uptake]", "Values[v_ace_net]")
+res_chemostat <- matrix(NA, nrow=n_step, ncol=length(fluxes)+1, dimnames=list(r=NULL, c=c("dilution_rate", fluxes)))
+for (i in seq(n_step)){
+  setGlobalQuantities(key = "_dilution_rate", initial_value = dilution_rates[i])
+  res_ss <- runSteadyState()
+  res_chemostat[i,] <- c(dilution_rates[i], unlist(res_ss$global_quantities[res_ss$global_quantities$key %in% fluxes, "value"]))
+}
+
+# acetate flux as function of dilution rate
+dilution_rate <- c(0.09586056644880175, 0.20043572984749464, 0.2997821350762528, 0.3468409586056645, 0.39912854030501094, 0.44618736383442276, 0.5002178649237474)
+q_ace <- c(0.40472342596168076, 0.7396156614846294, 1.477019302736899, 1.2154669794005626, 1.96934635755591, 2.0929143843289824, 2.006569318707304)
+q_ace_sd <- c(0.120440687823878, 0.15316333195082, 0.04595662724122, 0.0274214232252601, 0.28885933172199, 0.0777639526513201, 0.28664731148963)
+
+plot(res_chemostat[,"dilution_rate"], res_chemostat[,"Values[v_ace_net]"], type="l", las=1, xlim=c(0,0.6), ylim=c(0,4), main="Renilla_2012", lwd=2, xlab="dilution rate (h-1)", ylab="ace flux (mmol/gDW/h)", col="#D6685C")
+plot_points(dilution_rate, q_ace, q_ace_sd, offset=0.01, col="#D6685C")
+
+# acetate flux as function of glc uptake
+q_glc <- c(1.43478260869565, 2.7391304347826, 4.59130434782608, 4.69565217391304, 5.7391304347826, 5.92173913043478, 6.10434782608695, 7.12173913043477, 8.34782608695652)
+q_ace <- c(0.381358340437624, 0.762906128635029, 1.40509614473808, 1.17836506583309, 1.99602159704461, 2.08290233967983, 2.01292033721701, 2.44717249218528, 2.5848252344416)
+q_ace_sd <- c(0.139547219854126, 0.139471440750213, 0.15697641375391, 0.1045751633987, 0.19179691200152, 0.0174291938997801, 0.24397082504499, 0.52295159609737, 0.33130624230368)
+q_glc_sd <- c(0.20234760540444, 0.58899555210581, 0.36827270271402, 0.14607356337583, 0.630432119199, 0.13069807968161, 0.47630364392495, 0.99361847036576, 0.66185122193432)
+
+plot(res_chemostat[,"Values[v_glc_uptake]"], res_chemostat[,"Values[v_ace_net]"], type="l", las=1, xlim=c(0,10), ylim=c(0,4), main="Renilla_2012", lwd=2, xlab="glc uptake (mmol/gDW/h)", ylab="ace flux (mmol/gDW/h)", col="#D6685C")
+plot_points(q_glc, q_ace, q_ace_sd, offset=0.2, col="#D6685C")
+plot_points(q_glc, q_ace, q_glc_sd, offset=0.08, mode="h", col="#D6685C")
+
+# Steady-state fluxes for acetate concentration between 0.1 and 100mM (Enjalbert et al., 2017; Pinhal et al., 2019)
+##############################################################################################
+
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_3.cps")
+
+# remove events and fix concentrations of actate, glucose and biomass
+deleteEvent(getEvents()$key)
+setSpecies(key="Ace_out", type="fixed")
+setSpecies(key="Glc", type="fixed")
+setSpecies(key="X", type="fixed")
+
+# run simulations
+n_step <- 50
+ace_concentration <- 10**seq(-1, 2, length.out = n_step)
+fluxes <- c("Values[v_growth_rate]", "Values[v_glc_uptake]", "Values[v_ace_net]")
+res_ace_range <- matrix(NA, nrow=n_step, ncol=length(fluxes)+1, dimnames=list(r=NULL, c=c("ace_concentration", fluxes)))
+for (i in seq(n_step)){
+  setSpecies(key="Ace_out", initial_concentration=ace_concentration[i])
+  applyInitialState()
+  res_ss <- runSteadyState()
+  res_ace_range[i,] <- c(ace_concentration[i], unlist(res_ss$global_quantities[res_ss$global_quantities$key %in% fluxes, "value"]))
+}
+
+xlab_main <- c(0.1, 1, 10, 100)
+xlab_sec <- c(seq(0.2, 0.9, by=0.1), seq(2, 9, by=1), seq(20, 90, by=10))
+
+# growth rate as function of acetate concentration
+growth_rates <- c(0.521128511, 0.611148842625582, 0.613161998174498, 0.502533817, 0.496290415, 0.488201506, 0.547635665, 0.499830448, 0.474554197, 0.425356578, 0.377534684, 0.645724326, 0.618475601, 0.554887936, 0.564811523, 0.527571192, 0.434972836, 0.3824734, 0.583623355, 0.620905534, 0.564259247, 0.532148135, 0.483885215, 0.557074418, 0.630654409249223)
+sd_growth_rates <- c(0.001793104, 0.00204807928657914, 0.00219396182484705, 0.001709207, 0.001846205, 0.001757403, 0.001821375, 0.001025702, 0.001940912, 0.001204707, 0.001999188, 0.001418374, 0.001932601, 0.001455791, 0.001574234, 0.001206265, 0.001292476, 0.001068259, 0.001804648, 0.001643459, 0.001598405, 0.001121218, 0.000912408, 0.00194896, 0.00203369597574686)
+ace_conc <- c(0.451964624, 1.11600286648471, 2.04718732931708, 2.86252145, 5.285907977, 9.106164204, 16.67476528, 16.76626787, 17.00218707, 30.8667961, 57.92292091, 0.478352574, 4.55673229, 8.10163028, 8.22100734, 7.829591756, 33.53244905, 66.20361403, 0.436956014, 1.28468189, 1.555875222, 12.02564968, 30.24566673, 0.548011282, 2.29562227069566)
+sd_ace_conc <- c(0.262318006, 0.281361538208953, 0.289527601555302, 0.302351163, 0.327705513, 0.330782201, 0.277259011, 0.233956798, 0.31883929, 0.300578057, 0.313371784, 0.231202155, 0.264687437, 0.243480317, 0.289821733, 0.263808862, 0.289478134, 0.264861034, 0.22461248, 0.229031308, 0.241718918, 0.254111384, 0.187394292, 0.011107606, 0.290519090995892)
+plot(res_ace_range[,"ace_concentration"], xaxt='n', res_ace_range[,"Values[v_growth_rate]"], las=1, col="#2E75B6", lwd=2, type="l", xlim=c(0.1,100), ylim=c(0,0.8), log="x", main="Enjalbert_2017", xlab="[acetate] (mM)", ylab="growth rate (h-1)")
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+plot_points(ace_conc, growth_rates, sd_growth_rates, offset=0.01, col="#2E75B6")
+plot_points(ace_conc, growth_rates, sd_ace_conc, offset=0.02, mode="h", col="#2E75B6")
+
+# glc uptake as function of acetate concentration
+glc_upt <- c(8.654860167, 8.36127542981722, 7.98010111285252, 9.236935826, 8.274418986, 7.560431219, 7.339194455, 5.775312502, 6.423391263, 5.1544758, 3.938631573, 8.115447647, 9.28067031, 6.737153424, 7.172748804, 5.884186033, 5.684201497, 4.811576974, 9.632702365, 8.055042777, 9.708342814, 7.100081588, 5.505759496, 9.242859752, 8.18621623190759)
+sd_glc_upt <- c(0.337812425, 0.38531328268303, 0.373770045721031, 0.356787032, 0.334672954, 0.317509322, 0.288025925, 0.16053276, 0.375934255, 0.293148172, 0.359225607, 0.197331684, 0.360984112, 0.229372278, 0.241820396, 0.20450532, 0.260869273, 0.216134352, 0.34289286, 0.350305744, 0.293144783, 0.220135755, 0.153471508, 0.25245346, 0.396815184905029)
+ace_conc <- c(0.451964624, 1.11600286648471, 2.04718732931708, 2.86252145, 5.285907977, 9.106164204, 16.67476528, 16.76626787, 17.00218707, 30.8667961, 57.92292091, 0.478352574, 4.55673229, 8.10163028, 8.22100734, 7.829591756, 33.53244905, 66.20361403, 0.436956014, 1.28468189, 1.555875222, 12.02564968, 30.24566673, 0.548011282, 2.29562227069566)
+sd_ace_conc <- c(0.262318006, 0.281361538208953, 0.289527601555302, 0.302351163, 0.327705513, 0.330782201, 0.277259011, 0.233956798, 0.31883929, 0.300578057, 0.313371784, 0.231202155, 0.264687437, 0.243480317, 0.289821733, 0.263808862, 0.289478134, 0.264861034, 0.22461248, 0.229031308, 0.241718918, 0.254111384, 0.187394292, 0.011107606, 0.290519090995892)
+plot(res_ace_range[,"ace_concentration"], res_ace_range[,"Values[v_glc_uptake]"], xaxt='n', las=1, type="l", lwd=2, xlim=c(0.1,100), col="#70AD47", ylim=c(0,10), log="x", main="Enjalbert_2017", xlab="[acetate] (mM)", ylab="glc uptake (mmol/gDW/h)")
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+plot_points(ace_conc, glc_upt, sd_glc_upt, offset=0.02, col="#70AD47")
+plot_points(ace_conc, glc_upt, sd_ace_conc, offset=0.2, mode="h", col="#70AD47")
+
+# ace flux as function of acetate concentration
+ace_flx <- c(3.5, -2.7, 1.516999356, 1.26845123082679, 0.775821380507016, 0.678877137, 0.017366464, -0.991478151, -1.286687213, -2.078474994, -1.530841439, -1.525342269, -1.253581266, 1.984679487, 0.546462624, -0.136780389, -0.393883917, -0.610240984, -1.120767885, -1.277455315, 2.574285211, 2.051935093, 1.828415596, -1.262442483, -1.317987733, 2.333568565, 1.85234639824858)
+sd_ace_flx <- c(0.35, 0.27, 0.316118066, 0.388752117258161, 0.40715278851436, 0.33357638, 0.37333751, 0.347029894, 0.280501612, 0.195031303, 0.376252463, 0.226182385, 0.303661317, 0.253610517, 0.385450715, 0.243880325, 0.30665695, 0.257983739, 0.23844407, 0.198458448, 0.299832036, 0.334956504, 0.317134334, 0.263807154, 0.195219648, 0.016120887, 0.386174129654754)
+ace_conc <- c(0.2, 100, 0.451964624, 1.11600286648471, 2.04718732931708, 2.86252145, 5.285907977, 9.106164204, 16.67476528, 16.76626787, 17.00218707, 30.8667961, 57.92292091, 0.478352574, 4.55673229, 8.10163028, 8.22100734, 7.829591756, 33.53244905, 66.20361403, 0.436956014, 1.28468189, 1.555875222, 12.02564968, 30.24566673, 0.548011282, 2.29562227069566)
+sd_ace_conc <- c(0.05, 10, 0.262318006, 0.281361538208953, 0.289527601555302, 0.302351163, 0.327705513, 0.330782201, 0.277259011, 0.233956798, 0.31883929, 0.300578057, 0.313371784, 0.231202155, 0.264687437, 0.243480317, 0.289821733, 0.263808862, 0.289478134, 0.264861034, 0.22461248, 0.229031308, 0.241718918, 0.254111384, 0.187394292, 0.011107606, 0.290519090995892)
+plot(res_ace_range[,"ace_concentration"], res_ace_range[,"Values[v_ace_net]"], xaxt='n', las=1, type="l", lwd=2, xlim=c(0.1,100), ylim=c(-4,4), log="x", main="Enjalbert_2017, Pinhal_2019", col="#D6685C", xlab="[acetate] (mM)", ylab="ace flux (mmol/gDW/h)")
+abline(h=0)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+plot_points(ace_conc, ace_flx, sd_ace_flx, offset=0.04, col="#D6685C")
+plot_points(ace_conc, ace_flx, sd_ace_conc, offset=0.2, mode="h", col="#D6685C")
+
+dev.off()
+
+
+##################################################
+# Calculate variance weighted SSR for all models #
+##################################################
+
+# Pulse experiment (Enjalbert et al., 2017)
+###########################################
+
+# measurements
+# sampling time
+time_meas <- seq(0,8)/60
+# acetate pulse experiment
+glc <- c(0, -0.06931183, -0.151415145, -0.189227994, -0.269451057, -0.290764495, -0.230785281, -0.464084162, -0.551878527)
+sd_glc <- c(0.1, 0.032476344, 0.073133915, 0.113018846, 0.049485284, 0.005325541, 0.163377704, 0.034786419, 0.048477157)
+ace <- c(0, -0.027907926, -0.078000853, -0.155334163, -0.165031608, -0.111098424, -0.182877548, -0.237262298, -0.276903255)
+sd_ace <- c(0.01, 0.002740145, 0.025693594, 0.053641876, 0.089975321, 0.005875669, 0.085604161, 0.061930626, 0.099140975)
+# control experiment (pulse without acetate)
+glc_nopulse <- c(0, -0.195637774, -0.325512845, -0.433785334, -0.628518958, -0.726913548, -0.892908748, -1.071230579, -1.16285575)
+sd_glc_nopulse <- c(0.01, 0.058023617, 0.109115511, 0.047090371, 0.052331837, 0.065619906, 0.133896355, 0.16828754, 0.03515465)
+ace_nopulse <- c(0, 0.01012067, 0.05974009, 0.086787283, 0.086690257, 0.104329693, 0.128507087, 0.130026354, 0.187336965)
+sd_ace_nopulse <- c(0.01, 0.005117257, 0.022507218, 0.040319045, 0.037548873, 0.037235285, 0.044494365, 0.045029023, 0.023982374)
+
+setwd(model_dir)
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_4.cps")
+# set biomass concentration at which the pulse is performed
+setGlobalQuantities(key = "_X_conc_pulse", initial_value = 0.9)
+# simulate response to acetate pulse
+res_pulse <- runTimeCourse(intervals=10000)
+# get simulation results
+id_start <- which(res_pulse$result$Ace_out >= 30)[1]+1
+id_end <- which(res_pulse$result$Time >= (res_pulse$result$Time[id_start]+8/60))[1]+1
+t_pulse <- (res_pulse$result$Time[seq(id_start, id_end)] - res_pulse$result$Time[id_start])
+ace_conc_pulse <- res_pulse$result$Ace_out[seq(id_start, id_end)] - res_pulse$result$Ace_out[id_start]
+glc_conc_pulse <- res_pulse$result$Glc[seq(id_start, id_end)] - res_pulse$result$Glc[id_start]
+# set biomass concentration at which the pulse is performed
+setGlobalQuantities(key = "_X_conc_pulse", initial_value = 1000)
+res_nopulse <- runTimeCourse(intervals=10000)
+# get simulation results
+ace_conc_nopulse <- res_nopulse$result$Ace_out[seq(id_start, id_end)] - res_nopulse$result$Ace_out[id_start]
+glc_conc_nopulse <- res_nopulse$result$Glc[seq(id_start, id_end)] - res_nopulse$result$Glc[id_start]
+# get simulation times
+time_sim <- res_nopulse$result$Time[seq(id_start, id_end)] - res_nopulse$result$Time[id_start]
+idx_sim <- get_index_closest(time_meas, time_sim)
+# calculate variance weighted SSR
+SSR_model_4 <- sum((glc-glc_conc_pulse[idx_sim])**2/sd_glc**2, (ace-ace_conc_pulse[idx_sim])**2/sd_ace**2, (glc_nopulse-glc_conc_nopulse[idx_sim])**2/sd_glc_nopulse**2, (ace_nopulse-ace_conc_nopulse[idx_sim])**2/sd_ace_nopulse**2 )
+
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_1.cps")
+# set biomass concentration at which the pulse is performed
+setGlobalQuantities(key = "_X_conc_pulse", initial_value = 0.9)
+# simulate response to acetate pulse
+res_pulse <- runTimeCourse(intervals=10000)
+# get simulation results
+id_start <- which(res_pulse$result$Ace_out >= 30)[1]+1
+id_end <- which(res_pulse$result$Time >= (res_pulse$result$Time[id_start]+8/60))[1]+1
+t_pulse <- (res_pulse$result$Time[seq(id_start, id_end)] - res_pulse$result$Time[id_start])
+ace_conc_pulse <- res_pulse$result$Ace_out[seq(id_start, id_end)] - res_pulse$result$Ace_out[id_start]
+glc_conc_pulse <- res_pulse$result$Glc[seq(id_start, id_end)] - res_pulse$result$Glc[id_start]
+# set biomass concentration at which the pulse is performed
+setGlobalQuantities(key = "_X_conc_pulse", initial_value = 1000)
+res_nopulse <- runTimeCourse(intervals=10000)
+# get simulation results
+ace_conc_nopulse <- res_nopulse$result$Ace_out[seq(id_start, id_end)] - res_nopulse$result$Ace_out[id_start]
+glc_conc_nopulse <- res_nopulse$result$Glc[seq(id_start, id_end)] - res_nopulse$result$Glc[id_start]
+# get simulation times
+time_sim <- res_nopulse$result$Time[seq(id_start, id_end)] - res_nopulse$result$Time[id_start]
+idx_sim <- get_index_closest(time_meas, time_sim)
+# calculate variance weighted SSR
+SSR_model_1 <- sum((glc-glc_conc_pulse[idx_sim])**2/sd_glc**2, (ace-ace_conc_pulse[idx_sim])**2/sd_ace**2, (glc_nopulse-glc_conc_nopulse[idx_sim])**2/sd_glc_nopulse**2, (ace_nopulse-ace_conc_nopulse[idx_sim])**2/sd_ace_nopulse**2 )
+
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_2.cps")
+# set biomass concentration at which the pulse is performed
+setGlobalQuantities(key = "_X_conc_pulse", initial_value = 0.9)
+# simulate response to acetate pulse
+res_pulse <- runTimeCourse(intervals=10000)
+# get simulation results
+id_start <- which(res_pulse$result$Ace_out >= 30)[1]+1
+id_end <- which(res_pulse$result$Time >= (res_pulse$result$Time[id_start]+8/60))[1]+1
+t_pulse <- (res_pulse$result$Time[seq(id_start, id_end)] - res_pulse$result$Time[id_start])
+ace_conc_pulse <- res_pulse$result$Ace_out[seq(id_start, id_end)] - res_pulse$result$Ace_out[id_start]
+glc_conc_pulse <- res_pulse$result$Glc[seq(id_start, id_end)] - res_pulse$result$Glc[id_start]
+# set biomass concentration at which the pulse is performed
+setGlobalQuantities(key = "_X_conc_pulse", initial_value = 1000)
+res_nopulse <- runTimeCourse(intervals=10000)
+# get simulation results
+ace_conc_nopulse <- res_nopulse$result$Ace_out[seq(id_start, id_end)] - res_nopulse$result$Ace_out[id_start]
+glc_conc_nopulse <- res_nopulse$result$Glc[seq(id_start, id_end)] - res_nopulse$result$Glc[id_start]
+# get simulation times
+time_sim <- res_nopulse$result$Time[seq(id_start, id_end)] - res_nopulse$result$Time[id_start]
+idx_sim <- get_index_closest(time_meas, time_sim)
+# calculate variance weighted SSR
+SSR_model_2 <- sum((glc-glc_conc_pulse[idx_sim])**2/sd_glc**2, (ace-ace_conc_pulse[idx_sim])**2/sd_ace**2, (glc_nopulse-glc_conc_nopulse[idx_sim])**2/sd_glc_nopulse**2, (ace_nopulse-ace_conc_nopulse[idx_sim])**2/sd_ace_nopulse**2 )
+
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_3.cps")
+# set biomass concentration at which the pulse is performed
+setGlobalQuantities(key = "_X_conc_pulse", initial_value = 0.9)
+# simulate response to acetate pulse
+res_pulse <- runTimeCourse(intervals=10000)
+# get simulation results
+id_start <- which(res_pulse$result$Ace_out >= 30)[1]+1
+id_end <- which(res_pulse$result$Time >= (res_pulse$result$Time[id_start]+8/60))[1]+1
+t_pulse <- (res_pulse$result$Time[seq(id_start, id_end)] - res_pulse$result$Time[id_start])
+ace_conc_pulse <- res_pulse$result$Ace_out[seq(id_start, id_end)] - res_pulse$result$Ace_out[id_start]
+glc_conc_pulse <- res_pulse$result$Glc[seq(id_start, id_end)] - res_pulse$result$Glc[id_start]
+# set biomass concentration at which the pulse is performed
+setGlobalQuantities(key = "_X_conc_pulse", initial_value = 1000)
+res_nopulse <- runTimeCourse(intervals=10000)
+# get simulation results
+ace_conc_nopulse <- res_nopulse$result$Ace_out[seq(id_start, id_end)] - res_nopulse$result$Ace_out[id_start]
+glc_conc_nopulse <- res_nopulse$result$Glc[seq(id_start, id_end)] - res_nopulse$result$Glc[id_start]
+# get simulation times
+time_sim <- res_nopulse$result$Time[seq(id_start, id_end)] - res_nopulse$result$Time[id_start]
+idx_sim <- get_index_closest(time_meas, time_sim)
+# calculate variance weighted SSR
+SSR_model_3 <- sum((glc-glc_conc_pulse[idx_sim])**2/sd_glc**2, (ace-ace_conc_pulse[idx_sim])**2/sd_ace**2, (glc_nopulse-glc_conc_nopulse[idx_sim])**2/sd_glc_nopulse**2, (ace_nopulse-ace_conc_nopulse[idx_sim])**2/sd_ace_nopulse**2 )
+
+
+# Steady-state fluxes for acetate concentration between 0.1 and 100mM (Enjalbert et al., 2017; Pinhal et al., 2019)
+##############################################################################################
+
+growth_rates <- c(0.521128511, 0.611148842625582, 0.613161998174498, 0.502533817, 0.496290415, 0.488201506, 0.547635665, 0.499830448, 0.474554197, 0.425356578, 0.377534684, 0.645724326, 0.618475601, 0.554887936, 0.564811523, 0.527571192, 0.434972836, 0.3824734, 0.583623355, 0.620905534, 0.564259247, 0.532148135, 0.483885215, 0.557074418, 0.630654409249223)
+sd_growth_rates <- c(0.001793104, 0.00204807928657914, 0.00219396182484705, 0.001709207, 0.001846205, 0.001757403, 0.001821375, 0.001025702, 0.001940912, 0.001204707, 0.001999188, 0.001418374, 0.001932601, 0.001455791, 0.001574234, 0.001206265, 0.001292476, 0.001068259, 0.001804648, 0.001643459, 0.001598405, 0.001121218, 0.000912408, 0.00194896, 0.00203369597574686)
+sd_growth_rates <- sapply(sd_growth_rates, FUN=function(x) max(x,0.01))
+glc_upt <- c(8.654860167, 8.36127542981722, 7.98010111285252, 9.236935826, 8.274418986, 7.560431219, 7.339194455, 5.775312502, 6.423391263, 5.1544758, 3.938631573, 8.115447647, 9.28067031, 6.737153424, 7.172748804, 5.884186033, 5.684201497, 4.811576974, 9.632702365, 8.055042777, 9.708342814, 7.100081588, 5.505759496, 9.242859752, 8.18621623190759)
+sd_glc_upt <- c(0.337812425, 0.38531328268303, 0.373770045721031, 0.356787032, 0.334672954, 0.317509322, 0.288025925, 0.16053276, 0.375934255, 0.293148172, 0.359225607, 0.197331684, 0.360984112, 0.229372278, 0.241820396, 0.20450532, 0.260869273, 0.216134352, 0.34289286, 0.350305744, 0.293144783, 0.220135755, 0.153471508, 0.25245346, 0.396815184905029)
+sd_glc_upt <- sapply(sd_glc_upt, FUN=function(x) max(x,0.1))
+ace_flx <- c(3.5, -2.7, 1.516999356, 1.26845123082679, 0.775821380507016, 0.678877137, 0.017366464, -0.991478151, -1.286687213, -2.078474994, -1.530841439, -1.525342269, -1.253581266, 1.984679487, 0.546462624, -0.136780389, -0.393883917, -0.610240984, -1.120767885, -1.277455315, 2.574285211, 2.051935093, 1.828415596, -1.262442483, -1.317987733, 2.333568565, 1.85234639824858)
+sd_ace_flx <- c(0.35, 0.27, 0.316118066, 0.388752117258161, 0.40715278851436, 0.33357638, 0.37333751, 0.347029894, 0.280501612, 0.195031303, 0.376252463, 0.226182385, 0.303661317, 0.253610517, 0.385450715, 0.243880325, 0.30665695, 0.257983739, 0.23844407, 0.198458448, 0.299832036, 0.334956504, 0.317134334, 0.263807154, 0.195219648, 0.016120887, 0.386174129654754)
+sd_ace_flx <- sapply(sd_ace_flx, FUN=function(x) max(x,0.1))
+
+ace_conc <- c(0.451964624, 1.11600286648471, 2.04718732931708, 2.86252145, 5.285907977, 9.106164204, 16.67476528, 16.76626787, 17.00218707, 30.8667961, 57.92292091, 0.478352574, 4.55673229, 8.10163028, 8.22100734, 7.829591756, 33.53244905, 66.20361403, 0.436956014, 1.28468189, 1.555875222, 12.02564968, 30.24566673, 0.548011282, 2.29562227069566)
+
+fluxes <- c("Values[v_growth_rate]", "Values[v_glc_uptake]", "Values[v_ace_net]")
+
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_1.cps")
+# remove events and fix concentrations of actate, glucose and biomass
+deleteEvent(getEvents()$key)
+setSpecies(key="Ace_out", type="fixed")
+setSpecies(key="Glc", type="fixed")
+setSpecies(key="X", type="fixed")
+Enj_SS_SSR_model_1 <- c()
+for (j in seq(length(ace_conc))){
+  setSpecies(key="Ace_out", initial_concentration=ace_conc[j])
+  applyInitialState()
+  res_ss <- runSteadyState()
+  res_flx <- unlist(res_ss$global_quantities[res_ss$global_quantities$key %in% fluxes, "value"])
+  Enj_SS_SSR_model_1 <- c(Enj_SS_SSR_model_1, (res_flx[1]-growth_rates[j])**2/sd_growth_rates[j]**2 + (res_flx[2]-glc_upt[j])**2/sd_glc_upt[j]**2 + (res_flx[3]-ace_flx[j])**2/sd_ace_flx[j]**2)
+}
+Enj_SS_SSR_model_1 <- sum(Enj_SS_SSR_model_1)
+
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_2.cps")
+# remove events and fix concentrations of actate, glucose and biomass
+deleteEvent(getEvents()$key)
+setSpecies(key="Ace_out", type="fixed")
+setSpecies(key="Glc", type="fixed")
+setSpecies(key="X", type="fixed")
+Enj_SS_SSR_model_2 <- c()
+for (j in seq(length(ace_conc))){
+  setSpecies(key="Ace_out", initial_concentration=ace_conc[j])
+  applyInitialState()
+  res_ss <- runSteadyState()
+  res_flx <- unlist(res_ss$global_quantities[res_ss$global_quantities$key %in% fluxes, "value"])
+  Enj_SS_SSR_model_2 <- c(Enj_SS_SSR_model_2, (res_flx[1]-growth_rates[j])**2/sd_growth_rates[j]**2 + (res_flx[2]-glc_upt[j])**2/sd_glc_upt[j]**2 + (res_flx[3]-ace_flx[j])**2/sd_ace_flx[j]**2)
+}
+Enj_SS_SSR_model_2 <- sum(Enj_SS_SSR_model_2)
+
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_3.cps")
+# remove events and fix concentrations of actate, glucose and biomass
+deleteEvent(getEvents()$key)
+setSpecies(key="Ace_out", type="fixed")
+setSpecies(key="Glc", type="fixed")
+setSpecies(key="X", type="fixed")
+Enj_SS_SSR_model_3 <- c()
+for (j in seq(length(ace_conc))){
+  setSpecies(key="Ace_out", initial_concentration=ace_conc[j])
+  applyInitialState()
+  res_ss <- runSteadyState()
+  res_flx <- unlist(res_ss$global_quantities[res_ss$global_quantities$key %in% fluxes, "value"])
+  Enj_SS_SSR_model_3 <- c(Enj_SS_SSR_model_3, (res_flx[1]-growth_rates[j])**2/sd_growth_rates[j]**2 + (res_flx[2]-glc_upt[j])**2/sd_glc_upt[j]**2 + (res_flx[3]-ace_flx[j])**2/sd_ace_flx[j]**2)
+}
+Enj_SS_SSR_model_3 <- sum(Enj_SS_SSR_model_3)
+
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_4.cps")
+# remove events and fix concentrations of actate, glucose and biomass
+deleteEvent(getEvents()$key)
+setSpecies(key="Ace_out", type="fixed")
+setSpecies(key="Glc", type="fixed")
+setSpecies(key="X", type="fixed")
+Enj_SS_SSR_model_4 <- c()
+for (j in seq(length(ace_conc))){
+  setSpecies(key="Ace_out", initial_concentration=ace_conc[j])
+  applyInitialState()
+  res_ss <- runSteadyState()
+  res_flx <- unlist(res_ss$global_quantities[res_ss$global_quantities$key %in% fluxes, "value"])
+  Enj_SS_SSR_model_4 <- c(Enj_SS_SSR_model_4, (res_flx[1]-growth_rates[j])**2/sd_growth_rates[j]**2 + (res_flx[2]-glc_upt[j])**2/sd_glc_upt[j]**2 + (res_flx[3]-ace_flx[j])**2/sd_ace_flx[j]**2)
+}
+Enj_SS_SSR_model_4 <- sum(Enj_SS_SSR_model_4)
+
+
+# Chemostat experiment (Renilla et al., 2012)
+#############################################
+
+fluxes <- c("Values[v_growth_rate]", "Values[v_glc_uptake]", "Values[v_ace_net]")
+
+# acetate flux as function of dilution rate
+dilution_rate <- c(0.09586056644880175, 0.20043572984749464, 0.2997821350762528, 0.3468409586056645, 0.39912854030501094, 0.44618736383442276, 0.5002178649237474)
+# acetate flux as function of glc uptake
+q_glc <- c(1.43478260869565, 2.7391304347826, 4.59130434782608, 4.69565217391304, 5.7391304347826, 5.92173913043478, 6.10434782608695, 7.12173913043477, 8.34782608695652)
+q_ace <- c(0.381358340437624, 0.762906128635029, 1.40509614473808, 1.17836506583309, 1.99602159704461, 2.08290233967983, 2.01292033721701, 2.44717249218528, 2.5848252344416)
+q_ace_sd <- c(0.139547219854126, 0.139471440750213, 0.15697641375391, 0.1045751633987, 0.19179691200152, 0.0174291938997801, 0.24397082504499, 0.52295159609737, 0.33130624230368)
+q_glc_sd <- c(0.20234760540444, 0.58899555210581, 0.36827270271402, 0.14607356337583, 0.630432119199, 0.13069807968161, 0.47630364392495, 0.99361847036576, 0.66185122193432)
+q_ace_sd <- sapply(q_ace_sd, FUN=function(x) max(x,0.1))
+q_glc_sd <- sapply(q_glc_sd, FUN=function(x) max(x,0.1))
+
+
+setwd(model_dir)
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_1.cps")
+# delete events and set glc feed to 1
+deleteEvent(getEvents()$key)
+setGlobalQuantities(key = "_feed", initial_value = 1)
+Ren_SSR_model_1 <- c()
+for (j in seq(length(dilution_rate))){
+  setGlobalQuantities(key = "_dilution_rate", initial_value = dilution_rate[j], model=getCurrentModel())
+  applyInitialState(model=getCurrentModel())
+  res_ss <- runSteadyState(model=getCurrentModel())
+  val <- unlist(res_ss$global_quantities[res_ss$global_quantities$key %in% fluxes, "value"])
+  Ren_SSR_model_1 <- c(Ren_SSR_model_1,
+                          (val[2]-q_glc[j])**2/q_glc_sd[j]**2 + (val[3]-q_ace[j])**2/q_ace_sd[j]**2)
+}
+Ren_SSR_model_1 <- sum(Ren_SSR_model_1)
+
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_2.cps")
+# delete events and set glc feed to 1
+deleteEvent(getEvents()$key)
+setGlobalQuantities(key = "_feed", initial_value = 1)
+Ren_SSR_model_2 <- c()
+for (j in seq(length(dilution_rate))){
+  setGlobalQuantities(key = "_dilution_rate", initial_value = dilution_rate[j])
+  applyInitialState()
+  res_ss <- runSteadyState()
+  val <- unlist(res_ss$global_quantities[res_ss$global_quantities$key %in% fluxes, "value"])
+  Ren_SSR_model_2 <- c(Ren_SSR_model_2,
+                          (val[2]-q_glc[j])**2/q_glc_sd[j]**2 + (val[3]-q_ace[j])**2/q_ace_sd[j]**2)
+}
+Ren_SSR_model_2 <- sum(Ren_SSR_model_2)
+
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_3.cps")
+# delete events and set glc feed to 1
+deleteEvent(getEvents()$key)
+setGlobalQuantities(key = "_feed", initial_value = 1)
+Ren_SSR_model_3 <- c()
+for (j in seq(length(dilution_rate))){
+  setGlobalQuantities(key = "_dilution_rate", initial_value = dilution_rate[j], model=getCurrentModel())
+  applyInitialState(model=getCurrentModel())
+  res_ss <- runSteadyState(model=getCurrentModel())
+  val <- unlist(res_ss$global_quantities[res_ss$global_quantities$key %in% fluxes, "value"])
+  Ren_SSR_model_3 <- c(Ren_SSR_model_3,
+                          (val[2]-q_glc[j])**2/q_glc_sd[j]**2 + (val[3]-q_ace[j])**2/q_ace_sd[j]**2)
+}
+Ren_SSR_model_3 <- sum(Ren_SSR_model_3)
+
+
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_4.cps")
+# delete events and set glc feed to 1
+deleteEvent(getEvents()$key)
+setGlobalQuantities(key = "_feed", initial_value = 1)
+Ren_SSR_model_4 <- c()
+for (j in seq(length(dilution_rate))){
+  setGlobalQuantities(key = "_dilution_rate", initial_value = dilution_rate[j], model=getCurrentModel())
+  applyInitialState(model=getCurrentModel())
+  res_ss <- runSteadyState(model=getCurrentModel())
+  val <- unlist(res_ss$global_quantities[res_ss$global_quantities$key %in% fluxes, "value"])
+  Ren_SSR_model_4 <- c(Ren_SSR_model_4,
+                          (val[2]-q_glc[j])**2/q_glc_sd[j]**2 + (val[3]-q_ace[j])**2/q_ace_sd[j]**2)
+}
+Ren_SSR_model_4 <- sum(Ren_SSR_model_4)
+
+
+# Plot results
+setwd(results_dir)
+pdf(file="Figure 3-figure supplement 4.pdf", width = 5, height = 5)
+
+data <- c(SSR_model_1, SSR_model_2, SSR_model_3, SSR_model_4)
+xx <- barplot(data, las=1, ylab="variance-weighted SSR", log="y", names.arg=c("model_1", "model_2", "model_3", "model_4"))
+text(x = xx, y = round(data), label = round(data), pos = c(1,3,1,3))
+
+data <- c(Enj_SS_SSR_model_1, Enj_SS_SSR_model_2, Enj_SS_SSR_model_3, Enj_SS_SSR_model_4)
+xx <- barplot(data, las=1, ylab="variance-weighted SSR (steady-state data from Enjalbert 2017)", log="y", names.arg=c("model_1", "model_2", "model_3", "model_4"))
+text(x = xx, y = round(data), label = round(data), pos = c(1,3,1,3))
+
+data <- c(Ren_SSR_model_1, Ren_SSR_model_2, Ren_SSR_model_3, Ren_SSR_model_4)
+xx <- barplot(data, las=1, ylab="variance-weighted SSR", names.arg=c("model_1", "model_2", "model_3", "model_4"))
+text(x = xx, y = round(data), label = round(data), pos = 1)
+
+dev.off()
diff --git a/3-Metabolic_control_analyses.R b/3-Metabolic_control_analyses.R
new file mode 100644
index 0000000..b26a03b
--- /dev/null
+++ b/3-Metabolic_control_analyses.R
@@ -0,0 +1,379 @@
+
+
+###################
+# Set environment #
+###################
+
+# load libraries and initialize environment
+source("set_env.R")
+
+
+############################################
+# Load global sensitivity analysis results #
+############################################
+
+# This file is generated by script "1-Model_construction.R".
+setwd(results_dir)
+load("mc_results_100.RData")
+
+
+########################################
+# Metabolic control analyses - Model 4 #
+########################################
+
+setwd(model_dir)
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model.cps")
+setwd(results_dir)
+
+# delete events and fix concentrations of biomass and extracellular glc and acetate
+deleteEvent(getEvents()$key)
+setSpecies(key="Ace_out", type="fixed")
+setSpecies(key="Glc", type="fixed")
+setSpecies(key="X", type="fixed")
+
+# calculate flux control coefficients
+n_step <- 50
+ace_range <- 10**(seq(-1,2,length.out = n_step))
+res_ace_MCA <- matrix(NA, nrow=length(ace_range), ncol=7)
+res_ace_MCA[,1] <- ace_range
+for (i in seq(n_step)){
+  setSpecies(key="Ace_out{cell}", initial_concentration = ace_range[i], model = getCurrentModel())
+  applyInitialState(model = getCurrentModel())
+  res_MCA <- runMetabolicControlAnalysis(perform_steady_state_analysis=TRUE, model = getCurrentModel())
+  if (res_MCA$result_ss != "found"){
+    print("error")
+  }else{
+    fcc <- res_MCA$flux_control_coefficients_scaled
+    res_ace_MCA[i,seq(2,7)] <- fcc["(ackA)", colnames(fcc) != "'Summation Error'"]
+  }
+}
+colnames(res_ace_MCA) <- c("ace_conc", colnames(fcc)[colnames(fcc) != "'Summation Error'"])
+
+# plot results
+pdf(file = "Figure 4.pdf", height = 4, width = 5)
+
+setSpecies(key="Ace_out{cell}", initial_concentration = 0.1, model = getCurrentModel())
+applyInitialState(model = getCurrentModel())
+res_MCA <- runMetabolicControlAnalysis(model = getCurrentModel())
+
+hmc <- res_MCA$flux_control_coefficients_scaled[c("(glc_upt)", "(ackA)", "(sink)"), c("(glc_upt)", "(sink)", "(pta)", "(ackA)", "(ace_xch)")]
+colnames(hmc) <- c("glycolysis", "TCA", "Pta", "AckA", "Ace_xch")
+rownames(hmc) <- c("glycolysis", "acetate", "TCA")
+rgb.palette <- colorRampPalette(brewer.pal(n = 11, name = "RdBu"))
+breaks <- c(-1, -0.5, -0.2, -0.1, -0.05, -0.01, 0.01, 0.05, 0.1, 0.2, 0.5, 1, 1.5)
+col_scale <- rgb.palette(length(breaks)-1)
+col_scale[6] <- "#DDDDDD"
+heatmap.2(hmc, Rowv=FALSE, Colv=FALSE, dendrogram="none", col=col_scale, breaks=breaks,
+          scale="none", trace="none", colsep=seq(0,ncol(hmc)), rowsep=seq(0,nrow(hmc)), sepwidth=c(0.04,0.02))
+
+dev.off()
+
+# sensitivity analysis
+run_mca_sa <- function(){
+  n_step <- 50
+  ace_range <- 10**(seq(-1,2,length.out = n_step))
+  res_ace_MCA <- matrix(NA, nrow=length(ace_range), ncol=7)
+  res_ace_MCA[,1] <- ace_range
+  for (i in seq(n_step)){
+    setSpecies(key="Ace_out{cell}", initial_concentration = ace_range[i], model = getCurrentModel())
+    applyInitialState(model = getCurrentModel())
+    res_MCA <- runMetabolicControlAnalysis(perform_steady_state_analysis=TRUE, model = getCurrentModel())
+    if (res_MCA$result_ss != "found"){
+      print("error")
+    }else{
+      fcc <- res_MCA$flux_control_coefficients_scaled
+      res_ace_MCA[i,seq(2,7)] <- fcc["(ackA)", colnames(fcc) != "'Summation Error'"]
+    }
+  }
+  colnames(res_ace_MCA) <- c("ace_conc", colnames(fcc)[colnames(fcc) != "'Summation Error'"])
+  return(res_ace_MCA)
+}
+
+# create progress bar
+pb <- txtProgressBar(min=0, max=ncol(fit_results$res_par)-1, style=3)
+
+# sensitivity analysis
+res <- array(NA, dim=c(ncol(fit_results$res_par)-1, length(ace_range), 7), dimnames=list(iter=NULL, ace_conc=NULL, fcc=c("ace_conc", colnames(fcc)[colnames(fcc) != "'Summation Error'"])))
+for (i in seq(ncol(fit_results$res_par)-1)){
+  rp <- c(fit_results$res_par[,i+1])
+  names(rp) <- fit_results$res_par[,"parameter"]
+  model <- update_params(getCurrentModel(), rp)
+  res[i,,] <- run_mca_sa()
+  setTxtProgressBar(pb, i)
+}
+
+# close progress bar
+close(pb)
+
+# plot results
+pdf(file="Figure 5.pdf", width = 7, height = 9)
+par(mfrow=c(4,3))
+
+xlab_main <- c(0.1, 1, 10, 100)
+xlab_sec <- c(seq(0.2, 0.9, by=0.1), seq(2, 9, by=1), seq(20, 90, by=10))
+conc_threshold <- 13.27174
+
+ctrl_by_acetate_pathway <- apply(apply(res[,,c("(ackA)", "(pta)", "(ace_xch)")], c(1,2), sum), 2, mean)
+ctrl_by_glc_upt <- apply(res[,,"(glc_upt)"], 2, mean)
+ctrl_by_TCA <- apply(res[,,"(sink)"], 2, mean)
+
+plot(x=ace_range, y=ctrl_by_acetate_pathway, type="l", xaxt="n", las=1, ylim=c(0,1), log="x", xaxs="i", yaxs="i", xlab="[acetate] (mM)", ylab="control by acetate pathway", lwd=1.2)
+polygon(x=c(ace_range, rev(ace_range)),
+        y=c(apply(apply(res[,,c("(ackA)", "(pta)", "(ace_xch)")], c(1,2), sum), 2, max), rev(apply(apply(res[,,c("(ackA)", "(pta)", "(ace_xch)")], c(1,2), sum), 2, min))),
+        col="#00000055", border=NA)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+
+fconc <- 0.8
+lines_threshold(x=ace_range, y=ctrl_by_glc_upt, threshold=conc_threshold, new=TRUE, xaxt="n", xaxs="i", yaxs="i", las=1, xlim=c(0.1,100), type="l", ylim=c(-3,3), log="x", xlab="[acetate] (mM)", ylab="control by glycolysis", lwd=1.2)
+polygon(x=c(ace_range[ace_range < conc_threshold*fconc], rev(ace_range[ace_range < conc_threshold*fconc])),
+        y=c(apply(res[,ace_range < conc_threshold*fconc,"(glc_upt)"], 2, max), rev(apply(res[,ace_range < conc_threshold*fconc,"(glc_upt)"], 2, min))),
+        col="#00000055", border=NA)
+
+polygon(x=c(ace_range[ace_range > conc_threshold/fconc], rev(ace_range[ace_range > conc_threshold/fconc])),
+        y=c(apply(res[,ace_range > conc_threshold/fconc,"(glc_upt)"], 2, max), rev(apply(res[,ace_range > conc_threshold/fconc,"(glc_upt)"], 2, min))),
+        col="#00000055", border=NA)
+
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+abline(h=0)
+
+lines_threshold(x=ace_range, y=ctrl_by_TCA, threshold=conc_threshold, new=TRUE, xaxt="n", xaxs="i", yaxs="i", las=1, xlim=c(0.1,100), type="l", ylim=c(-3,3), log="x", xlab="[acetate] (mM)", ylab="control by TCA", lwd=1.2)
+polygon(x=c(ace_range[ace_range < conc_threshold*fconc], rev(ace_range[ace_range < conc_threshold*fconc])),
+        y=c(apply(res[,ace_range < conc_threshold*fconc,"(sink)"], 2, max), rev(apply(res[,ace_range < conc_threshold*fconc,"(sink)"], 2, min))),
+        col="#00000055", border=NA)
+
+polygon(x=c(ace_range[ace_range > conc_threshold/fconc], rev(ace_range[ace_range > conc_threshold/fconc])),
+        y=c(apply(res[,ace_range > conc_threshold/fconc,"(sink)"], 2, max), rev(apply(res[,ace_range > conc_threshold/fconc,"(sink)"], 2, min))),
+        col="#00000055", border=NA)
+
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+abline(h=0)
+
+plot(x=ace_range, y=ctrl_by_TCA+ctrl_by_glc_upt, type="l", ylim=c(0,1), xaxt="n", xaxs="i", yaxs="i", las=1, log="x", xlab="[acetate] (mM)", ylab="control by TCA+glycolysis", lwd=1.2)
+polygon(x=c(ace_range, rev(ace_range)),
+        y=c(apply(res[,,"(sink)"]+res[,,"(glc_upt)"], 2, max), rev(apply(res[,,"(sink)"]+res[,,"(glc_upt)"], 2, min))),
+        col="#00000055", border=NA)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+
+plot(x=ace_range, y=-ctrl_by_TCA/ctrl_by_glc_upt, type="l", ylim=c(0,2), xaxt="n", xaxs="i", yaxs="i", las=1, log="x", xlab="[acetate] (mM)", ylab="control by TCA/glycolysis", lwd=1.2)
+polygon(x=c(ace_range, rev(ace_range)),
+        y=c(apply(-res[,,"(sink)"]/res[,,"(glc_upt)"], 2, max), rev(apply(-res[,,"(sink)"]/res[,,"(glc_upt)"], 2, min))),
+        col="#00000055", border=NA)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+abline(h=1)
+
+dev.off()
+
+
+#####################################################
+# Metabolic control analyses for alternative models #
+#####################################################
+
+###########
+# Model 1 #
+###########
+
+setwd(model_dir)
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_1.cps")
+setwd(results_dir)
+
+# delete events and fix concentrations of biomass and extracellular glc and acetate
+deleteEvent(getEvents()$key)
+setSpecies(key="Ace_out", type="fixed")
+setSpecies(key="Glc", type="fixed")
+setSpecies(key="X", type="fixed")
+
+# calculate flux control coefficients
+n_step <- 50
+ace_range <- 10**(seq(-1,2,length.out = n_step))
+res_ace_MCA <- matrix(NA, nrow=length(ace_range), ncol=7)
+res_ace_MCA[,1] <- ace_range
+for (i in seq(n_step)){
+  setSpecies(key="Ace_out{cell}", initial_concentration = ace_range[i], model = getCurrentModel())
+  applyInitialState(model = getCurrentModel())
+  res_MCA <- runMetabolicControlAnalysis(model = getCurrentModel())
+  if (res_MCA$result_ss != "found"){
+    print("error")
+  }else{
+    fcc <- res_MCA$flux_control_coefficients_scaled
+    res_ace_MCA[i,seq(2,7)] <- fcc["(ackA)", colnames(fcc) != "'Summation Error'"]
+  }
+}
+colnames(res_ace_MCA) <- c("ace_conc", colnames(fcc)[colnames(fcc) != "'Summation Error'"])
+
+pdf(file="Figure 5-figure supplement 1.pdf", width = 7, height = 9)
+par(mfrow=c(4,3))
+
+xlab_main <- c(0.1, 1, 10, 100)
+xlab_sec <- c(seq(0.2, 0.9, by=0.1), seq(2, 9, by=1), seq(20, 90, by=10))
+conc_threshold <- 16
+
+ctrl_by_acetate_pathway <- apply(res_ace_MCA[,c("(ackA)", "(pta)", "(ace_xch)")], 1, sum)
+ctrl_by_glc_upt <- res_ace_MCA[,"(glc_upt)"]
+ctrl_by_TCA <- res_ace_MCA[,"(sink)"]
+
+plot(x=ace_range, y=ctrl_by_acetate_pathway, type="l", xaxt="n", las=1, ylim=c(0,1), log="x", xaxs="i", yaxs="i", xlab="[acetate] (mM)", ylab="control by acetate pathway", lwd=2)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+
+lines_threshold(x=ace_range, y=ctrl_by_glc_upt, threshold=conc_threshold, new=TRUE, xaxt="n", xaxs="i", yaxs="i", las=1, xlim=c(0.1,100), type="l", ylim=c(-3,3), log="x", xlab="[acetate] (mM)", ylab="control by glycolysis", lwd=2)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+abline(h=0)
+
+lines_threshold(x=ace_range, y=ctrl_by_TCA, threshold=conc_threshold, new=TRUE, xaxt="n", xaxs="i", yaxs="i", las=1, xlim=c(0.1,100), type="l", ylim=c(-3,3), log="x", xlab="[acetate] (mM)", ylab="control by TCA", lwd=2)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+abline(h=0)
+
+plot(x=ace_range, y=ctrl_by_TCA+ctrl_by_glc_upt, type="l", ylim=c(0,1), xaxt="n", xaxs="i", yaxs="i", las=1, log="x", xlab="[acetate] (mM)", ylab="control by TCA+glycolysis", lwd=2)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+
+plot(x=ace_range, y=-ctrl_by_TCA/ctrl_by_glc_upt, type="l", ylim=c(0,2), xaxt="n", xaxs="i", yaxs="i", las=1, log="x", xlab="[acetate] (mM)", ylab="control by TCA/glycolysis", lwd=2)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+abline(h=1)
+
+dev.off()
+
+###########
+# Model 2 #
+###########
+
+setwd(model_dir)
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_2.cps")
+setwd(results_dir)
+
+# delete events and fix concentrations of biomass and extracellular glc and acetate
+deleteEvent(getEvents()$key)
+setSpecies(key="Ace_out", type="fixed")
+setSpecies(key="Glc", type="fixed")
+setSpecies(key="X", type="fixed")
+
+# calculate flux control coefficients
+n_step <- 50
+ace_range <- 10**(seq(-1,2,length.out = n_step))
+res_ace_MCA <- matrix(NA, nrow=length(ace_range), ncol=7)
+res_ace_MCA[,1] <- ace_range
+for (i in seq(n_step)){
+  setSpecies(key="Ace_out{cell}", initial_concentration = ace_range[i], model = getCurrentModel())
+  applyInitialState(model = getCurrentModel())
+  res_MCA <- runMetabolicControlAnalysis(model = getCurrentModel())
+  if (res_MCA$result_ss != "found"){
+    print("error")
+  }else{
+    fcc <- res_MCA$flux_control_coefficients_scaled
+    res_ace_MCA[i,seq(2,7)] <- fcc["(ackA)", colnames(fcc) != "'Summation Error'"]
+  }
+}
+colnames(res_ace_MCA) <- c("ace_conc", colnames(fcc)[colnames(fcc) != "'Summation Error'"])
+
+pdf(file="Figure 5-figure supplement 2.pdf", width = 7, height = 9)
+par(mfrow=c(4,3))
+
+xlab_main <- c(0.1, 1, 10, 100)
+xlab_sec <- c(seq(0.2, 0.9, by=0.1), seq(2, 9, by=1), seq(20, 90, by=10))
+conc_threshold <- 14
+
+ctrl_by_acetate_pathway <- apply(res_ace_MCA[,c("(ackA)", "(pta)", "(ace_xch)")], 1, sum)
+ctrl_by_glc_upt <- res_ace_MCA[,"(glc_upt)"]
+ctrl_by_TCA <- res_ace_MCA[,"(sink)"]
+
+plot(x=ace_range, y=ctrl_by_acetate_pathway, type="l", xaxt="n", las=1, ylim=c(0,1), log="x", xaxs="i", yaxs="i", xlab="[acetate] (mM)", ylab="control by acetate pathway", lwd=2)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+
+lines_threshold(x=ace_range, y=ctrl_by_glc_upt, threshold=conc_threshold, new=TRUE, xaxt="n", xaxs="i", yaxs="i", las=1, xlim=c(0.1,100), type="l", ylim=c(-3,3), log="x", xlab="[acetate] (mM)", ylab="control by glycolysis", lwd=2)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+abline(h=0)
+
+lines_threshold(x=ace_range, y=ctrl_by_TCA, threshold=conc_threshold, new=TRUE, xaxt="n", xaxs="i", yaxs="i", las=1, xlim=c(0.1,100), type="l", ylim=c(-3,3), log="x", xlab="[acetate] (mM)", ylab="control by TCA", lwd=2)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+abline(h=0)
+
+plot(x=ace_range, y=ctrl_by_TCA+ctrl_by_glc_upt, type="l", ylim=c(0,1), xaxt="n", xaxs="i", yaxs="i", las=1, log="x", xlab="[acetate] (mM)", ylab="control by TCA+glycolysis", lwd=2)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+
+plot(x=ace_range, y=-ctrl_by_TCA/ctrl_by_glc_upt, type="l", ylim=c(0,2), xaxt="n", xaxs="i", yaxs="i", las=1, log="x", xlab="[acetate] (mM)", ylab="control by TCA/glycolysis", lwd=2)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+abline(h=1)
+
+dev.off()
+
+###########
+# Model 3 #
+###########
+
+setwd(model_dir)
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model_3.cps")
+setwd(results_dir)
+
+# delete events and fix concentrations of biomass and extracellular glc and acetate
+deleteEvent(getEvents()$key)
+setSpecies(key="Ace_out", type="fixed")
+setSpecies(key="Glc", type="fixed")
+setSpecies(key="X", type="fixed")
+
+# calculate flux control coefficients
+n_step <- 50
+ace_range <- 10**(seq(-1,2,length.out = n_step))
+res_ace_MCA <- matrix(NA, nrow=length(ace_range), ncol=7)
+res_ace_MCA[,1] <- ace_range
+for (i in seq(n_step)){
+  setSpecies(key="Ace_out{cell}", initial_concentration = ace_range[i], model = getCurrentModel())
+  applyInitialState(model = getCurrentModel())
+  res_MCA <- runMetabolicControlAnalysis(model = getCurrentModel())
+  if (res_MCA$result_ss != "found"){
+    print("error")
+  }else{
+    fcc <- res_MCA$flux_control_coefficients_scaled
+    res_ace_MCA[i,seq(2,7)] <- fcc["(ackA)", colnames(fcc) != "'Summation Error'"]
+  }
+}
+colnames(res_ace_MCA) <- c("ace_conc", colnames(fcc)[colnames(fcc) != "'Summation Error'"])
+
+pdf(file="Figure 5-figure supplement 3.pdf", width = 7, height = 9)
+par(mfrow=c(4,3))
+
+xlab_main <- c(0.1, 1, 10, 100)
+xlab_sec <- c(seq(0.2, 0.9, by=0.1), seq(2, 9, by=1), seq(20, 90, by=10))
+conc_threshold <- 2.3
+
+ctrl_by_acetate_pathway <- apply(res_ace_MCA[,c("(ackA)", "(pta)", "(ace_xch)")], 1, sum)
+ctrl_by_glc_upt <- res_ace_MCA[,"(glc_upt)"]
+ctrl_by_TCA <- res_ace_MCA[,"(sink)"]
+
+plot(x=ace_range, y=ctrl_by_acetate_pathway, type="l", xaxt="n", las=1, ylim=c(0,1), log="x", xaxs="i", yaxs="i", xlab="[acetate] (mM)", ylab="control by acetate pathway", lwd=2)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+
+lines_threshold(x=ace_range, y=ctrl_by_glc_upt, threshold=conc_threshold, new=TRUE, xaxt="n", xaxs="i", yaxs="i", las=1, xlim=c(0.1,100), type="l", ylim=c(-3,3), log="x", xlab="[acetate] (mM)", ylab="control by glycolysis", lwd=2)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+abline(h=0)
+
+lines_threshold(x=ace_range, y=ctrl_by_TCA, threshold=conc_threshold, new=TRUE, xaxt="n", xaxs="i", yaxs="i", las=1, xlim=c(0.1,100), type="l", ylim=c(-3,3), log="x", xlab="[acetate] (mM)", ylab="control by TCA", lwd=2)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+abline(h=0)
+
+plot(x=ace_range, y=ctrl_by_TCA+ctrl_by_glc_upt, type="l", ylim=c(0,1), xaxt="n", xaxs="i", yaxs="i", las=1, log="x", xlab="[acetate] (mM)", ylab="control by TCA+glycolysis", lwd=2)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+
+plot(x=ace_range, y=-ctrl_by_TCA/ctrl_by_glc_upt, type="l", ylim=c(0,2), xaxt="n", xaxs="i", yaxs="i", las=1, log="x", xlab="[acetate] (mM)", ylab="control by TCA/glycolysis", lwd=2)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+abline(h=1)
+
+dev.off()
+
diff --git a/4-Regulation_analyses.R b/4-Regulation_analyses.R
new file mode 100644
index 0000000..4555c50
--- /dev/null
+++ b/4-Regulation_analyses.R
@@ -0,0 +1,186 @@
+
+
+###################
+# Set environment #
+###################
+
+# load libraries and initialize environment
+source("set_env.R")
+
+
+############################################
+# Load global sensitivity analysis results #
+############################################
+
+# This file is generated by script "1-Model_construction.R".
+setwd(results_dir)
+load("mc_results_100.RData")
+
+
+#################################
+# Metabolic regulation analyses #
+#################################
+
+setwd(model_dir)
+loadModel("Millard2020_Ecoli_glc_ace_kinetic_model.cps")
+setwd(results_dir)
+# delete events and fix concentrations of biomass and extracellular glc and acetate
+deleteEvent(getEvents()$key)
+setSpecies(key="Ace_out", type="fixed")
+setSpecies(key="Glc", type="fixed")
+setSpecies(key="X", type="fixed")
+
+n_step <- 300
+delta_p <- 0.001
+conc_threshold <- 14.27174
+ace_range <- 10**(seq(-1, 2, length.out = n_step))
+ace_range <- ace_range[abs(ace_range - conc_threshold) > 0.1]
+
+res_reg <- array(NA, dim=c(ncol(fit_results$res_par)-1, length(ace_range), 4), dimnames=list(iter=NULL, r=NULL, c=c("ace_conc", "via_acetate_pathway", "via_glc_upt", "via_tca")))
+
+# create progress bar
+pb <- txtProgressBar(min=0, max=ncol(fit_results$res_par)-1, style=3)
+
+for (j in seq(ncol(fit_results$res_par)-1)){
+  
+  res_ace_regulation <- matrix(NA, nrow=length(ace_range), ncol=4, dimnames=list(r=NULL, c=c("ace_conc", "via_acetate_pathway", "via_glc_upt", "via_tca")))
+  
+  for (i in seq(length(ace_range))){
+    
+    rp <- c(fit_results$res_par[,j+1])
+    names(rp) <- fit_results$res_par[,"parameter"]
+    model <- update_params(getCurrentModel(), rp)
+    
+    # set ace concentration
+    setSpecies(key="Ace_out{cell}", initial_concentration = ace_range[i], model=model)
+    applyInitialState(model=model)
+    
+    # get steady-state
+    res_ss_i <- runSteadyState(update_model=TRUE, model=model)$global_quantities
+    
+    # calculate control coefficients
+    res_MCA_R <- runMCA(model=model)$flux_control_coefficients_scaled
+    
+    # calculate elasticities
+    
+    # fix acetylCoA concentration to calculate elasticity of each pathway wrt acetate
+    setSpecies(key="AcCoA", type="fixed", model=model)
+    
+    # change acetate concentration
+    setSpecies(key="Ace_out{cell}", initial_concentration = ace_range[i]*(1+delta_p), model=model)
+    applyInitialState(model=model)
+    
+    # get steady-state
+    res_ss_i_eps <- runSteadyState(model=model)$global_quantities
+    
+    # calculate elasticities (using the more stable numerical method, both being equivalent)
+    #elasticities <- (log(abs(res_ss_i_eps$value)) - log(abs(res_ss_i$value))) / log(1+delta_p)
+    #print(elasticities)
+    elasticities <- (res_ss_i_eps$value - res_ss_i$value) / delta_p / res_ss_i_eps$value
+    #print(elasticities)
+    
+    # reset balance on accoa
+    setSpecies(key="AcCoA", type="reactions", model=model)
+    
+    # calculate response coefficient
+    # acetate via Pta-AckA
+    res_reg_ace_ace <- sum(res_MCA_R["(ackA)", c("(ackA)", "(pta)", "(ace_xch)")]) * elasticities[res_ss_i_eps$key == "Values[v_ace_net]"]
+    # acetate via glc uptake
+    res_reg_ace_glc <- res_MCA_R["(ackA)", "(glc_upt)"] * elasticities[res_ss_i_eps$key == "Values[v_glc_uptake]"]
+    # acetate via sink
+    res_reg_ace_tca <- res_MCA_R["(ackA)", "(sink)"] * elasticities[res_ss_i_eps$key == "Values[v_growth_rate]"]
+    
+    res_ace_regulation[i,] <- c(ace_range[i], res_reg_ace_ace, res_reg_ace_glc, res_reg_ace_tca)
+  }
+  
+  # save results
+  res_reg[j,,] <- res_ace_regulation
+  
+  # update the progress bar
+  setTxtProgressBar(pb, j)
+}
+
+# close progress bar
+close(pb)
+
+# plot regulation results
+pdf(file="Figure 6.pdf", width = 7, height = 9)
+par(mfrow=c(4,3))
+
+xlab_main <- c(0.1, 1, 10, 100)
+xlab_sec <- c(seq(0.2, 0.9, by=0.1), seq(2, 9, by=1), seq(20, 90, by=10))
+conc_threshold <- 14.5
+
+
+# plot partitioned response coefficients
+fconc_max <- 1.12
+fconc_min <- 0.82
+lines_threshold(ace_range, apply(res_reg[,,"via_acetate_pathway"], 2, median), threshold=conc_threshold, new=TRUE, xaxt="n", las=1, xaxs="i", yaxs="i", col="#2E75B6", xlim=c(0.1,100), type="l", log="x", ylim=c(-5, 5), xlab="[acetate] (mM)", ylab="R_ace_pathway", lwd=1.2)
+polygon(x=c(ace_range[ace_range < conc_threshold*fconc_min], rev(ace_range[ace_range < conc_threshold*fconc_min])),
+        y=c(apply(res_reg[,ace_range < conc_threshold*fconc_min,"via_acetate_pathway"], 2, max), rev(apply(res_reg[,ace_range < conc_threshold*fconc_min,"via_acetate_pathway"], 2, min))),
+        col="#2E75B655", border=NA)
+polygon(x=c(ace_range[ace_range > conc_threshold*fconc_max], rev(ace_range[ace_range > conc_threshold*fconc_max])),
+        y=c(apply(res_reg[,ace_range > conc_threshold*fconc_max,"via_acetate_pathway"], 2, max), rev(apply(res_reg[,ace_range > conc_threshold*fconc_max,"via_acetate_pathway"], 2, min))),
+        col="#2E75B655", border=NA)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+abline(h=0)
+
+fconc_max <- 1.12
+fconc_min <- 0.84
+lines_threshold(ace_range, apply(res_reg[,,"via_glc_upt"], 2, median), threshold=conc_threshold, new=TRUE, xaxt="n", las=1, xaxs="i", yaxs="i", col="#D6685C", xlim=c(0.1,100), type="l", log="x", ylim=c(-5, 5), xlab="[acetate] (mM)", ylab="R_Glc_uptake", lwd=1.2)
+polygon(x=c(ace_range[ace_range < conc_threshold*fconc_min], rev(ace_range[ace_range < conc_threshold*fconc_min])),
+        y=c(apply(res_reg[,ace_range < conc_threshold*fconc_min,"via_glc_upt"], 2, max), rev(apply(res_reg[,ace_range < conc_threshold*fconc_min,"via_glc_upt"], 2, min))),
+        col="#D6685C55", border=NA)
+polygon(x=c(ace_range[ace_range > conc_threshold*fconc_max], rev(ace_range[ace_range > conc_threshold*fconc_max])),
+        y=c(apply(res_reg[,ace_range > conc_threshold*fconc_max,"via_glc_upt"], 2, max), rev(apply(res_reg[,ace_range > conc_threshold*fconc_max,"via_glc_upt"], 2, min))),
+        col="#D6685C55", border=NA)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+abline(h=0)
+
+lines_threshold(ace_range, apply(res_reg[,,"via_tca"], 2, median), threshold=conc_threshold, new=TRUE, xaxt="n", las=1, xaxs="i", yaxs="i", col="#70AD47", xlim=c(0.1,100), type="l", log="x", ylim=c(-5, 5), xlab="[acetate] (mM)", ylab="R_TCA", lwd=1.2)
+polygon(x=c(ace_range[ace_range < conc_threshold*fconc_min], rev(ace_range[ace_range < conc_threshold*fconc_min])),
+        y=c(apply(res_reg[,ace_range < conc_threshold*fconc_min,"via_tca"], 2, max), rev(apply(res_reg[,ace_range < conc_threshold*fconc_min,"via_tca"], 2, min))),
+        col="#70AD4755", border=NA)
+polygon(x=c(ace_range[ace_range > conc_threshold*fconc_max], rev(ace_range[ace_range > conc_threshold*fconc_max])),
+        y=c(apply(res_reg[,ace_range > conc_threshold*fconc_max,"via_tca"], 2, max), rev(apply(res_reg[,ace_range > conc_threshold*fconc_max,"via_tca"], 2, min))),
+        col="#70AD4755", border=NA)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+abline(h=0)
+
+# plot contribution of each pathway
+fconc_max <- 1.14
+fconc_min <- 0.84
+contributio_ace <- res_reg[,,"via_acetate_pathway"]/apply(res_reg[,,2:4], 1:2, FUN=function(x) sum(abs(x)))
+lines_threshold(ace_range, apply(contributio_ace, 2, median), threshold=conc_threshold, new=TRUE, xaxt="n", las=1, xaxs="i", yaxs="i", xlim=c(0.1,100), type="l", log="x", xlab="[acetate] (mM)", ylab="relative_R", ylim=c(-0.7, 0.7), lwd=1.2, col="#2E75B6")
+polygon(x=c(ace_range[ace_range < conc_threshold*fconc_min], rev(ace_range[ace_range < conc_threshold*fconc_min])),
+        y=c(apply(contributio_ace[,ace_range < conc_threshold*fconc_min], 2, max), rev(apply(contributio_ace[,ace_range < conc_threshold*fconc_min], 2, min))),
+        col="#2E75B655", border=NA)
+polygon(x=c(ace_range[ace_range > conc_threshold*fconc_max], rev(ace_range[ace_range > conc_threshold*fconc_max])),
+        y=c(apply(contributio_ace[,ace_range > conc_threshold*fconc_max], 2, max), rev(apply(contributio_ace[,ace_range > conc_threshold*fconc_max], 2, min))),
+        col="#2E75B655", border=NA)
+axis(side = 1, at = xlab_main, labels = TRUE)
+axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
+abline(h=0)
+contributio_glc_upt <- res_reg[,,"via_glc_upt"]/apply(res_reg[,,2:4], 1:2, FUN=function(x) sum(abs(x)))
+lines_threshold(ace_range, apply(contributio_glc_upt, 2, median), threshold=conc_threshold, new=FALSE, type="l", col="#D6685C", lwd=1.2)
+polygon(x=c(ace_range[ace_range < conc_threshold*fconc_min], rev(ace_range[ace_range < conc_threshold*fconc_min])),
+        y=c(apply(contributio_glc_upt[,ace_range < conc_threshold*fconc_min], 2, max), rev(apply(contributio_glc_upt[,ace_range < conc_threshold*fconc_min], 2, min))),
+        col="#D6685C55", border=NA)
+polygon(x=c(ace_range[ace_range > conc_threshold*fconc_max], rev(ace_range[ace_range > conc_threshold*fconc_max])),
+        y=c(apply(contributio_glc_upt[,ace_range > conc_threshold*fconc_max], 2, max), rev(apply(contributio_glc_upt[,ace_range > conc_threshold*fconc_max], 2, min))),
+        col="#D6685C55", border=NA)
+contributio_tca <- res_reg[,,"via_tca"]/apply(res_reg[,,2:4], 1:2, FUN=function(x) sum(abs(x)))
+lines_threshold(ace_range, apply(contributio_tca, 2, median), threshold=conc_threshold, new=FALSE, type="l", col="#70AD47", lwd=1.2)
+polygon(x=c(ace_range[ace_range < conc_threshold*fconc_min], rev(ace_range[ace_range < conc_threshold*fconc_min])),
+        y=c(apply(contributio_tca[,ace_range < conc_threshold*fconc_min], 2, max), rev(apply(contributio_tca[,ace_range < conc_threshold*fconc_min], 2, min))),
+        col="#70AD4755", border=NA)
+polygon(x=c(ace_range[ace_range > conc_threshold*fconc_max], rev(ace_range[ace_range > conc_threshold*fconc_max])),
+        y=c(apply(contributio_tca[,ace_range > conc_threshold*fconc_max], 2, max), rev(apply(contributio_tca[,ace_range > conc_threshold*fconc_max], 2, min))),
+        col="#70AD4755", border=NA)
+
+dev.off()
+
+
diff --git a/README.md b/README.md
index 0edb188..d95af71 100644
--- a/README.md
+++ b/README.md
@@ -1,8 +1,8 @@
-# Kinetic modeling of glucose and acetate metabolisms in *E. coli* - Millard et al., 2020.
+# Kinetic modeling of glucose and acetate metabolisms in *E. coli* - Millard et al., 2021.
 
 ## Overview
 
-This R script performs all analyses detailed in the following publication:
+These R scripts perform all analyses detailed in the following publication:
 
 > Control and regulation of acetate overflow in *Escherichia coli*
 > 
@@ -11,17 +11,17 @@ This R script performs all analyses detailed in the following publication:
 All models are available in COPASI format in the directory `/model/cps/`, with the experimental data used for model calibration. The final kinetic model is also available in SBML format in the 
 directory `/model/sbml/` and from the Biomodels database (http://www.ebi.ac.uk/biomodels/) under identifier MODEL2005050001.
 
-Details on the calculations can be found in the [publication](https://doi.org/10.1101/2020.08.18.255356) and in the script `run_analysis.R`.
+Details on the calculations can be found in the [original publication](https://doi.org/10.1101/2020.08.18.255356) and in the R scripts.
 
 ## Dependencies
 
 Some R packages are required.
 
-`RColorBrewer` and `gplots` can be installed
+`RColorBrewer`, `stringr` and `gplots` can be installed
 by running the following command in an R console:
 
 ```bash
-install.packages(c("RColorBrewer", "gplots"))
+install.packages(c("RColorBrewer", "gplots", "stringr"))
 ```
 
 `CoRC` can be installed
@@ -53,10 +53,22 @@ cd /home/usr/data/acetate_regulation/
 R
 ```
 
-- run calculations:
+- run calculations, starting from model construction to regulation analyses:
 
 ```bash
-source("run_analysis.R")
+source("1-Model_construction.R")
+```
+
+```bash
+source("2-Model_validation.R")
+```
+
+```bash
+source("3-Metabolic_control_analyses.R")
+```
+
+```bash
+source("4-Regulation_analyses.R")
 ```
 
 The code is open-source and available under GPLv3 license.
diff --git a/misc.R b/misc.R
new file mode 100644
index 0000000..9cb1723
--- /dev/null
+++ b/misc.R
@@ -0,0 +1,168 @@
+library(RColorBrewer)
+library(gplots)
+library(CoRC)
+library(stringr)
+
+test_khi2 <- function(nb_points, k_val, nb_par){
+  # Perform Khi2 statistical test.
+  #
+  # Args:
+  #   nb_points (int): number of data points
+  #   k_val (float): khi2 value (cost)
+  #   nb_par (int): number of free parameters
+  #
+  # Returns (list):
+  #   $'khi2 value' (float): khi2 value (cost)
+  #   $'data points' (int): number of data points
+  #   $'fitted parameters' (int): number of free parameters
+  #   $'degrees of freedom' (int): degrees of freedom
+  #   $'khi2 reduced value' (float): chi2 reduced value
+  #   $'p-value, i.e. P(X^2<=value)' (float): p value
+  #   $conclusion (str): message indicating whether the models fits (or not) the data at 95% confidence interval
+  #
+  df <- nb_points - nb_par
+  p_val <- pchisq(k_val, df=df)
+  khi2test <- list("khi2 value"                  = k_val,
+                   "data points"                 = nb_points,
+                   "fitted parameters"           = nb_par,
+                   "degrees of freedom"          = df,
+                   "khi2 reduced value"          = k_val/df,
+                   "p-value, i.e. P(X^2<=value)" = p_val)
+  if (p_val > 0.95){
+    khi2test$conclusion <- "At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD."
+  }else{
+    khi2test$conclusion <- "At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD."
+  }
+  return(khi2test)
+}
+
+plot_points <- function(x, y, sd, col="black", offset=1.5, mode="v", cex=1){
+  # Scatterplot with error bars.
+  #
+  # Args:
+  #   x (vector): x coordinates
+  #   y (vector): y coordinates
+  #   sd (vector): error bars
+  #   col (color code): color of points
+  #   offset (float): width (or height if mode = 'v') of error bars
+  #   mode ('v' or 'h'): errors of y (if mode='v') or x (if mode='h')
+  #
+  if (mode == "v"){
+    segments(x0=x, y0=y-sd, x1=x, y1=y+sd) 
+    segments(x0=x-offset, y0=y+sd, x1=x+offset, y1=y+sd) 
+    segments(x0=x-offset, y0=y-sd, x1=x+offset, y1=y-sd) 
+  }else if (mode == "h"){
+    segments(x0=x-sd, y0=y, x1=x+sd, y1=y) 
+    segments(x0=x+sd, y0=y-offset, x1=x+sd, y1=y+offset) 
+    segments(x0=x-sd, y0=y-offset, x1=x-sd, y1=y+offset) 
+  }
+  points(x, y, pch=21, bg=col, col="black", cex=cex)
+}
+
+lines_threshold <- function(x, y, threshold, new, ...){
+  # Split data according to a given threshold, and plot lines for
+  # each set.
+  #
+  # Args:
+  #   x (vector): x coordinates
+  #   y (vector): y coordinates
+  #   threshold (float): value of x at which lines should not
+  #                      be connected
+  #   new (bool): create a new plot if TRUE, otherwise add
+  #               lines to an existing plot
+  #
+  id_1 <- (x < threshold)
+  id_2 <- (x > threshold)
+  if (new){
+    plot(x[id_1], y[id_1], ...)
+  }else{
+    suppressWarnings(lines(x[id_1], y[id_1], ...))
+  }
+  suppressWarnings(lines(x[id_2], y[id_2], ...))
+}
+
+get_parameters_stats <- function(fit_results){
+  li <- grep("]_0", fit_results$res_par$parameter, fixed=TRUE, invert=TRUE)
+  tmp <- matrix(NA, nrow=length(li), ncol=6, dimnames=list(par=fit_results$res_par$parameter[li], stats=c("mean", "median", "ci95_lb", "ci95_up", "sd", "rsd")))
+  for (i in li){
+    data <- as.numeric(unlist(fit_results$res_par[i,-1]))
+    tmp[fit_results$res_par[i,1],] <- c(mean(data), median(data), quantile(data, probs = c(0.025, 0.975)), sd(data), sd(data)/mean(data))
+  }
+  return(tmp)
+}
+
+update_params <- function(model, rp){
+  setCurrentModel(model)
+  for (i in names(rp)){
+    if (grepl("_0", i, fixed = TRUE)){
+      next
+    }else if (grepl(".InitialValue", i, fixed = TRUE)){
+      k <- str_remove(i, ".InitialValue")
+      #print(getGlobalQuantities(key=k))
+      setGlobalQuantities(key=k, initial_value=rp[i])
+      #print(getGlobalQuantities(key=k))
+    }else{
+      #print(getParameters(key=i))
+      setParameters(key=i, value=rp[i])
+      #print(getParameters(key=i))
+    }
+  }
+  applyInitialState()
+  return(model)
+}
+
+plot_with_ci <- function(fit_results, cond, specie, col, ...){
+  if (specie %in% dimnames(fit_results[[cond]]$simulations)$specie){
+    specie_id <- specie
+  }else{
+    specie_id <- fit_results[[cond]]$mapping[specie]
+  }
+  plot(fit_results[[cond]]$simulations[1,,"Time"], apply(fit_results[[cond]]$simulations[,,specie_id], 2, mean), col=col, type="l", ...)
+  #polygon(x=c(fit_results[[cond]]$simulations[1,,"Time"], rev(fit_results[[cond]]$simulations[1,,"Time"])),
+  #        y=c(apply(fit_results[[cond]]$simulations[,,specie_id], 2, max), rev(apply(fit_results[[cond]]$simulations[,,specie_id], 2, min))),
+  #        col=paste(col, "33", sep=""), border=NA)
+  polygon(x=c(fit_results[[cond]]$simulations[1,,"Time"], rev(fit_results[[cond]]$simulations[1,,"Time"])),
+          y=c(apply(fit_results[[cond]]$simulations[,,specie_id], 2, max), rev(apply(fit_results[[cond]]$simulations[,,specie_id], 2, min))),
+          col=paste(col, "55", sep=""), border=NA)
+  plot_points(fit_results[[cond]]$data_exp$time,
+              fit_results[[cond]]$data_exp[, specie],
+              fit_results[[cond]]$sd[specie], offset=0.03, col=col, cex=1.2)
+}
+
+plot_with_ci_2 <- function(x1, y1, y2, x2, y3, sd_y3, col, h=NULL, ...){
+  plot(x1, y1, type="l", col=col, ...)
+  if (!is.null(h)){
+    abline(h=h)
+  }
+  polygon(x=c(x1, rev(x1)),
+          y=c(apply(y2, 2, max), rev(apply(y2, 2, min))),
+          col=paste(col, "55", sep=""), border=NA)
+  plot_points(x2, y3, sd_y3, offset=0.002, col=col)
+}
+
+plot_with_ci_3 <- function(sim_results, x, specie, col, ...){
+  plot(sim_results[1,,x], apply(sim_results[,,specie], 2, mean), col=col, type="l", ...)
+  polygon(x=c(sim_results[1,,x], rev(sim_results[1,,x])),
+          y=c(apply(sim_results[,,specie], 2, max), rev(apply(sim_results[,,specie], 2, min))),
+          col=paste(col, "55", sep=""), border=NA)
+}
+
+plot_no_ci <- function(fit_results, cond, specie, col, ...){
+  if (specie %in% dimnames(fit_results[[cond]]$simulations)$specie){
+    specie_id <- specie
+  }else{
+    specie_id <- fit_results[[cond]]$mapping[specie]
+  }
+  plot(fit_results[[cond]]$simulations[,"Time"], fit_results[[cond]]$simulations[,specie_id], col=col, type="l", ...)
+  plot_points(fit_results[[cond]]$data_exp$time,
+              fit_results[[cond]]$data_exp[, specie],
+              fit_results[[cond]]$sd[specie], offset=0.03, col=col, cex=1.2)
+}
+
+get_index_closest <- function(x, v){
+  idx <- c()
+  for (i in x){
+    idx <- c(idx, which.min(abs(v - i)))
+  }
+  return(idx)
+}
diff --git a/model/cps/Millard2020_Ecoli_glc_ace_model_1.cps b/model/cps/Millard2020_Ecoli_glc_ace_isotopic_model_1.cps
similarity index 100%
rename from model/cps/Millard2020_Ecoli_glc_ace_model_1.cps
rename to model/cps/Millard2020_Ecoli_glc_ace_isotopic_model_1.cps
diff --git a/model/cps/Millard2020_Ecoli_glc_ace_model_2.cps b/model/cps/Millard2020_Ecoli_glc_ace_isotopic_model_2.cps
similarity index 100%
rename from model/cps/Millard2020_Ecoli_glc_ace_model_2.cps
rename to model/cps/Millard2020_Ecoli_glc_ace_isotopic_model_2.cps
diff --git a/model/cps/Millard2020_Ecoli_glc_ace_model_3.cps b/model/cps/Millard2020_Ecoli_glc_ace_isotopic_model_3.cps
similarity index 100%
rename from model/cps/Millard2020_Ecoli_glc_ace_model_3.cps
rename to model/cps/Millard2020_Ecoli_glc_ace_isotopic_model_3.cps
diff --git a/model/cps/Millard2020_Ecoli_glc_ace_model_4.cps b/model/cps/Millard2020_Ecoli_glc_ace_isotopic_model_4.cps
similarity index 100%
rename from model/cps/Millard2020_Ecoli_glc_ace_model_4.cps
rename to model/cps/Millard2020_Ecoli_glc_ace_isotopic_model_4.cps
diff --git a/model/cps/Millard2020_Ecoli_glc_ace_isotopic_model_4_MC.cps b/model/cps/Millard2020_Ecoli_glc_ace_isotopic_model_4_MC.cps
new file mode 100644
index 0000000..432883f
--- /dev/null
+++ b/model/cps/Millard2020_Ecoli_glc_ace_isotopic_model_4_MC.cps
@@ -0,0 +1,3941 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- generated with COPASI 4.27 (Build 217) (http://www.copasi.org) at 2020-12-21T11:39:01Z -->
+<?oxygen RNGSchema="http://www.copasi.org/static/schema/CopasiML.rng" type="xml"?>
+<COPASI xmlns="http://www.copasi.org/static/schema" versionMajor="4" versionMinor="27" versionDevel="217" copasiSourcesModified="0">
+  <ListOfFunctions>
+    <Function key="Function_40" name="growth" type="UserDefined" reversible="unspecified">
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+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T12:10:06Z</dcterms:W3CDTF>
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+</rdf:RDF>
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+      <Expression>
+        Y*X*sink
+      </Expression>
+      <ListOfParameterDescriptions>
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+        <ParameterDescription key="FunctionParameter_263" name="X" order="1" role="product"/>
+        <ParameterDescription key="FunctionParameter_262" name="sink" order="2" role="constant"/>
+      </ListOfParameterDescriptions>
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+    <Function key="Function_41" name="Rate Law for r1" type="UserDefined" reversible="unspecified">
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+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+      </rdf:Description>
+    </dcterms:created>
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+      </MiriamAnnotation>
+      <Expression>
+        V*S/((KM+S)*(1+I/Ki))
+      </Expression>
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+        <ParameterDescription key="FunctionParameter_250" name="S" order="1" role="substrate"/>
+        <ParameterDescription key="FunctionParameter_261" name="KM" order="2" role="constant"/>
+        <ParameterDescription key="FunctionParameter_266" name="I" order="3" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_267" name="Ki" order="4" role="constant"/>
+      </ListOfParameterDescriptions>
+    </Function>
+    <Function key="Function_42" name="ackf_0_m" type="UserDefined" reversible="unspecified">
+      <MiriamAnnotation>
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+        AcP_0/AcP*v_ACK_Vmax*(ACP*ADP)/ (v_ACK_KmACP*v_ACK_KmADP)/((1+ACP/ v_ACK_KmACP+ACE/v_ACK_KmACE)*(1+ADP/v_ACK_KmADP+ATP/v_ACK_KmATP))
+      </Expression>
+      <ListOfParameterDescriptions>
+        <ParameterDescription key="FunctionParameter_272" name="AcP_0" order="0" role="substrate"/>
+        <ParameterDescription key="FunctionParameter_271" name="AcP" order="1" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_270" name="v_ACK_Vmax" order="2" role="constant"/>
+        <ParameterDescription key="FunctionParameter_269" name="ACP" order="3" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_268" name="ADP" order="4" role="constant"/>
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+        <ParameterDescription key="FunctionParameter_274" name="v_ACK_KmADP" order="6" role="constant"/>
+        <ParameterDescription key="FunctionParameter_275" name="ACE" order="7" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_276" name="v_ACK_KmACE" order="8" role="constant"/>
+        <ParameterDescription key="FunctionParameter_277" name="ATP" order="9" role="constant"/>
+        <ParameterDescription key="FunctionParameter_278" name="v_ACK_KmATP" order="10" role="constant"/>
+      </ListOfParameterDescriptions>
+    </Function>
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+      <MiriamAnnotation>
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+    <dcterms:created>
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+        AcP_1/AcP*v_ACK_Vmax*(ACP*ADP)/ (v_ACK_KmACP*v_ACK_KmADP)/((1+ACP/ v_ACK_KmACP+ACE/v_ACK_KmACE)*(1+ADP/v_ACK_KmADP+ATP/v_ACK_KmATP))
+      </Expression>
+      <ListOfParameterDescriptions>
+        <ParameterDescription key="FunctionParameter_289" name="AcP_1" order="0" role="substrate"/>
+        <ParameterDescription key="FunctionParameter_288" name="AcP" order="1" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_287" name="v_ACK_Vmax" order="2" role="constant"/>
+        <ParameterDescription key="FunctionParameter_286" name="ACP" order="3" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_285" name="ADP" order="4" role="constant"/>
+        <ParameterDescription key="FunctionParameter_284" name="v_ACK_KmACP" order="5" role="constant"/>
+        <ParameterDescription key="FunctionParameter_283" name="v_ACK_KmADP" order="6" role="constant"/>
+        <ParameterDescription key="FunctionParameter_282" name="ACE" order="7" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_281" name="v_ACK_KmACE" order="8" role="constant"/>
+        <ParameterDescription key="FunctionParameter_280" name="ATP" order="9" role="constant"/>
+        <ParameterDescription key="FunctionParameter_279" name="v_ACK_KmATP" order="10" role="constant"/>
+      </ListOfParameterDescriptions>
+    </Function>
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+      </Expression>
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+        <ParameterDescription key="FunctionParameter_299" name="Ace" order="1" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_298" name="v_ACK_Vmax" order="2" role="constant"/>
+        <ParameterDescription key="FunctionParameter_297" name="ACE" order="3" role="modifier"/>
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+        <ParameterDescription key="FunctionParameter_295" name="v_ACK_Keq" order="5" role="constant"/>
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+        <ParameterDescription key="FunctionParameter_292" name="ACP" order="8" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_291" name="v_ACK_KmACE" order="9" role="constant"/>
+        <ParameterDescription key="FunctionParameter_290" name="ADP" order="10" role="constant"/>
+        <ParameterDescription key="FunctionParameter_301" name="v_ACK_KmATP" order="11" role="constant"/>
+      </ListOfParameterDescriptions>
+    </Function>
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+        <dcterms:W3CDTF>2019-09-24T11:33:45Z</dcterms:W3CDTF>
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+    </dcterms:created>
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+      </MiriamAnnotation>
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+        Ace_1/Ace*v_ACK_Vmax*(ACE*ATP/v_ACK_Keq)/ (v_ACK_KmACP*v_ACK_KmADP)/((1+ACP/ v_ACK_KmACP+ACE/v_ACK_KmACE)*(1+ADP/v_ACK_KmADP+ATP/v_ACK_KmATP))
+      </Expression>
+      <ListOfParameterDescriptions>
+        <ParameterDescription key="FunctionParameter_313" name="Ace_1" order="0" role="substrate"/>
+        <ParameterDescription key="FunctionParameter_312" name="Ace" order="1" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_311" name="v_ACK_Vmax" order="2" role="constant"/>
+        <ParameterDescription key="FunctionParameter_310" name="ACE" order="3" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_309" name="ATP" order="4" role="constant"/>
+        <ParameterDescription key="FunctionParameter_308" name="v_ACK_Keq" order="5" role="constant"/>
+        <ParameterDescription key="FunctionParameter_307" name="v_ACK_KmACP" order="6" role="constant"/>
+        <ParameterDescription key="FunctionParameter_306" name="v_ACK_KmADP" order="7" role="constant"/>
+        <ParameterDescription key="FunctionParameter_305" name="ACP" order="8" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_304" name="v_ACK_KmACE" order="9" role="constant"/>
+        <ParameterDescription key="FunctionParameter_303" name="ADP" order="10" role="constant"/>
+        <ParameterDescription key="FunctionParameter_302" name="v_ACK_KmATP" order="11" role="constant"/>
+      </ListOfParameterDescriptions>
+    </Function>
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+      <MiriamAnnotation>
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+      </Expression>
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+        <ParameterDescription key="FunctionParameter_321" name="v_PTA_KiACCOA" order="4" role="constant"/>
+        <ParameterDescription key="FunctionParameter_320" name="v_PTA_KmP" order="5" role="constant"/>
+        <ParameterDescription key="FunctionParameter_319" name="v_PTA_KiP" order="6" role="constant"/>
+        <ParameterDescription key="FunctionParameter_318" name="ACP" order="7" role="modifier"/>
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+        <dcterms:W3CDTF>2019-09-24T11:40:53Z</dcterms:W3CDTF>
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+      </Expression>
+      <ListOfParameterDescriptions>
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+        <ParameterDescription key="FunctionParameter_336" name="ACCOA" order="1" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_335" name="v_PTA_Vmax" order="2" role="constant"/>
+        <ParameterDescription key="FunctionParameter_334" name="P" order="3" role="constant"/>
+        <ParameterDescription key="FunctionParameter_333" name="v_PTA_KiACCOA" order="4" role="constant"/>
+        <ParameterDescription key="FunctionParameter_332" name="v_PTA_KmP" order="5" role="constant"/>
+        <ParameterDescription key="FunctionParameter_331" name="v_PTA_KiP" order="6" role="constant"/>
+        <ParameterDescription key="FunctionParameter_330" name="ACP" order="7" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_329" name="v_PTA_KiACP" order="8" role="constant"/>
+        <ParameterDescription key="FunctionParameter_328" name="COA" order="9" role="constant"/>
+        <ParameterDescription key="FunctionParameter_327" name="v_PTA_KiCOA" order="10" role="constant"/>
+        <ParameterDescription key="FunctionParameter_326" name="v_PTA_KmACP" order="11" role="constant"/>
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+        <dcterms:W3CDTF>2019-09-24T11:32:27Z</dcterms:W3CDTF>
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+        (AcP_0/AcP)*v_PTA_Vmax*(ACP*COA/v_PTA_Keq)/ (v_PTA_KiACCOA*v_PTA_KmP)/(1+ACCOA/v_PTA_KiACCOA+P/ v_PTA_KiP+ACP/v_PTA_KiACP+COA/v_PTA_KiCOA+ACCOA*P/ (v_PTA_KiACCOA*v_PTA_KmP)+ACP*COA/(v_PTA_KmACP*v_PTA_KiCOA))
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+        <ParameterDescription key="FunctionParameter_348" name="AcP" order="1" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_347" name="v_PTA_Vmax" order="2" role="constant"/>
+        <ParameterDescription key="FunctionParameter_346" name="ACP" order="3" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_345" name="COA" order="4" role="constant"/>
+        <ParameterDescription key="FunctionParameter_344" name="v_PTA_Keq" order="5" role="constant"/>
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+        <ParameterDescription key="FunctionParameter_342" name="v_PTA_KmP" order="7" role="constant"/>
+        <ParameterDescription key="FunctionParameter_341" name="ACCOA" order="8" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_340" name="P" order="9" role="constant"/>
+        <ParameterDescription key="FunctionParameter_339" name="v_PTA_KiP" order="10" role="constant"/>
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+        <ParameterDescription key="FunctionParameter_351" name="v_PTA_KmACP" order="13" role="constant"/>
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+        (AcP_1/AcP)*v_PTA_Vmax*(ACP*COA/v_PTA_Keq)/ (v_PTA_KiACCOA*v_PTA_KmP)/(1+ACCOA/v_PTA_KiACCOA+P/ v_PTA_KiP+ACP/v_PTA_KiACP+COA/v_PTA_KiCOA+ACCOA*P/ (v_PTA_KiACCOA*v_PTA_KmP)+ACP*COA/(v_PTA_KmACP*v_PTA_KiCOA))
+      </Expression>
+      <ListOfParameterDescriptions>
+        <ParameterDescription key="FunctionParameter_365" name="AcP_1" order="0" role="substrate"/>
+        <ParameterDescription key="FunctionParameter_364" name="AcP" order="1" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_363" name="v_PTA_Vmax" order="2" role="constant"/>
+        <ParameterDescription key="FunctionParameter_362" name="ACP" order="3" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_361" name="COA" order="4" role="constant"/>
+        <ParameterDescription key="FunctionParameter_360" name="v_PTA_Keq" order="5" role="constant"/>
+        <ParameterDescription key="FunctionParameter_359" name="v_PTA_KiACCOA" order="6" role="constant"/>
+        <ParameterDescription key="FunctionParameter_358" name="v_PTA_KmP" order="7" role="constant"/>
+        <ParameterDescription key="FunctionParameter_357" name="ACCOA" order="8" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_356" name="P" order="9" role="constant"/>
+        <ParameterDescription key="FunctionParameter_355" name="v_PTA_KiP" order="10" role="constant"/>
+        <ParameterDescription key="FunctionParameter_354" name="v_PTA_KiACP" order="11" role="constant"/>
+        <ParameterDescription key="FunctionParameter_353" name="v_PTA_KiCOA" order="12" role="constant"/>
+        <ParameterDescription key="FunctionParameter_352" name="v_PTA_KmACP" order="13" role="constant"/>
+      </ListOfParameterDescriptions>
+    </Function>
+    <Function key="Function_50" name="function_sink" type="UserDefined" reversible="unspecified">
+      <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+        <dcterms:W3CDTF>2019-09-24T14:21:54Z</dcterms:W3CDTF>
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+      <Expression>
+        A/At*V*At^n/((At^n+Km)*(1+I/Ki))
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+        <ParameterDescription key="FunctionParameter_379" name="A" order="0" role="substrate"/>
+        <ParameterDescription key="FunctionParameter_378" name="At" order="1" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_377" name="V" order="2" role="constant"/>
+        <ParameterDescription key="FunctionParameter_376" name="n" order="3" role="constant"/>
+        <ParameterDescription key="FunctionParameter_375" name="Km" order="4" role="constant"/>
+        <ParameterDescription key="FunctionParameter_374" name="I" order="5" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_373" name="Ki" order="6" role="constant"/>
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+      </MiriamAnnotation>
+      <Expression>
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+        <ParameterDescription key="FunctionParameter_366" name="Sx" order="0" role="substrate"/>
+        <ParameterDescription key="FunctionParameter_367" name="S" order="1" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_368" name="Vmax" order="2" role="constant"/>
+        <ParameterDescription key="FunctionParameter_369" name="KM" order="3" role="constant"/>
+        <ParameterDescription key="FunctionParameter_370" name="P" order="4" role="modifier"/>
+      </ListOfParameterDescriptions>
+    </Function>
+  </ListOfFunctions>
+  <Model key="Model_1" name="E. coli model - Glc-Ace metabolism" simulationType="time" timeUnit="h" volumeUnit="l" areaUnit="m²" lengthUnit="m" quantityUnit="mmol" type="deterministic" avogadroConstant="6.0221408570000002e+23">
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+Kinetic and isotopic model, inhibition of glycolysis and TCA by acetate.
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+model #4 of Millard et al., 2020
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+      </Metabolite>
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+      </Metabolite>
+      <Metabolite key="Metabolite_9" name="Acet" simulationType="assignment" compartment="Compartment_0" addNoise="false">
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+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_317">
+              <SourceParameter reference="ModelValue_7"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_316">
+              <SourceParameter reference="ModelValue_11"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_315">
+              <SourceParameter reference="ModelValue_8"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_314">
+              <SourceParameter reference="ModelValue_9"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_2" name="ack_f0" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_2">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:28:35Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_1" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_2" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_10" stoichiometry="1"/>
+          <Modifier metabolite="Metabolite_9" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5362" name="v_ACK_Vmax" value="336940"/>
+          <Constant key="Parameter_5361" name="ACP" value="1"/>
+          <Constant key="Parameter_5360" name="ADP" value="0.606"/>
+          <Constant key="Parameter_5359" name="v_ACK_KmACP" value="0.16"/>
+          <Constant key="Parameter_5358" name="v_ACK_KmADP" value="0.5"/>
+          <Constant key="Parameter_5357" name="ACE" value="1"/>
+          <Constant key="Parameter_5356" name="v_ACK_KmACE" value="7"/>
+          <Constant key="Parameter_5355" name="ATP" value="2.4"/>
+          <Constant key="Parameter_5354" name="v_ACK_KmATP" value="0.07"/>
+          <Constant key="Parameter_5678" name="AcP" value="1"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_42" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_272">
+              <SourceParameter reference="Metabolite_1"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_271">
+              <SourceParameter reference="Metabolite_10"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_270">
+              <SourceParameter reference="ModelValue_13"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_269">
+              <SourceParameter reference="Metabolite_10"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_268">
+              <SourceParameter reference="ModelValue_14"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_273">
+              <SourceParameter reference="ModelValue_15"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_274">
+              <SourceParameter reference="ModelValue_16"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_275">
+              <SourceParameter reference="Metabolite_9"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_276">
+              <SourceParameter reference="ModelValue_17"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_277">
+              <SourceParameter reference="ModelValue_18"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_278">
+              <SourceParameter reference="ModelValue_19"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_3" name="sink0" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_3">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:28:46Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_5" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_8" stoichiometry="1"/>
+          <Modifier metabolite="Metabolite_13" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5679" name="V" value="740860"/>
+          <Constant key="Parameter_5677" name="n" value="1"/>
+          <Constant key="Parameter_5680" name="Km" value="24.7592"/>
+          <Constant key="Parameter_5707" name="Ki" value="2.32617"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_50" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_379">
+              <SourceParameter reference="Metabolite_5"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_378">
+              <SourceParameter reference="Metabolite_8"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_377">
+              <SourceParameter reference="ModelValue_21"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_376">
+              <SourceParameter reference="ModelValue_27"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_375">
+              <SourceParameter reference="ModelValue_22"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_374">
+              <SourceParameter reference="Metabolite_13"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_373">
+              <SourceParameter reference="ModelValue_28"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_4" name="ack_r0" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_4">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:34:27Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_2" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_1" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_9" stoichiometry="1"/>
+          <Modifier metabolite="Metabolite_10" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5708" name="v_ACK_Vmax" value="336940"/>
+          <Constant key="Parameter_5706" name="ACE" value="1"/>
+          <Constant key="Parameter_5709" name="ATP" value="2.4"/>
+          <Constant key="Parameter_5691" name="v_ACK_Keq" value="174"/>
+          <Constant key="Parameter_5692" name="v_ACK_KmACP" value="0.16"/>
+          <Constant key="Parameter_5690" name="v_ACK_KmADP" value="0.5"/>
+          <Constant key="Parameter_5693" name="ACP" value="1"/>
+          <Constant key="Parameter_5353" name="v_ACK_KmACE" value="7"/>
+          <Constant key="Parameter_5352" name="ADP" value="0.606"/>
+          <Constant key="Parameter_5351" name="v_ACK_KmATP" value="0.07"/>
+          <Constant key="Parameter_5350" name="Ace" value="1"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_44" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_300">
+              <SourceParameter reference="Metabolite_2"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_299">
+              <SourceParameter reference="Metabolite_9"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_298">
+              <SourceParameter reference="ModelValue_13"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_297">
+              <SourceParameter reference="Metabolite_9"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_296">
+              <SourceParameter reference="ModelValue_18"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_295">
+              <SourceParameter reference="ModelValue_20"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_294">
+              <SourceParameter reference="ModelValue_15"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_293">
+              <SourceParameter reference="ModelValue_16"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_292">
+              <SourceParameter reference="Metabolite_10"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_291">
+              <SourceParameter reference="ModelValue_17"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_290">
+              <SourceParameter reference="ModelValue_14"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_301">
+              <SourceParameter reference="ModelValue_19"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_5" name="pta_r0" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_5">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:35:06Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_1" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_5" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_10" stoichiometry="1"/>
+          <Modifier metabolite="Metabolite_8" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5349" name="v_PTA_Vmax" value="9.56552e+06"/>
+          <Constant key="Parameter_5348" name="ACP" value="1"/>
+          <Constant key="Parameter_5347" name="COA" value="1.22"/>
+          <Constant key="Parameter_5346" name="v_PTA_Keq" value="0.0281"/>
+          <Constant key="Parameter_5345" name="v_PTA_KiACCOA" value="0.2"/>
+          <Constant key="Parameter_5344" name="v_PTA_KmP" value="2.6"/>
+          <Constant key="Parameter_5343" name="ACCOA" value="1"/>
+          <Constant key="Parameter_5342" name="P" value="10"/>
+          <Constant key="Parameter_5341" name="v_PTA_KiP" value="2.6"/>
+          <Constant key="Parameter_5340" name="v_PTA_KiACP" value="0.2"/>
+          <Constant key="Parameter_5339" name="v_PTA_KiCOA" value="0.029"/>
+          <Constant key="Parameter_5338" name="v_PTA_KmACP" value="0.7"/>
+          <Constant key="Parameter_5646" name="AcP" value="1"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_48" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_349">
+              <SourceParameter reference="Metabolite_1"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_348">
+              <SourceParameter reference="Metabolite_10"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_347">
+              <SourceParameter reference="ModelValue_3"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_346">
+              <SourceParameter reference="Metabolite_10"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_345">
+              <SourceParameter reference="ModelValue_11"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_344">
+              <SourceParameter reference="ModelValue_12"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_343">
+              <SourceParameter reference="ModelValue_4"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_342">
+              <SourceParameter reference="ModelValue_5"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_341">
+              <SourceParameter reference="Metabolite_8"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_340">
+              <SourceParameter reference="ModelValue_10"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_339">
+              <SourceParameter reference="ModelValue_6"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_338">
+              <SourceParameter reference="ModelValue_7"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_350">
+              <SourceParameter reference="ModelValue_8"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_351">
+              <SourceParameter reference="ModelValue_9"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_6" name="ack_f1" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_6">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:28:35Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_3" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_4" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_10" stoichiometry="1"/>
+          <Modifier metabolite="Metabolite_9" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5647" name="v_ACK_Vmax" value="336940"/>
+          <Constant key="Parameter_5645" name="ACP" value="1"/>
+          <Constant key="Parameter_5648" name="ADP" value="0.606"/>
+          <Constant key="Parameter_5337" name="v_ACK_KmACP" value="0.16"/>
+          <Constant key="Parameter_5336" name="v_ACK_KmADP" value="0.5"/>
+          <Constant key="Parameter_5335" name="ACE" value="1"/>
+          <Constant key="Parameter_5334" name="v_ACK_KmACE" value="7"/>
+          <Constant key="Parameter_5333" name="ATP" value="2.4"/>
+          <Constant key="Parameter_5332" name="v_ACK_KmATP" value="0.07"/>
+          <Constant key="Parameter_5331" name="AcP" value="1"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_43" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_289">
+              <SourceParameter reference="Metabolite_3"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_288">
+              <SourceParameter reference="Metabolite_10"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_287">
+              <SourceParameter reference="ModelValue_13"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_286">
+              <SourceParameter reference="Metabolite_10"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_285">
+              <SourceParameter reference="ModelValue_14"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_284">
+              <SourceParameter reference="ModelValue_15"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_283">
+              <SourceParameter reference="ModelValue_16"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_282">
+              <SourceParameter reference="Metabolite_9"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_281">
+              <SourceParameter reference="ModelValue_17"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_280">
+              <SourceParameter reference="ModelValue_18"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_279">
+              <SourceParameter reference="ModelValue_19"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_7" name="ack_r1" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_7">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:34:27Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_4" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_3" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_9" stoichiometry="1"/>
+          <Modifier metabolite="Metabolite_10" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5328" name="v_ACK_Vmax" value="336940"/>
+          <Constant key="Parameter_5329" name="ACE" value="1"/>
+          <Constant key="Parameter_5327" name="ATP" value="2.4"/>
+          <Constant key="Parameter_5326" name="v_ACK_Keq" value="174"/>
+          <Constant key="Parameter_5330" name="v_ACK_KmACP" value="0.16"/>
+          <Constant key="Parameter_5325" name="v_ACK_KmADP" value="0.5"/>
+          <Constant key="Parameter_5324" name="ACP" value="1"/>
+          <Constant key="Parameter_5323" name="v_ACK_KmACE" value="7"/>
+          <Constant key="Parameter_5322" name="ADP" value="0.606"/>
+          <Constant key="Parameter_5321" name="v_ACK_KmATP" value="0.07"/>
+          <Constant key="Parameter_5320" name="Ace" value="1"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_45" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_313">
+              <SourceParameter reference="Metabolite_4"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_312">
+              <SourceParameter reference="Metabolite_9"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_311">
+              <SourceParameter reference="ModelValue_13"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_310">
+              <SourceParameter reference="Metabolite_9"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_309">
+              <SourceParameter reference="ModelValue_18"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_308">
+              <SourceParameter reference="ModelValue_20"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_307">
+              <SourceParameter reference="ModelValue_15"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_306">
+              <SourceParameter reference="ModelValue_16"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_305">
+              <SourceParameter reference="Metabolite_10"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_304">
+              <SourceParameter reference="ModelValue_17"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_303">
+              <SourceParameter reference="ModelValue_14"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_302">
+              <SourceParameter reference="ModelValue_19"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_8" name="pta_f1" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_8">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:28:06Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_6" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_3" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_8" stoichiometry="1"/>
+          <Modifier metabolite="Metabolite_10" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5319" name="v_PTA_Vmax" value="9.56552e+06"/>
+          <Constant key="Parameter_5318" name="ACCOA" value="1"/>
+          <Constant key="Parameter_5317" name="P" value="10"/>
+          <Constant key="Parameter_5311" name="ACP" value="1"/>
+          <Constant key="Parameter_5310" name="COA" value="1.22"/>
+          <Constant key="Parameter_5309" name="v_PTA_KiACCOA" value="0.2"/>
+          <Constant key="Parameter_5308" name="v_PTA_KmP" value="2.6"/>
+          <Constant key="Parameter_5307" name="v_PTA_KiP" value="2.6"/>
+          <Constant key="Parameter_5306" name="v_PTA_KiACP" value="0.2"/>
+          <Constant key="Parameter_5305" name="v_PTA_KiCOA" value="0.029"/>
+          <Constant key="Parameter_5304" name="v_PTA_KmACP" value="0.7"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_47" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_337">
+              <SourceParameter reference="Metabolite_6"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_336">
+              <SourceParameter reference="Metabolite_8"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_335">
+              <SourceParameter reference="ModelValue_3"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_334">
+              <SourceParameter reference="ModelValue_10"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_333">
+              <SourceParameter reference="ModelValue_4"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_332">
+              <SourceParameter reference="ModelValue_5"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_331">
+              <SourceParameter reference="ModelValue_6"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_330">
+              <SourceParameter reference="Metabolite_10"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_329">
+              <SourceParameter reference="ModelValue_7"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_328">
+              <SourceParameter reference="ModelValue_11"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_327">
+              <SourceParameter reference="ModelValue_8"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_326">
+              <SourceParameter reference="ModelValue_9"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_9" name="pta_r1" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_9">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:35:06Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_3" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_6" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_10" stoichiometry="1"/>
+          <Modifier metabolite="Metabolite_8" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5303" name="v_PTA_Vmax" value="9.56552e+06"/>
+          <Constant key="Parameter_5302" name="ACP" value="1"/>
+          <Constant key="Parameter_5301" name="COA" value="1.22"/>
+          <Constant key="Parameter_5300" name="v_PTA_Keq" value="0.0281"/>
+          <Constant key="Parameter_5299" name="v_PTA_KiACCOA" value="0.2"/>
+          <Constant key="Parameter_5298" name="v_PTA_KmP" value="2.6"/>
+          <Constant key="Parameter_5297" name="ACCOA" value="1"/>
+          <Constant key="Parameter_5296" name="P" value="10"/>
+          <Constant key="Parameter_5295" name="v_PTA_KiP" value="2.6"/>
+          <Constant key="Parameter_5294" name="v_PTA_KiACP" value="0.2"/>
+          <Constant key="Parameter_5293" name="v_PTA_KiCOA" value="0.029"/>
+          <Constant key="Parameter_5292" name="v_PTA_KmACP" value="0.7"/>
+          <Constant key="Parameter_5291" name="AcP" value="1"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_49" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_365">
+              <SourceParameter reference="Metabolite_3"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_364">
+              <SourceParameter reference="Metabolite_10"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_363">
+              <SourceParameter reference="ModelValue_3"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_362">
+              <SourceParameter reference="Metabolite_10"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_361">
+              <SourceParameter reference="ModelValue_11"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_360">
+              <SourceParameter reference="ModelValue_12"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_359">
+              <SourceParameter reference="ModelValue_4"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_358">
+              <SourceParameter reference="ModelValue_5"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_357">
+              <SourceParameter reference="Metabolite_8"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_356">
+              <SourceParameter reference="ModelValue_10"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_355">
+              <SourceParameter reference="ModelValue_6"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_354">
+              <SourceParameter reference="ModelValue_7"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_353">
+              <SourceParameter reference="ModelValue_8"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_352">
+              <SourceParameter reference="ModelValue_9"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_10" name="sink1" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_10">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:28:46Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_6" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_8" stoichiometry="1"/>
+          <Modifier metabolite="Metabolite_13" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5290" name="n" value="1"/>
+          <Constant key="Parameter_5289" name="Km" value="24.7592"/>
+          <Constant key="Parameter_5288" name="Ki" value="2.32617"/>
+          <Constant key="Parameter_5287" name="V" value="740860"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_50" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_379">
+              <SourceParameter reference="Metabolite_6"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_378">
+              <SourceParameter reference="Metabolite_8"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_377">
+              <SourceParameter reference="ModelValue_21"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_376">
+              <SourceParameter reference="ModelValue_27"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_375">
+              <SourceParameter reference="ModelValue_22"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_374">
+              <SourceParameter reference="Metabolite_13"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_373">
+              <SourceParameter reference="ModelValue_28"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_11" name="growth" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_11">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T12:07:54Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_7" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfConstants>
+          <Constant key="Parameter_5286" name="Y" value="9.98043e-05"/>
+          <Constant key="Parameter_5285" name="sink" value="29662.2"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_40" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_264">
+              <SourceParameter reference="ModelValue_24"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_263">
+              <SourceParameter reference="Metabolite_7"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_262">
+              <SourceParameter reference="ModelValue_23"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_12" name="trp_ace_f0" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_12">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-02-26T10:33:46Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_2" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_11" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_9" stoichiometry="1"/>
+          <Modifier metabolite="Metabolite_13" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5284" name="Vmax" value="480035"/>
+          <Constant key="Parameter_5283" name="KM" value="33.1536"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_51" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_366">
+              <SourceParameter reference="Metabolite_2"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_367">
+              <SourceParameter reference="Metabolite_9"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_368">
+              <SourceParameter reference="ModelValue_31"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_369">
+              <SourceParameter reference="ModelValue_30"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_370">
+              <SourceParameter reference="Metabolite_13"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_13" name="trp_ace_f1" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_13">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-02-26T10:33:46Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_4" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_12" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_9" stoichiometry="1"/>
+          <Modifier metabolite="Metabolite_13" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5282" name="Vmax" value="480035"/>
+          <Constant key="Parameter_5281" name="KM" value="33.1536"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_51" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_366">
+              <SourceParameter reference="Metabolite_4"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_367">
+              <SourceParameter reference="Metabolite_9"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_368">
+              <SourceParameter reference="ModelValue_31"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_369">
+              <SourceParameter reference="ModelValue_30"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_370">
+              <SourceParameter reference="Metabolite_13"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_14" name="trp_ace_r0" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_14">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-02-26T10:33:46Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_11" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_2" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_13" stoichiometry="1"/>
+          <Modifier metabolite="Metabolite_9" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5280" name="Vmax" value="480035"/>
+          <Constant key="Parameter_5279" name="KM" value="33.1536"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_51" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_366">
+              <SourceParameter reference="Metabolite_11"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_367">
+              <SourceParameter reference="Metabolite_13"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_368">
+              <SourceParameter reference="ModelValue_31"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_369">
+              <SourceParameter reference="ModelValue_30"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_370">
+              <SourceParameter reference="Metabolite_9"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_15" name="trp_ace_r1" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_15">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-02-26T10:33:46Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_12" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_4" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_13" stoichiometry="1"/>
+          <Modifier metabolite="Metabolite_9" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5278" name="Vmax" value="480035"/>
+          <Constant key="Parameter_5277" name="KM" value="33.1536"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_51" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_366">
+              <SourceParameter reference="Metabolite_12"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_367">
+              <SourceParameter reference="Metabolite_13"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_368">
+              <SourceParameter reference="ModelValue_31"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_369">
+              <SourceParameter reference="ModelValue_30"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_370">
+              <SourceParameter reference="Metabolite_9"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+    </ListOfReactions>
+    <ListOfModelParameterSets activeSet="ModelParameterSet_1">
+      <ModelParameterSet key="ModelParameterSet_1" name="Initial State">
+        <MiriamAnnotation>
+<rdf:RDF
+xmlns:dcterms="http://purl.org/dc/terms/"
+xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+<rdf:Description rdf:about="#ModelParameterSet_1">
+<dcterms:created>
+<rdf:Description>
+<dcterms:W3CDTF>2020-12-21T11:38:18Z</dcterms:W3CDTF>
+</rdf:Description>
+</dcterms:created>
+</rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ModelParameterGroup cn="String=Initial Time" type="Group">
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism" value="0" type="Model" simulationType="time"/>
+        </ModelParameterGroup>
+        <ModelParameterGroup cn="String=Initial Compartment Sizes" type="Group">
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]" value="1" type="Compartment" simulationType="fixed"/>
+        </ModelParameterGroup>
+        <ModelParameterGroup cn="String=Initial Species Values" type="Group">
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Glc]" value="7.7685596306705115e+21" type="Species" simulationType="ode"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[AcP0]" value="5.9326521219652067e+21" type="Species" simulationType="reactions"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace0]" value="5.7661288689345823e+20" type="Species" simulationType="reactions"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[AcP1]" value="0" type="Species" simulationType="reactions"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace1]" value="0" type="Species" simulationType="reactions"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[AcCoA0]" value="8.7923256512199996e+20" type="Species" simulationType="reactions"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[AcCoA1]" value="6.0221408570000005e+18" type="Species" simulationType="reactions"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[X]" value="4.2154949148271837e+19" type="Species" simulationType="ode"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[AcCoAt]" value="8.8525470597899996e+20" type="Species" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Acet]" value="5.7661288689345823e+20" type="Species" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[AcPt]" value="5.9326521219652067e+21" type="Species" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace0_out]" value="5.5403817796619515e+20" type="Species" simulationType="ode"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace1_out]" value="6.0153929090582774e+18" type="Species" simulationType="ode"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Acet_out]" value="5.6005357087525346e+20" type="Species" simulationType="assignment"/>
+        </ModelParameterGroup>
+        <ModelParameterGroup cn="String=Initial Global Quantities" type="Group">
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[AcCoA]" value="1.47" type="ModelValue" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[AcP]" value="9.8514004617962829" type="ModelValue" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[Ace]" value="0.95748820990000005" type="ModelValue" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Vmax]" value="9565521.7634551357" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACCOA]" value="0.20000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmP]" value="2.6000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiP]" value="2.6000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACP]" value="0.20000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiCOA]" value="0.029000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmACP]" value="0.69999999999999996" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[P]" value="10" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[CoA]" value="1.22" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Keq]" value="0.0281" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Vmax]" value="336940.01763224584" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ADP]" value="0.60599999999999998" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACP]" value="0.16" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmADP]" value="0.5" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACE]" value="7" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ATP]" value="2.3999999999999999" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmATP]" value="0.070000000000000007" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Keq]" value="174" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Vmax]" value="740859.87349901034" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Km]" value="24.759179607035055" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[v_sink]" value="29662.247991208762" type="ModelValue" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[Y]" value="9.980425734506176e-05" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[Ace_enr]" value="0" type="ModelValue" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[volume]" value="0.0017700000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[sink_n]" value="1" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Ki]" value="2.3261654310710522" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_STEADY_STATE]" value="0" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Km]" value="33.153580532659561" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Vmax]" value="480034.55363364267" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[growth_rate]" value="2.9604186319476407" type="ModelValue" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[acetate_net]" value="376.69231041352646" type="ModelValue" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Ki]" value="60" type="ModelValue" simulationType="fixed"/>
+        </ModelParameterGroup>
+        <ModelParameterGroup cn="String=Kinetic Parameters" type="Group">
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt],ParameterGroup=Parameters,Parameter=V" value="5557.6400000000003" type="ReactionParameter" simulationType="fixed"/>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt],ParameterGroup=Parameters,Parameter=KM" value="0.02" type="ReactionParameter" simulationType="fixed"/>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt],ParameterGroup=Parameters,Parameter=Ki" value="36.677599999999998" type="ReactionParameter" simulationType="fixed"/>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f0]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f0],ParameterGroup=Parameters,Parameter=v_PTA_Vmax" value="9565521.7634551357" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f0],ParameterGroup=Parameters,Parameter=P" value="10" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[P],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f0],ParameterGroup=Parameters,Parameter=COA" value="1.22" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[CoA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f0],ParameterGroup=Parameters,Parameter=v_PTA_KiACCOA" value="0.20000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACCOA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f0],ParameterGroup=Parameters,Parameter=v_PTA_KmP" value="2.6000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f0],ParameterGroup=Parameters,Parameter=v_PTA_KiP" value="2.6000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f0],ParameterGroup=Parameters,Parameter=v_PTA_KiACP" value="0.20000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f0],ParameterGroup=Parameters,Parameter=v_PTA_KiCOA" value="0.029000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiCOA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f0],ParameterGroup=Parameters,Parameter=v_PTA_KmACP" value="0.69999999999999996" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_f0]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_f0],ParameterGroup=Parameters,Parameter=v_ACK_Vmax" value="336940.01763224584" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_f0],ParameterGroup=Parameters,Parameter=ADP" value="0.60599999999999998" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ADP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_f0],ParameterGroup=Parameters,Parameter=v_ACK_KmACP" value="0.16" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_f0],ParameterGroup=Parameters,Parameter=v_ACK_KmADP" value="0.5" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmADP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_f0],ParameterGroup=Parameters,Parameter=v_ACK_KmACE" value="7" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACE],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_f0],ParameterGroup=Parameters,Parameter=ATP" value="2.3999999999999999" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ATP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_f0],ParameterGroup=Parameters,Parameter=v_ACK_KmATP" value="0.070000000000000007" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmATP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink0]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink0],ParameterGroup=Parameters,Parameter=V" value="740859.87349901034" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink0],ParameterGroup=Parameters,Parameter=n" value="1" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[sink_n],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink0],ParameterGroup=Parameters,Parameter=Km" value="24.759179607035055" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Km],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink0],ParameterGroup=Parameters,Parameter=Ki" value="2.3261654310710522" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Ki],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_r0]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_r0],ParameterGroup=Parameters,Parameter=v_ACK_Vmax" value="336940.01763224584" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_r0],ParameterGroup=Parameters,Parameter=ATP" value="2.3999999999999999" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ATP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_r0],ParameterGroup=Parameters,Parameter=v_ACK_Keq" value="174" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Keq],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_r0],ParameterGroup=Parameters,Parameter=v_ACK_KmACP" value="0.16" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_r0],ParameterGroup=Parameters,Parameter=v_ACK_KmADP" value="0.5" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmADP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_r0],ParameterGroup=Parameters,Parameter=v_ACK_KmACE" value="7" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACE],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_r0],ParameterGroup=Parameters,Parameter=ADP" value="0.60599999999999998" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ADP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_r0],ParameterGroup=Parameters,Parameter=v_ACK_KmATP" value="0.070000000000000007" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmATP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r0]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r0],ParameterGroup=Parameters,Parameter=v_PTA_Vmax" value="9565521.7634551357" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r0],ParameterGroup=Parameters,Parameter=COA" value="1.22" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[CoA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r0],ParameterGroup=Parameters,Parameter=v_PTA_Keq" value="0.0281" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Keq],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r0],ParameterGroup=Parameters,Parameter=v_PTA_KiACCOA" value="0.20000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACCOA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r0],ParameterGroup=Parameters,Parameter=v_PTA_KmP" value="2.6000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r0],ParameterGroup=Parameters,Parameter=P" value="10" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[P],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r0],ParameterGroup=Parameters,Parameter=v_PTA_KiP" value="2.6000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r0],ParameterGroup=Parameters,Parameter=v_PTA_KiACP" value="0.20000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r0],ParameterGroup=Parameters,Parameter=v_PTA_KiCOA" value="0.029000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiCOA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r0],ParameterGroup=Parameters,Parameter=v_PTA_KmACP" value="0.69999999999999996" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_f1]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_f1],ParameterGroup=Parameters,Parameter=v_ACK_Vmax" value="336940.01763224584" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_f1],ParameterGroup=Parameters,Parameter=ADP" value="0.60599999999999998" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ADP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_f1],ParameterGroup=Parameters,Parameter=v_ACK_KmACP" value="0.16" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_f1],ParameterGroup=Parameters,Parameter=v_ACK_KmADP" value="0.5" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmADP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_f1],ParameterGroup=Parameters,Parameter=v_ACK_KmACE" value="7" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACE],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_f1],ParameterGroup=Parameters,Parameter=ATP" value="2.3999999999999999" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ATP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_f1],ParameterGroup=Parameters,Parameter=v_ACK_KmATP" value="0.070000000000000007" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmATP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_r1]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_r1],ParameterGroup=Parameters,Parameter=v_ACK_Vmax" value="336940.01763224584" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_r1],ParameterGroup=Parameters,Parameter=ATP" value="2.3999999999999999" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ATP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_r1],ParameterGroup=Parameters,Parameter=v_ACK_Keq" value="174" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Keq],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_r1],ParameterGroup=Parameters,Parameter=v_ACK_KmACP" value="0.16" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_r1],ParameterGroup=Parameters,Parameter=v_ACK_KmADP" value="0.5" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmADP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_r1],ParameterGroup=Parameters,Parameter=v_ACK_KmACE" value="7" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACE],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_r1],ParameterGroup=Parameters,Parameter=ADP" value="0.60599999999999998" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ADP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ack_r1],ParameterGroup=Parameters,Parameter=v_ACK_KmATP" value="0.070000000000000007" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmATP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f1]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f1],ParameterGroup=Parameters,Parameter=v_PTA_Vmax" value="9565521.7634551357" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f1],ParameterGroup=Parameters,Parameter=P" value="10" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[P],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f1],ParameterGroup=Parameters,Parameter=COA" value="1.22" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[CoA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f1],ParameterGroup=Parameters,Parameter=v_PTA_KiACCOA" value="0.20000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACCOA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f1],ParameterGroup=Parameters,Parameter=v_PTA_KmP" value="2.6000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f1],ParameterGroup=Parameters,Parameter=v_PTA_KiP" value="2.6000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f1],ParameterGroup=Parameters,Parameter=v_PTA_KiACP" value="0.20000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f1],ParameterGroup=Parameters,Parameter=v_PTA_KiCOA" value="0.029000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiCOA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_f1],ParameterGroup=Parameters,Parameter=v_PTA_KmACP" value="0.69999999999999996" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r1]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r1],ParameterGroup=Parameters,Parameter=v_PTA_Vmax" value="9565521.7634551357" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r1],ParameterGroup=Parameters,Parameter=COA" value="1.22" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[CoA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r1],ParameterGroup=Parameters,Parameter=v_PTA_Keq" value="0.0281" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Keq],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r1],ParameterGroup=Parameters,Parameter=v_PTA_KiACCOA" value="0.20000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACCOA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r1],ParameterGroup=Parameters,Parameter=v_PTA_KmP" value="2.6000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r1],ParameterGroup=Parameters,Parameter=P" value="10" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[P],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r1],ParameterGroup=Parameters,Parameter=v_PTA_KiP" value="2.6000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r1],ParameterGroup=Parameters,Parameter=v_PTA_KiACP" value="0.20000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r1],ParameterGroup=Parameters,Parameter=v_PTA_KiCOA" value="0.029000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiCOA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta_r1],ParameterGroup=Parameters,Parameter=v_PTA_KmACP" value="0.69999999999999996" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink1]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink1],ParameterGroup=Parameters,Parameter=n" value="1" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[sink_n],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink1],ParameterGroup=Parameters,Parameter=Km" value="24.759179607035055" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Km],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink1],ParameterGroup=Parameters,Parameter=Ki" value="2.3261654310710522" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Ki],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink1],ParameterGroup=Parameters,Parameter=V" value="740859.87349901034" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[growth]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[growth],ParameterGroup=Parameters,Parameter=Y" value="9.980425734506176e-05" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[Y],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[growth],ParameterGroup=Parameters,Parameter=sink" value="29662.247991208762" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[v_sink],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[trp_ace_f0]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[trp_ace_f0],ParameterGroup=Parameters,Parameter=Vmax" value="480034.55363364267" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[trp_ace_f0],ParameterGroup=Parameters,Parameter=KM" value="33.153580532659561" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Km],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[trp_ace_f1]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[trp_ace_f1],ParameterGroup=Parameters,Parameter=Vmax" value="480034.55363364267" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[trp_ace_f1],ParameterGroup=Parameters,Parameter=KM" value="33.153580532659561" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Km],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[trp_ace_r0]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[trp_ace_r0],ParameterGroup=Parameters,Parameter=Vmax" value="480034.55363364267" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[trp_ace_r0],ParameterGroup=Parameters,Parameter=KM" value="33.153580532659561" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Km],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[trp_ace_r1]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[trp_ace_r1],ParameterGroup=Parameters,Parameter=Vmax" value="480034.55363364267" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[trp_ace_r1],ParameterGroup=Parameters,Parameter=KM" value="33.153580532659561" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Km],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+        </ModelParameterGroup>
+      </ModelParameterSet>
+    </ListOfModelParameterSets>
+    <StateTemplate>
+      <StateTemplateVariable objectReference="Model_1"/>
+      <StateTemplateVariable objectReference="Metabolite_0"/>
+      <StateTemplateVariable objectReference="Metabolite_7"/>
+      <StateTemplateVariable objectReference="Metabolite_11"/>
+      <StateTemplateVariable objectReference="Metabolite_12"/>
+      <StateTemplateVariable objectReference="Metabolite_6"/>
+      <StateTemplateVariable objectReference="Metabolite_2"/>
+      <StateTemplateVariable objectReference="Metabolite_4"/>
+      <StateTemplateVariable objectReference="Metabolite_5"/>
+      <StateTemplateVariable objectReference="Metabolite_3"/>
+      <StateTemplateVariable objectReference="Metabolite_1"/>
+      <StateTemplateVariable objectReference="Metabolite_8"/>
+      <StateTemplateVariable objectReference="Metabolite_9"/>
+      <StateTemplateVariable objectReference="Metabolite_10"/>
+      <StateTemplateVariable objectReference="Metabolite_13"/>
+      <StateTemplateVariable objectReference="ModelValue_0"/>
+      <StateTemplateVariable objectReference="ModelValue_1"/>
+      <StateTemplateVariable objectReference="ModelValue_2"/>
+      <StateTemplateVariable objectReference="ModelValue_23"/>
+      <StateTemplateVariable objectReference="ModelValue_25"/>
+      <StateTemplateVariable objectReference="ModelValue_32"/>
+      <StateTemplateVariable objectReference="ModelValue_33"/>
+      <StateTemplateVariable objectReference="Compartment_0"/>
+      <StateTemplateVariable objectReference="ModelValue_3"/>
+      <StateTemplateVariable objectReference="ModelValue_4"/>
+      <StateTemplateVariable objectReference="ModelValue_5"/>
+      <StateTemplateVariable objectReference="ModelValue_6"/>
+      <StateTemplateVariable objectReference="ModelValue_7"/>
+      <StateTemplateVariable objectReference="ModelValue_8"/>
+      <StateTemplateVariable objectReference="ModelValue_9"/>
+      <StateTemplateVariable objectReference="ModelValue_10"/>
+      <StateTemplateVariable objectReference="ModelValue_11"/>
+      <StateTemplateVariable objectReference="ModelValue_12"/>
+      <StateTemplateVariable objectReference="ModelValue_13"/>
+      <StateTemplateVariable objectReference="ModelValue_14"/>
+      <StateTemplateVariable objectReference="ModelValue_15"/>
+      <StateTemplateVariable objectReference="ModelValue_16"/>
+      <StateTemplateVariable objectReference="ModelValue_17"/>
+      <StateTemplateVariable objectReference="ModelValue_18"/>
+      <StateTemplateVariable objectReference="ModelValue_19"/>
+      <StateTemplateVariable objectReference="ModelValue_20"/>
+      <StateTemplateVariable objectReference="ModelValue_21"/>
+      <StateTemplateVariable objectReference="ModelValue_22"/>
+      <StateTemplateVariable objectReference="ModelValue_24"/>
+      <StateTemplateVariable objectReference="ModelValue_26"/>
+      <StateTemplateVariable objectReference="ModelValue_27"/>
+      <StateTemplateVariable objectReference="ModelValue_28"/>
+      <StateTemplateVariable objectReference="ModelValue_29"/>
+      <StateTemplateVariable objectReference="ModelValue_30"/>
+      <StateTemplateVariable objectReference="ModelValue_31"/>
+      <StateTemplateVariable objectReference="ModelValue_34"/>
+    </StateTemplate>
+    <InitialState type="initialState">
+      0 7.7685596306705115e+21 4.2154949148271837e+19 5.5403817796619515e+20 6.0153929090582774e+18 6.0221408570000005e+18 5.7661288689345823e+20 0 8.7923256512199996e+20 0 5.9326521219652067e+21 8.8525470597899996e+20 5.7661288689345823e+20 5.9326521219652067e+21 5.6005357087525346e+20 1.47 9.8514004617962829 0.95748820990000005 29662.247991208762 0 2.9604186319476407 376.69231041352646 1 9565521.7634551357 0.20000000000000001 2.6000000000000001 2.6000000000000001 0.20000000000000001 0.029000000000000001 0.69999999999999996 10 1.22 0.0281 336940.01763224584 0.60599999999999998 0.16 0.5 7 2.3999999999999999 0.070000000000000007 174 740859.87349901034 24.759179607035055 9.980425734506176e-05 0.0017700000000000001 1 2.3261654310710522 0 33.153580532659561 480034.55363364267 60 
+    </InitialState>
+  </Model>
+  <ListOfTasks>
+    <Task key="Task_15" name="Steady-State" type="steadyState" scheduled="false" updateModel="false">
+      <Report reference="Report_10" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="JacobianRequested" type="bool" value="1"/>
+        <Parameter name="StabilityAnalysisRequested" type="bool" value="1"/>
+      </Problem>
+      <Method name="Enhanced Newton" type="EnhancedNewton">
+        <Parameter name="Resolution" type="unsignedFloat" value="1.0000000000000001e-09"/>
+        <Parameter name="Derivation Factor" type="unsignedFloat" value="0.001"/>
+        <Parameter name="Use Newton" type="bool" value="1"/>
+        <Parameter name="Use Integration" type="bool" value="1"/>
+        <Parameter name="Use Back Integration" type="bool" value="0"/>
+        <Parameter name="Accept Negative Concentrations" type="bool" value="0"/>
+        <Parameter name="Iteration Limit" type="unsignedInteger" value="50"/>
+        <Parameter name="Maximum duration for forward integration" type="unsignedFloat" value="1000000000"/>
+        <Parameter name="Maximum duration for backward integration" type="unsignedFloat" value="1000000"/>
+      </Method>
+    </Task>
+    <Task key="Task_16" name="Time-Course" type="timeCourse" scheduled="false" updateModel="false">
+      <Problem>
+        <Parameter name="AutomaticStepSize" type="bool" value="0"/>
+        <Parameter name="StepNumber" type="unsignedInteger" value="1000"/>
+        <Parameter name="StepSize" type="float" value="0.01"/>
+        <Parameter name="Duration" type="float" value="10"/>
+        <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
+        <Parameter name="OutputStartTime" type="float" value="0"/>
+        <Parameter name="Output Event" type="bool" value="1"/>
+        <Parameter name="Start in Steady State" type="bool" value="0"/>
+        <Parameter name="Use Values" type="bool" value="0"/>
+        <Parameter name="Values" type="string" value=""/>
+      </Problem>
+      <Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
+        <Parameter name="Integrate Reduced Model" type="bool" value="0"/>
+        <Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-07"/>
+        <Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
+        <Parameter name="Max Internal Steps" type="unsignedInteger" value="100000"/>
+        <Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
+      </Method>
+    </Task>
+    <Task key="Task_17" name="Scan" type="scan" scheduled="false" updateModel="false">
+      <Problem>
+        <Parameter name="Subtask" type="unsignedInteger" value="0"/>
+        <ParameterGroup name="ScanItems">
+          <ParameterGroup name="ScanItem">
+            <Parameter name="Number of steps" type="unsignedInteger" value="100"/>
+            <Parameter name="Type" type="unsignedInteger" value="1"/>
+            <Parameter name="Object" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace0_out],Reference=InitialConcentration"/>
+            <Parameter name="Minimum" type="float" value="0.0011000000000000001"/>
+            <Parameter name="Maximum" type="float" value="99.989999999999995"/>
+            <Parameter name="log" type="bool" value="1"/>
+            <Parameter name="Values" type="string" value=""/>
+            <Parameter name="Use Values" type="bool" value="0"/>
+          </ParameterGroup>
+        </ParameterGroup>
+        <Parameter name="Output in subtask" type="bool" value="0"/>
+        <Parameter name="Adjust initial conditions" type="bool" value="0"/>
+        <Parameter name="Continue on Error" type="bool" value="0"/>
+      </Problem>
+      <Method name="Scan Framework" type="ScanFramework">
+      </Method>
+    </Task>
+    <Task key="Task_18" name="Elementary Flux Modes" type="fluxMode" scheduled="false" updateModel="false">
+      <Report reference="Report_11" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+      </Problem>
+      <Method name="EFM Algorithm" type="EFMAlgorithm">
+      </Method>
+    </Task>
+    <Task key="Task_19" name="Optimization" type="optimization" scheduled="false" updateModel="false">
+      <Report reference="Report_12" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="Subtask" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
+        <ParameterText name="ObjectiveExpression" type="expression">
+          
+        </ParameterText>
+        <Parameter name="Maximize" type="bool" value="0"/>
+        <Parameter name="Randomize Start Values" type="bool" value="0"/>
+        <Parameter name="Calculate Statistics" type="bool" value="1"/>
+        <ParameterGroup name="OptimizationItemList">
+        </ParameterGroup>
+        <ParameterGroup name="OptimizationConstraintList">
+        </ParameterGroup>
+      </Problem>
+      <Method name="Random Search" type="RandomSearch">
+        <Parameter name="Log Verbosity" type="unsignedInteger" value="0"/>
+        <Parameter name="Number of Iterations" type="unsignedInteger" value="100000"/>
+        <Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
+        <Parameter name="Seed" type="unsignedInteger" value="0"/>
+      </Method>
+    </Task>
+    <Task key="Task_20" name="Parameter Estimation" type="parameterFitting" scheduled="false" updateModel="false">
+      <Report reference="Report_13" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="Maximize" type="bool" value="0"/>
+        <Parameter name="Randomize Start Values" type="bool" value="0"/>
+        <Parameter name="Calculate Statistics" type="bool" value="1"/>
+        <ParameterGroup name="OptimizationItemList">
+          <ParameterGroup name="FitItem">
+            <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace0_out],Reference=InitialConcentration"/>
+            <Parameter name="LowerBound" type="cn" value="0.92"/>
+            <Parameter name="UpperBound" type="cn" value="0.98"/>
+            <Parameter name="StartValue" type="float" value="0.92000202440000001"/>
+            <ParameterGroup name="Affected Experiments">
+              <Parameter name="Experiment Key" type="key" value="Experiment_1"/>
+            </ParameterGroup>
+            <ParameterGroup name="Affected Cross Validation Experiments">
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="FitItem">
+            <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[X],Reference=InitialConcentration"/>
+            <Parameter name="LowerBound" type="cn" value="0.05"/>
+            <Parameter name="UpperBound" type="cn" value="0.07"/>
+            <Parameter name="StartValue" type="float" value="0.069999938807927209"/>
+            <ParameterGroup name="Affected Experiments">
+              <Parameter name="Experiment Key" type="key" value="Experiment_1"/>
+            </ParameterGroup>
+            <ParameterGroup name="Affected Cross Validation Experiments">
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="FitItem">
+            <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Glc],Reference=InitialConcentration"/>
+            <Parameter name="LowerBound" type="cn" value="12.4"/>
+            <Parameter name="UpperBound" type="cn" value="12.9"/>
+            <Parameter name="StartValue" type="float" value="12.899996554614816"/>
+            <ParameterGroup name="Affected Experiments">
+              <Parameter name="Experiment Key" type="key" value="Experiment_1"/>
+            </ParameterGroup>
+            <ParameterGroup name="Affected Cross Validation Experiments">
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="FitItem">
+            <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace0_out],Reference=InitialConcentration"/>
+            <Parameter name="LowerBound" type="cn" value="8.8"/>
+            <Parameter name="UpperBound" type="cn" value="9.1"/>
+            <Parameter name="StartValue" type="float" value="9.0039719980000008"/>
+            <ParameterGroup name="Affected Experiments">
+              <Parameter name="Experiment Key" type="key" value="Experiment_0"/>
+            </ParameterGroup>
+            <ParameterGroup name="Affected Cross Validation Experiments">
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="FitItem">
+            <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Glc],Reference=InitialConcentration"/>
+            <Parameter name="LowerBound" type="cn" value="12.3"/>
+            <Parameter name="UpperBound" type="cn" value="15"/>
+            <Parameter name="StartValue" type="float" value="14.192231189999999"/>
+            <ParameterGroup name="Affected Experiments">
+              <Parameter name="Experiment Key" type="key" value="Experiment_0"/>
+            </ParameterGroup>
+            <ParameterGroup name="Affected Cross Validation Experiments">
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="FitItem">
+            <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[X],Reference=InitialConcentration"/>
+            <Parameter name="LowerBound" type="cn" value="0.058"/>
+            <Parameter name="UpperBound" type="cn" value="0.08"/>
+            <Parameter name="StartValue" type="float" value="0.067137097156835912"/>
+            <ParameterGroup name="Affected Experiments">
+              <Parameter name="Experiment Key" type="key" value="Experiment_0"/>
+            </ParameterGroup>
+            <ParameterGroup name="Affected Cross Validation Experiments">
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="FitItem">
+            <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Glc],Reference=InitialConcentration"/>
+            <Parameter name="LowerBound" type="cn" value="12.5"/>
+            <Parameter name="UpperBound" type="cn" value="14"/>
+            <Parameter name="StartValue" type="float" value="12.50000275"/>
+            <ParameterGroup name="Affected Experiments">
+              <Parameter name="Experiment Key" type="key" value="Experiment_2"/>
+            </ParameterGroup>
+            <ParameterGroup name="Affected Cross Validation Experiments">
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="FitItem">
+            <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[X],Reference=InitialConcentration"/>
+            <Parameter name="LowerBound" type="cn" value="0.04"/>
+            <Parameter name="UpperBound" type="cn" value="0.08"/>
+            <Parameter name="StartValue" type="float" value="0.072266202289999998"/>
+            <ParameterGroup name="Affected Experiments">
+              <Parameter name="Experiment Key" type="key" value="Experiment_2"/>
+            </ParameterGroup>
+            <ParameterGroup name="Affected Cross Validation Experiments">
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="FitItem">
+            <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace0_out],Reference=InitialConcentration"/>
+            <Parameter name="LowerBound" type="cn" value="29.5"/>
+            <Parameter name="UpperBound" type="cn" value="30.5"/>
+            <Parameter name="StartValue" type="float" value="30.244809336536925"/>
+            <ParameterGroup name="Affected Experiments">
+              <Parameter name="Experiment Key" type="key" value="Experiment_2"/>
+            </ParameterGroup>
+            <ParameterGroup name="Affected Cross Validation Experiments">
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="FitItem">
+            <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Km],Reference=InitialValue"/>
+            <Parameter name="LowerBound" type="cn" value="1"/>
+            <Parameter name="UpperBound" type="cn" value="100"/>
+            <Parameter name="StartValue" type="float" value="33.153580529999999"/>
+            <ParameterGroup name="Affected Experiments">
+            </ParameterGroup>
+            <ParameterGroup name="Affected Cross Validation Experiments">
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="FitItem">
+            <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Vmax],Reference=InitialValue"/>
+            <Parameter name="LowerBound" type="cn" value="1e+3"/>
+            <Parameter name="UpperBound" type="cn" value="1e+08"/>
+            <Parameter name="StartValue" type="float" value="480034.55363364267"/>
+            <ParameterGroup name="Affected Experiments">
+            </ParameterGroup>
+            <ParameterGroup name="Affected Cross Validation Experiments">
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="FitItem">
+            <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[Y],Reference=InitialValue"/>
+            <Parameter name="LowerBound" type="cn" value="3.05738e-05"/>
+            <Parameter name="UpperBound" type="cn" value="0.000229304"/>
+            <Parameter name="StartValue" type="float" value="9.980425734506176e-05"/>
+            <ParameterGroup name="Affected Experiments">
+            </ParameterGroup>
+            <ParameterGroup name="Affected Cross Validation Experiments">
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="FitItem">
+            <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Ki],Reference=InitialValue"/>
+            <Parameter name="LowerBound" type="cn" value="1"/>
+            <Parameter name="UpperBound" type="cn" value="1e3"/>
+            <Parameter name="StartValue" type="float" value="2.3261654310710522"/>
+            <ParameterGroup name="Affected Experiments">
+            </ParameterGroup>
+            <ParameterGroup name="Affected Cross Validation Experiments">
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="FitItem">
+            <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Km],Reference=InitialValue"/>
+            <Parameter name="LowerBound" type="cn" value="1"/>
+            <Parameter name="UpperBound" type="cn" value="1e3"/>
+            <Parameter name="StartValue" type="float" value="24.759179607035055"/>
+            <ParameterGroup name="Affected Experiments">
+            </ParameterGroup>
+            <ParameterGroup name="Affected Cross Validation Experiments">
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="FitItem">
+            <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Vmax],Reference=InitialValue"/>
+            <Parameter name="LowerBound" type="cn" value="3818.88"/>
+            <Parameter name="UpperBound" type="cn" value="1e8"/>
+            <Parameter name="StartValue" type="float" value="740859.87349999999"/>
+            <ParameterGroup name="Affected Experiments">
+            </ParameterGroup>
+            <ParameterGroup name="Affected Cross Validation Experiments">
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="FitItem">
+            <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Vmax],Reference=InitialValue"/>
+            <Parameter name="LowerBound" type="cn" value="1e3"/>
+            <Parameter name="UpperBound" type="cn" value="1e7"/>
+            <Parameter name="StartValue" type="float" value="336940.01763224584"/>
+            <ParameterGroup name="Affected Experiments">
+            </ParameterGroup>
+            <ParameterGroup name="Affected Cross Validation Experiments">
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="FitItem">
+            <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Vmax],Reference=InitialValue"/>
+            <Parameter name="LowerBound" type="cn" value="1e4"/>
+            <Parameter name="UpperBound" type="cn" value="1e7"/>
+            <Parameter name="StartValue" type="float" value="9565521.7634551357"/>
+            <ParameterGroup name="Affected Experiments">
+            </ParameterGroup>
+            <ParameterGroup name="Affected Cross Validation Experiments">
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="FitItem">
+            <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt],ParameterGroup=Parameters,Parameter=Ki,Reference=Value"/>
+            <Parameter name="LowerBound" type="cn" value="14.3334"/>
+            <Parameter name="UpperBound" type="cn" value="107.5"/>
+            <Parameter name="StartValue" type="float" value="36.677582885785789"/>
+            <ParameterGroup name="Affected Experiments">
+            </ParameterGroup>
+            <ParameterGroup name="Affected Cross Validation Experiments">
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="FitItem">
+            <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt],ParameterGroup=Parameters,Parameter=V,Reference=Value"/>
+            <Parameter name="LowerBound" type="cn" value="1e3"/>
+            <Parameter name="UpperBound" type="cn" value="1e7"/>
+            <Parameter name="StartValue" type="float" value="5557.6413849999999"/>
+            <ParameterGroup name="Affected Experiments">
+            </ParameterGroup>
+            <ParameterGroup name="Affected Cross Validation Experiments">
+            </ParameterGroup>
+          </ParameterGroup>
+        </ParameterGroup>
+        <ParameterGroup name="OptimizationConstraintList">
+        </ParameterGroup>
+        <Parameter name="Steady-State" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
+        <Parameter name="Time-Course" type="cn" value="CN=Root,Vector=TaskList[Time-Course]"/>
+        <Parameter name="Create Parameter Sets" type="bool" value="0"/>
+        <ParameterGroup name="Experiment Set">
+          <ParameterGroup name="Exp_8mM">
+            <Parameter name="Key" type="key" value="Experiment_0"/>
+            <Parameter name="File Name" type="file" value="data_10mM_MC.txt"/>
+            <Parameter name="First Row" type="unsignedInteger" value="1"/>
+            <Parameter name="Last Row" type="unsignedInteger" value="12"/>
+            <Parameter name="Experiment Type" type="unsignedInteger" value="1"/>
+            <Parameter name="Normalize Weights per Experiment" type="bool" value="0"/>
+            <Parameter name="Separator" type="string" value="&#x09;"/>
+            <Parameter name="Weight Method" type="unsignedInteger" value="0"/>
+            <Parameter name="Data is Row Oriented" type="bool" value="1"/>
+            <Parameter name="Row containing Names" type="unsignedInteger" value="1"/>
+            <Parameter name="Number of Columns" type="unsignedInteger" value="5"/>
+            <ParameterGroup name="Object Map">
+              <ParameterGroup name="0">
+                <Parameter name="Role" type="unsignedInteger" value="3"/>
+              </ParameterGroup>
+              <ParameterGroup name="1">
+                <Parameter name="Role" type="unsignedInteger" value="2"/>
+                <Parameter name="Object CN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Acet_out],Reference=Concentration"/>
+                <Parameter name="Weight" type="unsignedFloat" value="25"/>
+              </ParameterGroup>
+              <ParameterGroup name="2">
+                <Parameter name="Role" type="unsignedInteger" value="2"/>
+                <Parameter name="Object CN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[X],Reference=Concentration"/>
+                <Parameter name="Weight" type="unsignedFloat" value="500"/>
+              </ParameterGroup>
+              <ParameterGroup name="3">
+                <Parameter name="Role" type="unsignedInteger" value="2"/>
+                <Parameter name="Object CN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Glc],Reference=Concentration"/>
+                <Parameter name="Weight" type="unsignedFloat" value="4"/>
+              </ParameterGroup>
+              <ParameterGroup name="4">
+                <Parameter name="Role" type="unsignedInteger" value="2"/>
+                <Parameter name="Object CN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[Ace_enr],Reference=Value"/>
+                <Parameter name="Weight" type="unsignedFloat" value="1100"/>
+              </ParameterGroup>
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="Exp_1mM">
+            <Parameter name="Key" type="key" value="Experiment_1"/>
+            <Parameter name="File Name" type="file" value="data_1mM_MC.txt"/>
+            <Parameter name="First Row" type="unsignedInteger" value="1"/>
+            <Parameter name="Last Row" type="unsignedInteger" value="13"/>
+            <Parameter name="Experiment Type" type="unsignedInteger" value="1"/>
+            <Parameter name="Normalize Weights per Experiment" type="bool" value="0"/>
+            <Parameter name="Separator" type="string" value="&#x09;"/>
+            <Parameter name="Weight Method" type="unsignedInteger" value="0"/>
+            <Parameter name="Data is Row Oriented" type="bool" value="1"/>
+            <Parameter name="Row containing Names" type="unsignedInteger" value="1"/>
+            <Parameter name="Number of Columns" type="unsignedInteger" value="5"/>
+            <ParameterGroup name="Object Map">
+              <ParameterGroup name="0">
+                <Parameter name="Role" type="unsignedInteger" value="3"/>
+              </ParameterGroup>
+              <ParameterGroup name="1">
+                <Parameter name="Role" type="unsignedInteger" value="2"/>
+                <Parameter name="Object CN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Acet_out],Reference=Concentration"/>
+                <Parameter name="Weight" type="unsignedFloat" value="25"/>
+              </ParameterGroup>
+              <ParameterGroup name="2">
+                <Parameter name="Role" type="unsignedInteger" value="2"/>
+                <Parameter name="Object CN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[X],Reference=Concentration"/>
+                <Parameter name="Weight" type="unsignedFloat" value="500"/>
+              </ParameterGroup>
+              <ParameterGroup name="3">
+                <Parameter name="Role" type="unsignedInteger" value="2"/>
+                <Parameter name="Object CN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Glc],Reference=Concentration"/>
+                <Parameter name="Weight" type="unsignedFloat" value="4"/>
+              </ParameterGroup>
+              <ParameterGroup name="4">
+                <Parameter name="Role" type="unsignedInteger" value="2"/>
+                <Parameter name="Object CN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[Ace_enr],Reference=Value"/>
+                <Parameter name="Weight" type="unsignedFloat" value="1100"/>
+              </ParameterGroup>
+            </ParameterGroup>
+          </ParameterGroup>
+          <ParameterGroup name="Exp_32mM">
+            <Parameter name="Key" type="key" value="Experiment_2"/>
+            <Parameter name="File Name" type="file" value="data_30mM_MC.txt"/>
+            <Parameter name="First Row" type="unsignedInteger" value="1"/>
+            <Parameter name="Last Row" type="unsignedInteger" value="16"/>
+            <Parameter name="Experiment Type" type="unsignedInteger" value="1"/>
+            <Parameter name="Normalize Weights per Experiment" type="bool" value="0"/>
+            <Parameter name="Separator" type="string" value="&#x09;"/>
+            <Parameter name="Weight Method" type="unsignedInteger" value="0"/>
+            <Parameter name="Data is Row Oriented" type="bool" value="1"/>
+            <Parameter name="Row containing Names" type="unsignedInteger" value="1"/>
+            <Parameter name="Number of Columns" type="unsignedInteger" value="5"/>
+            <ParameterGroup name="Object Map">
+              <ParameterGroup name="0">
+                <Parameter name="Role" type="unsignedInteger" value="3"/>
+              </ParameterGroup>
+              <ParameterGroup name="1">
+                <Parameter name="Role" type="unsignedInteger" value="2"/>
+                <Parameter name="Object CN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Acet_out],Reference=Concentration"/>
+                <Parameter name="Weight" type="unsignedFloat" value="25"/>
+              </ParameterGroup>
+              <ParameterGroup name="2">
+                <Parameter name="Role" type="unsignedInteger" value="2"/>
+                <Parameter name="Object CN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[X],Reference=Concentration"/>
+                <Parameter name="Weight" type="unsignedFloat" value="500"/>
+              </ParameterGroup>
+              <ParameterGroup name="3">
+                <Parameter name="Role" type="unsignedInteger" value="2"/>
+                <Parameter name="Object CN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Glc],Reference=Concentration"/>
+                <Parameter name="Weight" type="unsignedFloat" value="4"/>
+              </ParameterGroup>
+              <ParameterGroup name="4">
+                <Parameter name="Role" type="unsignedInteger" value="2"/>
+                <Parameter name="Object CN" type="cn" value="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[Ace_enr],Reference=Value"/>
+                <Parameter name="Weight" type="unsignedFloat" value="1100"/>
+              </ParameterGroup>
+            </ParameterGroup>
+          </ParameterGroup>
+        </ParameterGroup>
+        <ParameterGroup name="Validation Set">
+          <Parameter name="Weight" type="unsignedFloat" value="1"/>
+          <Parameter name="Threshold" type="unsignedInteger" value="5"/>
+        </ParameterGroup>
+      </Problem>
+      <Method name="Current Solution Statistics" type="CurrentSolutionStatistics">
+        <Parameter name="Log Verbosity" type="unsignedInteger" value="0"/>
+      </Method>
+    </Task>
+    <Task key="Task_21" name="Metabolic Control Analysis" type="metabolicControlAnalysis" scheduled="false" updateModel="false">
+      <Report reference="Report_14" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="Steady-State" type="key" value="Task_15"/>
+      </Problem>
+      <Method name="MCA Method (Reder)" type="MCAMethod(Reder)">
+        <Parameter name="Modulation Factor" type="unsignedFloat" value="1.0000000000000001e-09"/>
+        <Parameter name="Use Reder" type="bool" value="1"/>
+        <Parameter name="Use Smallbone" type="bool" value="1"/>
+      </Method>
+    </Task>
+    <Task key="Task_22" name="Lyapunov Exponents" type="lyapunovExponents" scheduled="false" updateModel="false">
+      <Report reference="Report_15" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="ExponentNumber" type="unsignedInteger" value="3"/>
+        <Parameter name="DivergenceRequested" type="bool" value="1"/>
+        <Parameter name="TransientTime" type="float" value="0"/>
+      </Problem>
+      <Method name="Wolf Method" type="WolfMethod">
+        <Parameter name="Orthonormalization Interval" type="unsignedFloat" value="1"/>
+        <Parameter name="Overall time" type="unsignedFloat" value="1000"/>
+        <Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-07"/>
+        <Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
+        <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
+      </Method>
+    </Task>
+    <Task key="Task_23" name="Time Scale Separation Analysis" type="timeScaleSeparationAnalysis" scheduled="false" updateModel="false">
+      <Report reference="Report_16" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="StepNumber" type="unsignedInteger" value="100"/>
+        <Parameter name="StepSize" type="float" value="0.01"/>
+        <Parameter name="Duration" type="float" value="1"/>
+        <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
+        <Parameter name="OutputStartTime" type="float" value="0"/>
+      </Problem>
+      <Method name="ILDM (LSODA,Deuflhard)" type="TimeScaleSeparation(ILDM,Deuflhard)">
+        <Parameter name="Deuflhard Tolerance" type="unsignedFloat" value="0.0001"/>
+      </Method>
+    </Task>
+    <Task key="Task_24" name="Sensitivities" type="sensitivities" scheduled="false" updateModel="false">
+      <Report reference="Report_17" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="SubtaskType" type="unsignedInteger" value="1"/>
+        <ParameterGroup name="TargetFunctions">
+          <Parameter name="SingleObject" type="cn" value=""/>
+          <Parameter name="ObjectListType" type="unsignedInteger" value="7"/>
+        </ParameterGroup>
+        <ParameterGroup name="ListOfVariables">
+          <ParameterGroup name="Variables">
+            <Parameter name="SingleObject" type="cn" value=""/>
+            <Parameter name="ObjectListType" type="unsignedInteger" value="41"/>
+          </ParameterGroup>
+          <ParameterGroup name="Variables">
+            <Parameter name="SingleObject" type="cn" value=""/>
+            <Parameter name="ObjectListType" type="unsignedInteger" value="0"/>
+          </ParameterGroup>
+        </ParameterGroup>
+      </Problem>
+      <Method name="Sensitivities Method" type="SensitivitiesMethod">
+        <Parameter name="Delta factor" type="unsignedFloat" value="0.001"/>
+        <Parameter name="Delta minimum" type="unsignedFloat" value="9.9999999999999998e-13"/>
+      </Method>
+    </Task>
+    <Task key="Task_25" name="Moieties" type="moieties" scheduled="false" updateModel="false">
+      <Report reference="Report_18" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+      </Problem>
+      <Method name="Householder Reduction" type="Householder">
+      </Method>
+    </Task>
+    <Task key="Task_26" name="Cross Section" type="crosssection" scheduled="false" updateModel="false">
+      <Problem>
+        <Parameter name="AutomaticStepSize" type="bool" value="0"/>
+        <Parameter name="StepNumber" type="unsignedInteger" value="100"/>
+        <Parameter name="StepSize" type="float" value="0.01"/>
+        <Parameter name="Duration" type="float" value="1"/>
+        <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
+        <Parameter name="OutputStartTime" type="float" value="0"/>
+        <Parameter name="Output Event" type="bool" value="0"/>
+        <Parameter name="Start in Steady State" type="bool" value="0"/>
+        <Parameter name="Use Values" type="bool" value="0"/>
+        <Parameter name="Values" type="string" value=""/>
+        <Parameter name="LimitCrossings" type="bool" value="0"/>
+        <Parameter name="NumCrossingsLimit" type="unsignedInteger" value="0"/>
+        <Parameter name="LimitOutTime" type="bool" value="0"/>
+        <Parameter name="LimitOutCrossings" type="bool" value="0"/>
+        <Parameter name="PositiveDirection" type="bool" value="1"/>
+        <Parameter name="NumOutCrossingsLimit" type="unsignedInteger" value="0"/>
+        <Parameter name="LimitUntilConvergence" type="bool" value="0"/>
+        <Parameter name="ConvergenceTolerance" type="float" value="9.9999999999999995e-07"/>
+        <Parameter name="Threshold" type="float" value="0"/>
+        <Parameter name="DelayOutputUntilConvergence" type="bool" value="0"/>
+        <Parameter name="OutputConvergenceTolerance" type="float" value="9.9999999999999995e-07"/>
+        <ParameterText name="TriggerExpression" type="expression">
+          
+        </ParameterText>
+        <Parameter name="SingleVariable" type="cn" value=""/>
+      </Problem>
+      <Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
+        <Parameter name="Integrate Reduced Model" type="bool" value="0"/>
+        <Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-07"/>
+        <Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
+        <Parameter name="Max Internal Steps" type="unsignedInteger" value="100000"/>
+        <Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
+      </Method>
+    </Task>
+    <Task key="Task_27" name="Linear Noise Approximation" type="linearNoiseApproximation" scheduled="false" updateModel="false">
+      <Report reference="Report_19" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="Steady-State" type="key" value="Task_15"/>
+      </Problem>
+      <Method name="Linear Noise Approximation" type="LinearNoiseApproximation">
+      </Method>
+    </Task>
+    <Task key="Task_28" name="Time-Course Sensitivities" type="timeSensitivities" scheduled="false" updateModel="false">
+      <Problem>
+        <Parameter name="AutomaticStepSize" type="bool" value="0"/>
+        <Parameter name="StepNumber" type="unsignedInteger" value="100"/>
+        <Parameter name="StepSize" type="float" value="0.01"/>
+        <Parameter name="Duration" type="float" value="1"/>
+        <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
+        <Parameter name="OutputStartTime" type="float" value="0"/>
+        <Parameter name="Output Event" type="bool" value="0"/>
+        <Parameter name="Start in Steady State" type="bool" value="0"/>
+        <Parameter name="Use Values" type="bool" value="0"/>
+        <Parameter name="Values" type="string" value=""/>
+        <ParameterGroup name="ListOfParameters">
+        </ParameterGroup>
+        <ParameterGroup name="ListOfTargets">
+        </ParameterGroup>
+      </Problem>
+      <Method name="LSODA Sensitivities" type="Sensitivities(LSODA)">
+        <Parameter name="Integrate Reduced Model" type="bool" value="0"/>
+        <Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-07"/>
+        <Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
+        <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
+        <Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
+      </Method>
+    </Task>
+  </ListOfTasks>
+  <ListOfReports>
+    <Report key="Report_10" name="Steady-State" taskType="steadyState" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Footer>
+        <Object cn="CN=Root,Vector=TaskList[Steady-State]"/>
+      </Footer>
+    </Report>
+    <Report key="Report_11" name="Elementary Flux Modes" taskType="fluxMode" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Footer>
+        <Object cn="CN=Root,Vector=TaskList[Elementary Flux Modes],Object=Result"/>
+      </Footer>
+    </Report>
+    <Report key="Report_12" name="Optimization" taskType="optimization" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Header>
+        <Object cn="CN=Root,Vector=TaskList[Optimization],Object=Description"/>
+        <Object cn="String=\[Function Evaluations\]"/>
+        <Object cn="Separator=&#x09;"/>
+        <Object cn="String=\[Best Value\]"/>
+        <Object cn="Separator=&#x09;"/>
+        <Object cn="String=\[Best Parameters\]"/>
+      </Header>
+      <Body>
+        <Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Function Evaluations"/>
+        <Object cn="Separator=&#x09;"/>
+        <Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Best Value"/>
+        <Object cn="Separator=&#x09;"/>
+        <Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Best Parameters"/>
+      </Body>
+      <Footer>
+        <Object cn="String=&#x0a;"/>
+        <Object cn="CN=Root,Vector=TaskList[Optimization],Object=Result"/>
+      </Footer>
+    </Report>
+    <Report key="Report_13" name="Parameter Estimation" taskType="parameterFitting" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Header>
+        <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Object=Description"/>
+        <Object cn="String=\[Function Evaluations\]"/>
+        <Object cn="Separator=&#x09;"/>
+        <Object cn="String=\[Best Value\]"/>
+        <Object cn="Separator=&#x09;"/>
+        <Object cn="String=\[Best Parameters\]"/>
+      </Header>
+      <Body>
+        <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Function Evaluations"/>
+        <Object cn="Separator=&#x09;"/>
+        <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Best Value"/>
+        <Object cn="Separator=&#x09;"/>
+        <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Best Parameters"/>
+      </Body>
+      <Footer>
+        <Object cn="String=&#x0a;"/>
+        <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Object=Result"/>
+      </Footer>
+    </Report>
+    <Report key="Report_14" name="Metabolic Control Analysis" taskType="metabolicControlAnalysis" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Header>
+        <Object cn="CN=Root,Vector=TaskList[Metabolic Control Analysis],Object=Description"/>
+      </Header>
+      <Footer>
+        <Object cn="String=&#x0a;"/>
+        <Object cn="CN=Root,Vector=TaskList[Metabolic Control Analysis],Object=Result"/>
+      </Footer>
+    </Report>
+    <Report key="Report_15" name="Lyapunov Exponents" taskType="lyapunovExponents" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Header>
+        <Object cn="CN=Root,Vector=TaskList[Lyapunov Exponents],Object=Description"/>
+      </Header>
+      <Footer>
+        <Object cn="String=&#x0a;"/>
+        <Object cn="CN=Root,Vector=TaskList[Lyapunov Exponents],Object=Result"/>
+      </Footer>
+    </Report>
+    <Report key="Report_16" name="Time Scale Separation Analysis" taskType="timeScaleSeparationAnalysis" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Header>
+        <Object cn="CN=Root,Vector=TaskList[Time Scale Separation Analysis],Object=Description"/>
+      </Header>
+      <Footer>
+        <Object cn="String=&#x0a;"/>
+        <Object cn="CN=Root,Vector=TaskList[Time Scale Separation Analysis],Object=Result"/>
+      </Footer>
+    </Report>
+    <Report key="Report_17" name="Sensitivities" taskType="sensitivities" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Header>
+        <Object cn="CN=Root,Vector=TaskList[Sensitivities],Object=Description"/>
+      </Header>
+      <Footer>
+        <Object cn="String=&#x0a;"/>
+        <Object cn="CN=Root,Vector=TaskList[Sensitivities],Object=Result"/>
+      </Footer>
+    </Report>
+    <Report key="Report_18" name="Moieties" taskType="moieties" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Header>
+        <Object cn="CN=Root,Vector=TaskList[Moieties],Object=Description"/>
+      </Header>
+      <Footer>
+        <Object cn="String=&#x0a;"/>
+        <Object cn="CN=Root,Vector=TaskList[Moieties],Object=Result"/>
+      </Footer>
+    </Report>
+    <Report key="Report_19" name="Linear Noise Approximation" taskType="linearNoiseApproximation" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Header>
+        <Object cn="CN=Root,Vector=TaskList[Linear Noise Approximation],Object=Description"/>
+      </Header>
+      <Footer>
+        <Object cn="String=&#x0a;"/>
+        <Object cn="CN=Root,Vector=TaskList[Linear Noise Approximation],Object=Result"/>
+      </Footer>
+    </Report>
+  </ListOfReports>
+  <ListOfPlots>
+    <PlotSpecification name="Parameter Estimation Result" type="Plot2D" active="1" taskTypes="Parameter Estimation">
+      <Parameter name="log X" type="bool" value="0"/>
+      <Parameter name="log Y" type="bool" value="0"/>
+      <ListOfPlotItems>
+        <PlotItem name="Exp_1mM,[Acet_out](Measured Value)" type="Curve2D">
+          <Parameter name="Line type" type="unsignedInteger" value="3"/>
+          <Parameter name="Line subtype" type="unsignedInteger" value="1"/>
+          <Parameter name="Line width" type="unsignedFloat" value="1"/>
+          <Parameter name="Symbol subtype" type="unsignedInteger" value="1"/>
+          <Parameter name="Color" type="string" value="#FF0000"/>
+          <Parameter name="Recording Activity" type="string" value="after"/>
+          <ListOfChannels>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[0],Reference=Independent Value"/>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[0],Reference=Measured Value"/>
+          </ListOfChannels>
+        </PlotItem>
+        <PlotItem name="Exp_1mM,[Acet_out](Fitted Value)" type="Curve2D">
+          <Parameter name="Line type" type="unsignedInteger" value="0"/>
+          <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
+          <Parameter name="Line width" type="unsignedFloat" value="1"/>
+          <Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
+          <Parameter name="Color" type="string" value="#FF0000"/>
+          <Parameter name="Recording Activity" type="string" value="after"/>
+          <ListOfChannels>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[0],Reference=Independent Value"/>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[0],Reference=Fitted Value"/>
+          </ListOfChannels>
+        </PlotItem>
+        <PlotItem name="Exp_1mM,[Acet_out](Weighted Error)" type="Curve2D">
+          <Parameter name="Line type" type="unsignedInteger" value="2"/>
+          <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
+          <Parameter name="Line width" type="unsignedFloat" value="1"/>
+          <Parameter name="Symbol subtype" type="unsignedInteger" value="2"/>
+          <Parameter name="Color" type="string" value="#FF0000"/>
+          <Parameter name="Recording Activity" type="string" value="after"/>
+          <ListOfChannels>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[0],Reference=Independent Value"/>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[0],Reference=Weighted Error"/>
+          </ListOfChannels>
+        </PlotItem>
+        <PlotItem name="Exp_1mM,[X](Measured Value)" type="Curve2D">
+          <Parameter name="Line type" type="unsignedInteger" value="3"/>
+          <Parameter name="Line subtype" type="unsignedInteger" value="1"/>
+          <Parameter name="Line width" type="unsignedFloat" value="1"/>
+          <Parameter name="Symbol subtype" type="unsignedInteger" value="1"/>
+          <Parameter name="Color" type="string" value="#0000FF"/>
+          <Parameter name="Recording Activity" type="string" value="after"/>
+          <ListOfChannels>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[0],Reference=Independent Value"/>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[1],Reference=Measured Value"/>
+          </ListOfChannels>
+        </PlotItem>
+        <PlotItem name="Exp_1mM,[X](Fitted Value)" type="Curve2D">
+          <Parameter name="Line type" type="unsignedInteger" value="0"/>
+          <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
+          <Parameter name="Line width" type="unsignedFloat" value="1"/>
+          <Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
+          <Parameter name="Color" type="string" value="#0000FF"/>
+          <Parameter name="Recording Activity" type="string" value="after"/>
+          <ListOfChannels>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[0],Reference=Independent Value"/>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[1],Reference=Fitted Value"/>
+          </ListOfChannels>
+        </PlotItem>
+        <PlotItem name="Exp_1mM,[X](Weighted Error)" type="Curve2D">
+          <Parameter name="Line type" type="unsignedInteger" value="2"/>
+          <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
+          <Parameter name="Line width" type="unsignedFloat" value="1"/>
+          <Parameter name="Symbol subtype" type="unsignedInteger" value="2"/>
+          <Parameter name="Color" type="string" value="#0000FF"/>
+          <Parameter name="Recording Activity" type="string" value="after"/>
+          <ListOfChannels>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[0],Reference=Independent Value"/>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[1],Reference=Weighted Error"/>
+          </ListOfChannels>
+        </PlotItem>
+        <PlotItem name="Exp_1mM,[Glc](Measured Value)" type="Curve2D">
+          <Parameter name="Line type" type="unsignedInteger" value="3"/>
+          <Parameter name="Line subtype" type="unsignedInteger" value="1"/>
+          <Parameter name="Line width" type="unsignedFloat" value="1"/>
+          <Parameter name="Symbol subtype" type="unsignedInteger" value="1"/>
+          <Parameter name="Color" type="string" value="#00E600"/>
+          <Parameter name="Recording Activity" type="string" value="after"/>
+          <ListOfChannels>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[0],Reference=Independent Value"/>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[2],Reference=Measured Value"/>
+          </ListOfChannels>
+        </PlotItem>
+        <PlotItem name="Exp_1mM,[Glc](Fitted Value)" type="Curve2D">
+          <Parameter name="Line type" type="unsignedInteger" value="0"/>
+          <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
+          <Parameter name="Line width" type="unsignedFloat" value="1"/>
+          <Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
+          <Parameter name="Color" type="string" value="#00E600"/>
+          <Parameter name="Recording Activity" type="string" value="after"/>
+          <ListOfChannels>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[0],Reference=Independent Value"/>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[2],Reference=Fitted Value"/>
+          </ListOfChannels>
+        </PlotItem>
+        <PlotItem name="Exp_1mM,[Glc](Weighted Error)" type="Curve2D">
+          <Parameter name="Line type" type="unsignedInteger" value="2"/>
+          <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
+          <Parameter name="Line width" type="unsignedFloat" value="1"/>
+          <Parameter name="Symbol subtype" type="unsignedInteger" value="2"/>
+          <Parameter name="Color" type="string" value="#00E600"/>
+          <Parameter name="Recording Activity" type="string" value="after"/>
+          <ListOfChannels>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[0],Reference=Independent Value"/>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[2],Reference=Weighted Error"/>
+          </ListOfChannels>
+        </PlotItem>
+        <PlotItem name="Exp_1mM,Values[Ace_enr](Measured Value)" type="Curve2D">
+          <Parameter name="Line type" type="unsignedInteger" value="3"/>
+          <Parameter name="Line subtype" type="unsignedInteger" value="1"/>
+          <Parameter name="Line width" type="unsignedFloat" value="1"/>
+          <Parameter name="Symbol subtype" type="unsignedInteger" value="1"/>
+          <Parameter name="Color" type="string" value="#00BEF0"/>
+          <Parameter name="Recording Activity" type="string" value="after"/>
+          <ListOfChannels>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[0],Reference=Independent Value"/>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[3],Reference=Measured Value"/>
+          </ListOfChannels>
+        </PlotItem>
+        <PlotItem name="Exp_1mM,Values[Ace_enr](Fitted Value)" type="Curve2D">
+          <Parameter name="Line type" type="unsignedInteger" value="0"/>
+          <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
+          <Parameter name="Line width" type="unsignedFloat" value="1"/>
+          <Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
+          <Parameter name="Color" type="string" value="#00BEF0"/>
+          <Parameter name="Recording Activity" type="string" value="after"/>
+          <ListOfChannels>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[0],Reference=Independent Value"/>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[3],Reference=Fitted Value"/>
+          </ListOfChannels>
+        </PlotItem>
+        <PlotItem name="Exp_1mM,Values[Ace_enr](Weighted Error)" type="Curve2D">
+          <Parameter name="Line type" type="unsignedInteger" value="2"/>
+          <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
+          <Parameter name="Line width" type="unsignedFloat" value="1"/>
+          <Parameter name="Symbol subtype" type="unsignedInteger" value="2"/>
+          <Parameter name="Color" type="string" value="#00BEF0"/>
+          <Parameter name="Recording Activity" type="string" value="after"/>
+          <ListOfChannels>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[0],Reference=Independent Value"/>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_1mM,Vector=Fitted Points[3],Reference=Weighted Error"/>
+          </ListOfChannels>
+        </PlotItem>
+        <PlotItem name="Exp_32mM,[Acet_out](Measured Value)" type="Curve2D">
+          <Parameter name="Line type" type="unsignedInteger" value="3"/>
+          <Parameter name="Line subtype" type="unsignedInteger" value="1"/>
+          <Parameter name="Line width" type="unsignedFloat" value="1"/>
+          <Parameter name="Symbol subtype" type="unsignedInteger" value="1"/>
+          <Parameter name="Color" type="string" value="#F000FF"/>
+          <Parameter name="Recording Activity" type="string" value="after"/>
+          <ListOfChannels>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_32mM,Vector=Fitted Points[0],Reference=Independent Value"/>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_32mM,Vector=Fitted Points[0],Reference=Measured Value"/>
+          </ListOfChannels>
+        </PlotItem>
+        <PlotItem name="Exp_32mM,[Acet_out](Fitted Value)" type="Curve2D">
+          <Parameter name="Line type" type="unsignedInteger" value="0"/>
+          <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
+          <Parameter name="Line width" type="unsignedFloat" value="1"/>
+          <Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
+          <Parameter name="Color" type="string" value="#F000FF"/>
+          <Parameter name="Recording Activity" type="string" value="after"/>
+          <ListOfChannels>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_32mM,Vector=Fitted Points[0],Reference=Independent Value"/>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_32mM,Vector=Fitted Points[0],Reference=Fitted Value"/>
+          </ListOfChannels>
+        </PlotItem>
+        <PlotItem name="Exp_32mM,[Acet_out](Weighted Error)" type="Curve2D">
+          <Parameter name="Line type" type="unsignedInteger" value="2"/>
+          <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
+          <Parameter name="Line width" type="unsignedFloat" value="1"/>
+          <Parameter name="Symbol subtype" type="unsignedInteger" value="2"/>
+          <Parameter name="Color" type="string" value="#F000FF"/>
+          <Parameter name="Recording Activity" type="string" value="after"/>
+          <ListOfChannels>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_32mM,Vector=Fitted Points[0],Reference=Independent Value"/>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_32mM,Vector=Fitted Points[0],Reference=Weighted Error"/>
+          </ListOfChannels>
+        </PlotItem>
+        <PlotItem name="Exp_32mM,[X](Measured Value)" type="Curve2D">
+          <Parameter name="Line type" type="unsignedInteger" value="3"/>
+          <Parameter name="Line subtype" type="unsignedInteger" value="1"/>
+          <Parameter name="Line width" type="unsignedFloat" value="1"/>
+          <Parameter name="Symbol subtype" type="unsignedInteger" value="1"/>
+          <Parameter name="Color" type="string" value="#F0C800"/>
+          <Parameter name="Recording Activity" type="string" value="after"/>
+          <ListOfChannels>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_32mM,Vector=Fitted Points[0],Reference=Independent Value"/>
+            <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Exp_32mM,Vector=Fitted Points[1],Reference=Measured Value"/>
+          </ListOfChannels>
+        </PlotItem>
+        <PlotItem name="Exp_32mM,[X](Fitted Value)" type="Curve2D">
+          <Parameter name="Line type" type="unsignedInteger" value="0"/>
+          <Parameter name="Line subtype" type="unsignedInteger" value="0"/>
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diff --git a/model/cps/Millard2020_Ecoli_glc_ace_kinetic_model_1.cps b/model/cps/Millard2020_Ecoli_glc_ace_kinetic_model_1.cps
new file mode 100644
index 0000000..f611c2a
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+<COPASI xmlns="http://www.copasi.org/static/schema" versionMajor="4" versionMinor="27" versionDevel="217" copasiSourcesModified="0">
+  <ListOfFunctions>
+    <Function key="Function_28" name="Reversible Michaelis-Menten" type="PreDefined" reversible="true">
+      <MiriamAnnotation>
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+<dcterms:created>
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+<dcterms:W3CDTF>2020-04-30T11:06:43Z</dcterms:W3CDTF>
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+</rdf:RDF>
+      </MiriamAnnotation>
+      <Expression>
+        (Vf*substrate/Kms-Vr*product/Kmp)/(1+substrate/Kms+product/Kmp)
+      </Expression>
+      <ListOfParameterDescriptions>
+        <ParameterDescription key="FunctionParameter_195" name="substrate" order="0" role="substrate"/>
+        <ParameterDescription key="FunctionParameter_196" name="product" order="1" role="product"/>
+        <ParameterDescription key="FunctionParameter_197" name="Kms" order="2" role="constant"/>
+        <ParameterDescription key="FunctionParameter_198" name="Kmp" order="3" role="constant"/>
+        <ParameterDescription key="FunctionParameter_199" name="Vf" order="4" role="constant"/>
+        <ParameterDescription key="FunctionParameter_200" name="Vr" order="5" role="constant"/>
+      </ListOfParameterDescriptions>
+    </Function>
+    <Function key="Function_40" name="growth" type="UserDefined" reversible="unspecified">
+      <MiriamAnnotation>
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+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T12:10:06Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+      </MiriamAnnotation>
+      <Expression>
+        Y*X*sink
+      </Expression>
+      <ListOfParameterDescriptions>
+        <ParameterDescription key="FunctionParameter_264" name="Y" order="0" role="constant"/>
+        <ParameterDescription key="FunctionParameter_263" name="X" order="1" role="product"/>
+        <ParameterDescription key="FunctionParameter_262" name="sink" order="2" role="constant"/>
+      </ListOfParameterDescriptions>
+    </Function>
+    <Function key="Function_41" name="Rate Law for r1" type="UserDefined" reversible="unspecified">
+      <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T12:15:09Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+      </MiriamAnnotation>
+      <Expression>
+        V*S/((KM+S)*(1+I/Ki))
+      </Expression>
+      <ListOfParameterDescriptions>
+        <ParameterDescription key="FunctionParameter_265" name="V" order="0" role="constant"/>
+        <ParameterDescription key="FunctionParameter_250" name="S" order="1" role="substrate"/>
+        <ParameterDescription key="FunctionParameter_261" name="KM" order="2" role="constant"/>
+        <ParameterDescription key="FunctionParameter_266" name="I" order="3" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_267" name="Ki" order="4" role="constant"/>
+      </ListOfParameterDescriptions>
+    </Function>
+    <Function key="Function_42" name="function_sink" type="UserDefined" reversible="unspecified">
+      <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Function_42">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T14:21:54Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+      </MiriamAnnotation>
+      <Expression>
+        A/At*V*At^n/((At^n+Km)*(1+I/Ki))
+      </Expression>
+      <ListOfParameterDescriptions>
+        <ParameterDescription key="FunctionParameter_272" name="A" order="0" role="substrate"/>
+        <ParameterDescription key="FunctionParameter_271" name="At" order="1" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_270" name="V" order="2" role="constant"/>
+        <ParameterDescription key="FunctionParameter_269" name="n" order="3" role="constant"/>
+        <ParameterDescription key="FunctionParameter_268" name="Km" order="4" role="constant"/>
+        <ParameterDescription key="FunctionParameter_273" name="I" order="5" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_274" name="Ki" order="6" role="constant"/>
+      </ListOfParameterDescriptions>
+    </Function>
+    <Function key="Function_43" name="ack" type="UserDefined" reversible="unspecified">
+      <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Function_43">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-04-30T11:17:51Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+      </MiriamAnnotation>
+      <Expression>
+        v_ACK_Vmax*(ACP*ADP-ACE*ATP/v_ACK_Keq)/ (v_ACK_KmACP*v_ACK_KmADP)/((1+ACP/ v_ACK_KmACP+ACE/v_ACK_KmACE)*(1+ADP/v_ACK_KmADP+ATP/v_ACK_KmATP))
+      </Expression>
+      <ListOfParameterDescriptions>
+        <ParameterDescription key="FunctionParameter_281" name="v_ACK_Vmax" order="0" role="constant"/>
+        <ParameterDescription key="FunctionParameter_280" name="ACP" order="1" role="substrate"/>
+        <ParameterDescription key="FunctionParameter_279" name="ADP" order="2" role="constant"/>
+        <ParameterDescription key="FunctionParameter_278" name="ATP" order="3" role="constant"/>
+        <ParameterDescription key="FunctionParameter_277" name="v_ACK_KmACP" order="4" role="constant"/>
+        <ParameterDescription key="FunctionParameter_276" name="v_ACK_KmADP" order="5" role="constant"/>
+        <ParameterDescription key="FunctionParameter_275" name="ACE" order="6" role="product"/>
+        <ParameterDescription key="FunctionParameter_282" name="v_ACK_KmACE" order="7" role="constant"/>
+        <ParameterDescription key="FunctionParameter_283" name="v_ACK_KmATP" order="8" role="constant"/>
+        <ParameterDescription key="FunctionParameter_284" name="v_ACK_Keq" order="9" role="constant"/>
+      </ListOfParameterDescriptions>
+    </Function>
+    <Function key="Function_44" name="pta" type="UserDefined" reversible="unspecified">
+      <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Function_44">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:31:22Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+      </MiriamAnnotation>
+      <Expression>
+        v_PTA_Vmax*(ACCOA*P-ACP*COA/KEQ)/ (v_PTA_KiACCOA*v_PTA_KmP)/(1+ACCOA/v_PTA_KiACCOA+P/ v_PTA_KiP+ACP/v_PTA_KiACP+COA/v_PTA_KiCOA+ACCOA*P/ (v_PTA_KiACCOA*v_PTA_KmP)+ACP*COA/(v_PTA_KmACP*v_PTA_KiCOA))
+      </Expression>
+      <ListOfParameterDescriptions>
+        <ParameterDescription key="FunctionParameter_294" name="v_PTA_Vmax" order="0" role="constant"/>
+        <ParameterDescription key="FunctionParameter_293" name="ACCOA" order="1" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_292" name="P" order="2" role="constant"/>
+        <ParameterDescription key="FunctionParameter_291" name="ACP" order="3" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_290" name="COA" order="4" role="constant"/>
+        <ParameterDescription key="FunctionParameter_289" name="KEQ" order="5" role="constant"/>
+        <ParameterDescription key="FunctionParameter_288" name="v_PTA_KiACCOA" order="6" role="constant"/>
+        <ParameterDescription key="FunctionParameter_287" name="v_PTA_KmP" order="7" role="constant"/>
+        <ParameterDescription key="FunctionParameter_286" name="v_PTA_KiP" order="8" role="constant"/>
+        <ParameterDescription key="FunctionParameter_285" name="v_PTA_KiACP" order="9" role="constant"/>
+        <ParameterDescription key="FunctionParameter_295" name="v_PTA_KiCOA" order="10" role="constant"/>
+        <ParameterDescription key="FunctionParameter_296" name="v_PTA_KmACP" order="11" role="constant"/>
+      </ListOfParameterDescriptions>
+    </Function>
+  </ListOfFunctions>
+  <Model key="Model_1" name="E. coli model - Glc-Ace metabolism" simulationType="time" timeUnit="h" volumeUnit="l" areaUnit="m²" lengthUnit="m" quantityUnit="mmol" type="deterministic" avogadroConstant="6.0221408570000002e+23">
+    <MiriamAnnotation>
+<rdf:RDF
+   xmlns:dcterms="http://purl.org/dc/terms/"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Model_1">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:27:30Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+
+    </MiriamAnnotation>
+    <Comment>
+      Calibrated model of E. coli glucose and acetate metabolism
+
+see Millard et al., 2020 for details
+    </Comment>
+    <ListOfCompartments>
+      <Compartment key="Compartment_0" name="cell" simulationType="fixed" dimensionality="3" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Compartment_0">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:27:54Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </Compartment>
+    </ListOfCompartments>
+    <ListOfMetabolites>
+      <Metabolite key="Metabolite_0" name="Glc" simulationType="ode" compartment="Compartment_0" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Metabolite_0">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:27:54Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <Expression>
+          -&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[X],Reference=Concentration>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt],Reference=Flux>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[volume],Reference=InitialValue>+&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_feed],Reference=InitialValue>-&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_dilution_rate],Reference=InitialValue>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Glc],Reference=Concentration>
+        </Expression>
+      </Metabolite>
+      <Metabolite key="Metabolite_1" name="AcP" simulationType="reactions" compartment="Compartment_0" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Metabolite_1">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:46:12Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </Metabolite>
+      <Metabolite key="Metabolite_2" name="Ace" simulationType="reactions" compartment="Compartment_0" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Metabolite_2">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:46:12Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </Metabolite>
+      <Metabolite key="Metabolite_3" name="AcCoA" simulationType="reactions" compartment="Compartment_0" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Metabolite_3">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:47:47Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </Metabolite>
+      <Metabolite key="Metabolite_4" name="X" simulationType="ode" compartment="Compartment_0" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Metabolite_4">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T12:08:24Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <Expression>
+          &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[growth],Reference=Flux>-&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_dilution_rate],Reference=InitialValue>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[X],Reference=Concentration>
+        </Expression>
+      </Metabolite>
+      <Metabolite key="Metabolite_5" name="Ace_out" simulationType="ode" compartment="Compartment_0" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Metabolite_5">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-02-26T10:12:50Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <Comment>
+          calibrated with 0.009988794769
+        </Comment>
+        <Expression>
+          &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[X],Reference=Concentration>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch],Reference=Flux>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[volume],Reference=InitialValue>-&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_dilution_rate],Reference=InitialValue>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace_out],Reference=Concentration>
+        </Expression>
+      </Metabolite>
+    </ListOfMetabolites>
+    <ListOfModelValues>
+      <ModelValue key="ModelValue_0" name="r_PTA_Vmax" simulationType="fixed" addNoise="false">
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+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:53:52Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_1" name="r_PTA_KiACCOA" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+        <dcterms:W3CDTF>2019-09-24T11:54:01Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_2" name="r_PTA_KmP" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_2">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:54:06Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_3" name="r_PTA_KiP" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:54:10Z</dcterms:W3CDTF>
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+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_4" name="r_PTA_KiACP" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+        <dcterms:W3CDTF>2019-09-24T11:54:14Z</dcterms:W3CDTF>
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+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_5" name="r_PTA_KiCOA" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:54:18Z</dcterms:W3CDTF>
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+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_6" name="r_PTA_KmACP" simulationType="fixed" addNoise="false">
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+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:54:21Z</dcterms:W3CDTF>
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+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_7" name="P" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_8" name="CoA" simulationType="fixed" addNoise="false">
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+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
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+      <ModelValue key="ModelValue_26" name="v_growth_rate" simulationType="assignment" addNoise="false">
+        <MiriamAnnotation>
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+        <MiriamAnnotation>
+<rdf:RDF
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+  <rdf:Description rdf:about="#ModelValue_27">
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+        <dcterms:W3CDTF>2020-04-29T19:12:37Z</dcterms:W3CDTF>
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+
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+      </ModelValue>
+      <ModelValue key="ModelValue_28" name="v_glc_uptake" simulationType="assignment" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_28">
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+        </MiriamAnnotation>
+        <Expression>
+          &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt],Reference=Flux>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[volume],Reference=InitialValue>
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+      <ModelValue key="ModelValue_29" name="v_ace_net" simulationType="assignment" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+        <dcterms:W3CDTF>2020-04-30T12:35:57Z</dcterms:W3CDTF>
+      </rdf:Description>
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+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <Expression>
+          &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch],Reference=Flux>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[volume],Reference=InitialValue>
+        </Expression>
+      </ModelValue>
+      <ModelValue key="ModelValue_30" name="_dilution_rate" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_30">
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+</rdf:RDF>
+        </MiriamAnnotation>
+        <Comment>
+          dilution rate (in h-1), used to simulate chemostat experiment
+
+default value: 0
+        </Comment>
+      </ModelValue>
+      <ModelValue key="ModelValue_31" name="_feed" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+        </MiriamAnnotation>
+        <Comment>
+          feed (in mmolGlc/h-1), used to simulate chemostat experiment
+
+default value: 0
+        </Comment>
+      </ModelValue>
+      <ModelValue key="ModelValue_32" name="_X_conc_pulse" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+        </MiriamAnnotation>
+        <Comment>
+          biomass concentration at which a 30mM acetate pulse it performed
+
+default value: 10000 (i.e., no pulse)
+        </Comment>
+      </ModelValue>
+    </ListOfModelValues>
+    <ListOfReactions>
+      <Reaction key="Reaction_0" name="glc_upt" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF
+   xmlns:dcterms="http://purl.org/dc/terms/"
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+  <rdf:Description rdf:about="#Reaction_0">
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+
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_0" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_3" stoichiometry="1.4"/>
+        </ListOfProducts>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_5" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5378" name="V" value="5007.02"/>
+          <Constant key="Parameter_5377" name="KM" value="0.02"/>
+          <Constant key="Parameter_5376" name="Ki" value="1e+10"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_41" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_265">
+              <SourceParameter reference="Parameter_5378"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_250">
+              <SourceParameter reference="Metabolite_0"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_261">
+              <SourceParameter reference="Parameter_5377"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_266">
+              <SourceParameter reference="Metabolite_5"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_267">
+              <SourceParameter reference="Parameter_5376"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_1" name="ackA" reversible="true" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_1" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_2" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfConstants>
+          <Constant key="Parameter_5375" name="v_ACK_Vmax" value="94788.6"/>
+          <Constant key="Parameter_5374" name="ACP" value="1"/>
+          <Constant key="Parameter_5373" name="ADP" value="0.606"/>
+          <Constant key="Parameter_5372" name="v_ACK_KmACP" value="0.16"/>
+          <Constant key="Parameter_5371" name="v_ACK_KmADP" value="0.5"/>
+          <Constant key="Parameter_5370" name="ACE" value="1"/>
+          <Constant key="Parameter_5369" name="v_ACK_KmACE" value="7"/>
+          <Constant key="Parameter_5368" name="ATP" value="2.4"/>
+          <Constant key="Parameter_5367" name="v_ACK_KmATP" value="0.07"/>
+          <Constant key="Parameter_5366" name="v_ACK_Keq" value="174"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_43" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_281">
+              <SourceParameter reference="ModelValue_10"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_280">
+              <SourceParameter reference="Metabolite_1"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_279">
+              <SourceParameter reference="ModelValue_11"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_278">
+              <SourceParameter reference="ModelValue_15"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_277">
+              <SourceParameter reference="ModelValue_12"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_276">
+              <SourceParameter reference="ModelValue_13"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_275">
+              <SourceParameter reference="Metabolite_2"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_282">
+              <SourceParameter reference="ModelValue_14"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_283">
+              <SourceParameter reference="ModelValue_16"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_284">
+              <SourceParameter reference="ModelValue_17"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_2" name="pta" reversible="true" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+    <dcterms:created>
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+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_3" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_1" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_3" stoichiometry="1"/>
+          <Modifier metabolite="Metabolite_1" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5365" name="v_PTA_Vmax" value="9.75624e+06"/>
+          <Constant key="Parameter_5364" name="ACCOA" value="1"/>
+          <Constant key="Parameter_5363" name="P" value="10"/>
+          <Constant key="Parameter_5362" name="ACP" value="1"/>
+          <Constant key="Parameter_5361" name="COA" value="1.22"/>
+          <Constant key="Parameter_5360" name="v_PTA_KiACCOA" value="0.2"/>
+          <Constant key="Parameter_5359" name="v_PTA_KmP" value="2.6"/>
+          <Constant key="Parameter_5358" name="v_PTA_KiP" value="2.6"/>
+          <Constant key="Parameter_5357" name="v_PTA_KiACP" value="0.2"/>
+          <Constant key="Parameter_5356" name="v_PTA_KiCOA" value="0.029"/>
+          <Constant key="Parameter_5355" name="v_PTA_KmACP" value="0.7"/>
+          <Constant key="Parameter_5679" name="KEQ" value="0.0281"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_44" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_294">
+              <SourceParameter reference="ModelValue_0"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_293">
+              <SourceParameter reference="Metabolite_3"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_292">
+              <SourceParameter reference="ModelValue_7"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_291">
+              <SourceParameter reference="Metabolite_1"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_290">
+              <SourceParameter reference="ModelValue_8"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_289">
+              <SourceParameter reference="ModelValue_9"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_288">
+              <SourceParameter reference="ModelValue_1"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_287">
+              <SourceParameter reference="ModelValue_2"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_286">
+              <SourceParameter reference="ModelValue_3"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_285">
+              <SourceParameter reference="ModelValue_4"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_295">
+              <SourceParameter reference="ModelValue_5"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_296">
+              <SourceParameter reference="ModelValue_6"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_3" name="sink" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_3">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:28:46Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_3" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_3" stoichiometry="1"/>
+          <Modifier metabolite="Metabolite_5" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5680" name="n" value="1"/>
+          <Constant key="Parameter_5678" name="Km" value="345.699"/>
+          <Constant key="Parameter_5681" name="Ki" value="1e+10"/>
+          <Constant key="Parameter_5708" name="V" value="1.52803e+06"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_42" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_272">
+              <SourceParameter reference="Metabolite_3"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_271">
+              <SourceParameter reference="Metabolite_3"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_270">
+              <SourceParameter reference="ModelValue_18"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_269">
+              <SourceParameter reference="Parameter_5680"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_268">
+              <SourceParameter reference="ModelValue_19"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_273">
+              <SourceParameter reference="Metabolite_5"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_274">
+              <SourceParameter reference="ModelValue_23"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_4" name="growth" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_4">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T12:07:54Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_4" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfConstants>
+          <Constant key="Parameter_5709" name="Y" value="7.99554e-05"/>
+          <Constant key="Parameter_5707" name="sink" value="6426.21"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_40" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_264">
+              <SourceParameter reference="ModelValue_21"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_263">
+              <SourceParameter reference="Metabolite_4"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_262">
+              <SourceParameter reference="ModelValue_20"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_5" name="ace_xch" reversible="true" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_5">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-02-26T10:33:46Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_2" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_5" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfConstants>
+          <Constant key="Parameter_5710" name="Kmp" value="7.12633"/>
+          <Constant key="Parameter_5692" name="Vf" value="22099.7"/>
+          <Constant key="Parameter_5693" name="Vr" value="22099.7"/>
+          <Constant key="Parameter_5691" name="Kms" value="7.12633"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_28" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_195">
+              <SourceParameter reference="Metabolite_2"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_196">
+              <SourceParameter reference="Metabolite_5"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_197">
+              <SourceParameter reference="ModelValue_24"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_198">
+              <SourceParameter reference="ModelValue_24"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_199">
+              <SourceParameter reference="ModelValue_25"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_200">
+              <SourceParameter reference="ModelValue_25"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+    </ListOfReactions>
+    <ListOfEvents>
+      <Event key="Event_0" name="pulse_acetate" fireAtInitialTime="0" persistentTrigger="0">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Event_0">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-04-30T20:08:42Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <TriggerExpression>
+          &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[X],Reference=Concentration> >= &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_X_conc_pulse],Reference=InitialValue>
+        </TriggerExpression>
+        <ListOfAssignments>
+          <Assignment target="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace_out]" targetKey="Metabolite_5">
+            <Expression>
+              &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace_out],Reference=Concentration>+30
+            </Expression>
+          </Assignment>
+        </ListOfAssignments>
+      </Event>
+    </ListOfEvents>
+    <ListOfModelParameterSets activeSet="ModelParameterSet_1">
+      <ModelParameterSet key="ModelParameterSet_1" name="Initial State">
+        <MiriamAnnotation>
+<rdf:RDF
+xmlns:dcterms="http://purl.org/dc/terms/"
+xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+<rdf:Description rdf:about="#ModelParameterSet_1">
+<dcterms:created>
+<rdf:Description>
+<dcterms:W3CDTF>2020-12-28T16:33:11Z</dcterms:W3CDTF>
+</rdf:Description>
+</dcterms:created>
+</rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ModelParameterGroup cn="String=Initial Time" type="Group">
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism" value="0" type="Model" simulationType="time"/>
+        </ModelParameterGroup>
+        <ModelParameterGroup cn="String=Initial Compartment Sizes" type="Group">
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]" value="1" type="Compartment" simulationType="fixed"/>
+        </ModelParameterGroup>
+        <ModelParameterGroup cn="String=Initial Species Values" type="Group">
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Glc]" value="1.2044281714000001e+22" type="Species" simulationType="ode"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[AcP]" value="6.0221408570000002e+20" type="Species" simulationType="reactions"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace]" value="6.0221408570000002e+20" type="Species" simulationType="reactions"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[AcCoA]" value="8.7923256512199996e+20" type="Species" simulationType="reactions"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[X]" value="6.0221408570000007e+19" type="Species" simulationType="ode"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace_out]" value="6.0221408570000007e+19" type="Species" simulationType="ode"/>
+        </ModelParameterGroup>
+        <ModelParameterGroup cn="String=Initial Global Quantities" type="Group">
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Vmax]" value="9756242.9959999993" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACCOA]" value="0.20000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmP]" value="2.6000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiP]" value="2.6000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACP]" value="0.20000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiCOA]" value="0.029000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmACP]" value="0.69999999999999996" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[P]" value="10" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[CoA]" value="1.22" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Keq]" value="0.0281" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Vmax]" value="94788.645690000005" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ADP]" value="0.60599999999999998" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACP]" value="0.16" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmADP]" value="0.5" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACE]" value="7" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ATP]" value="2.3999999999999999" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmATP]" value="0.070000000000000007" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Keq]" value="174" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Vmax]" value="1528025.1410000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Km]" value="345.69920159999998" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[v_sink]" value="6426.206465378883" type="ModelValue" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[Y]" value="7.9955412690000001e-05" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[volume]" value="0.0017700000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Ki]" value="10000000000" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Km]" value="7.1263327710000004" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Vmax]" value="22099.742200000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[v_growth_rate]" value="0.51380998997051475" type="ModelValue" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Ki]" value="60" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[v_glc_uptake]" value="8.8535718280832931" type="ModelValue" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[v_ace_net]" value="4.2795362532265351" type="ModelValue" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_dilution_rate]" value="0" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_feed]" value="0" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_X_conc_pulse]" value="10000" type="ModelValue" simulationType="fixed"/>
+        </ModelParameterGroup>
+        <ModelParameterGroup cn="String=Kinetic Parameters" type="Group">
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt],ParameterGroup=Parameters,Parameter=V" value="5007.0200000000004" type="ReactionParameter" simulationType="fixed"/>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt],ParameterGroup=Parameters,Parameter=KM" value="0.02" type="ReactionParameter" simulationType="fixed"/>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt],ParameterGroup=Parameters,Parameter=Ki" value="10000000000" type="ReactionParameter" simulationType="fixed"/>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=v_ACK_Vmax" value="94788.645690000005" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=ADP" value="0.60599999999999998" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ADP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=v_ACK_KmACP" value="0.16" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=v_ACK_KmADP" value="0.5" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmADP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=v_ACK_KmACE" value="7" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACE],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=ATP" value="2.3999999999999999" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ATP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=v_ACK_KmATP" value="0.070000000000000007" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmATP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=v_ACK_Keq" value="174" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Keq],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_Vmax" value="9756242.9959999993" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=P" value="10" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[P],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=COA" value="1.22" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[CoA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_KiACCOA" value="0.20000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACCOA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_KmP" value="2.6000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_KiP" value="2.6000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_KiACP" value="0.20000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_KiCOA" value="0.029000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiCOA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_KmACP" value="0.69999999999999996" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=KEQ" value="0.0281" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Keq],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink],ParameterGroup=Parameters,Parameter=n" value="1" type="ReactionParameter" simulationType="fixed"/>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink],ParameterGroup=Parameters,Parameter=Km" value="345.69920159999998" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Km],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink],ParameterGroup=Parameters,Parameter=Ki" value="10000000000" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Ki],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink],ParameterGroup=Parameters,Parameter=V" value="1528025.1410000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[growth]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[growth],ParameterGroup=Parameters,Parameter=Y" value="7.9955412690000001e-05" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[Y],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[growth],ParameterGroup=Parameters,Parameter=sink" value="6426.206465378883" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[v_sink],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch],ParameterGroup=Parameters,Parameter=Kmp" value="7.1263327710000004" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Km],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch],ParameterGroup=Parameters,Parameter=Vf" value="22099.742200000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch],ParameterGroup=Parameters,Parameter=Vr" value="22099.742200000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch],ParameterGroup=Parameters,Parameter=Kms" value="7.1263327710000004" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Km],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+        </ModelParameterGroup>
+      </ModelParameterSet>
+    </ListOfModelParameterSets>
+    <StateTemplate>
+      <StateTemplateVariable objectReference="Model_1"/>
+      <StateTemplateVariable objectReference="Metabolite_0"/>
+      <StateTemplateVariable objectReference="Metabolite_4"/>
+      <StateTemplateVariable objectReference="Metabolite_5"/>
+      <StateTemplateVariable objectReference="Metabolite_3"/>
+      <StateTemplateVariable objectReference="Metabolite_2"/>
+      <StateTemplateVariable objectReference="Metabolite_1"/>
+      <StateTemplateVariable objectReference="ModelValue_20"/>
+      <StateTemplateVariable objectReference="ModelValue_26"/>
+      <StateTemplateVariable objectReference="ModelValue_28"/>
+      <StateTemplateVariable objectReference="ModelValue_29"/>
+      <StateTemplateVariable objectReference="Compartment_0"/>
+      <StateTemplateVariable objectReference="ModelValue_0"/>
+      <StateTemplateVariable objectReference="ModelValue_1"/>
+      <StateTemplateVariable objectReference="ModelValue_2"/>
+      <StateTemplateVariable objectReference="ModelValue_3"/>
+      <StateTemplateVariable objectReference="ModelValue_4"/>
+      <StateTemplateVariable objectReference="ModelValue_5"/>
+      <StateTemplateVariable objectReference="ModelValue_6"/>
+      <StateTemplateVariable objectReference="ModelValue_7"/>
+      <StateTemplateVariable objectReference="ModelValue_8"/>
+      <StateTemplateVariable objectReference="ModelValue_9"/>
+      <StateTemplateVariable objectReference="ModelValue_10"/>
+      <StateTemplateVariable objectReference="ModelValue_11"/>
+      <StateTemplateVariable objectReference="ModelValue_12"/>
+      <StateTemplateVariable objectReference="ModelValue_13"/>
+      <StateTemplateVariable objectReference="ModelValue_14"/>
+      <StateTemplateVariable objectReference="ModelValue_15"/>
+      <StateTemplateVariable objectReference="ModelValue_16"/>
+      <StateTemplateVariable objectReference="ModelValue_17"/>
+      <StateTemplateVariable objectReference="ModelValue_18"/>
+      <StateTemplateVariable objectReference="ModelValue_19"/>
+      <StateTemplateVariable objectReference="ModelValue_21"/>
+      <StateTemplateVariable objectReference="ModelValue_22"/>
+      <StateTemplateVariable objectReference="ModelValue_23"/>
+      <StateTemplateVariable objectReference="ModelValue_24"/>
+      <StateTemplateVariable objectReference="ModelValue_25"/>
+      <StateTemplateVariable objectReference="ModelValue_27"/>
+      <StateTemplateVariable objectReference="ModelValue_30"/>
+      <StateTemplateVariable objectReference="ModelValue_31"/>
+      <StateTemplateVariable objectReference="ModelValue_32"/>
+    </StateTemplate>
+    <InitialState type="initialState">
+      0 1.2044281714000001e+22 6.0221408570000007e+19 6.0221408570000007e+19 8.7923256512199996e+20 6.0221408570000002e+20 6.0221408570000002e+20 6426.206465378883 0.51380998997051475 8.8535718280832931 4.2795362532265351 1 9756242.9959999993 0.20000000000000001 2.6000000000000001 2.6000000000000001 0.20000000000000001 0.029000000000000001 0.69999999999999996 10 1.22 0.0281 94788.645690000005 0.60599999999999998 0.16 0.5 7 2.3999999999999999 0.070000000000000007 174 1528025.1410000001 345.69920159999998 7.9955412690000001e-05 0.0017700000000000001 10000000000 7.1263327710000004 22099.742200000001 60 0 0 10000 
+    </InitialState>
+  </Model>
+  <ListOfTasks>
+    <Task key="Task_15" name="Steady-State" type="steadyState" scheduled="false" updateModel="false">
+      <Report reference="Report_10" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="JacobianRequested" type="bool" value="1"/>
+        <Parameter name="StabilityAnalysisRequested" type="bool" value="1"/>
+      </Problem>
+      <Method name="Enhanced Newton" type="EnhancedNewton">
+        <Parameter name="Resolution" type="unsignedFloat" value="1.0000000000000001e-09"/>
+        <Parameter name="Derivation Factor" type="unsignedFloat" value="0.001"/>
+        <Parameter name="Use Newton" type="bool" value="0"/>
+        <Parameter name="Use Integration" type="bool" value="1"/>
+        <Parameter name="Use Back Integration" type="bool" value="0"/>
+        <Parameter name="Accept Negative Concentrations" type="bool" value="0"/>
+        <Parameter name="Iteration Limit" type="unsignedInteger" value="50"/>
+        <Parameter name="Maximum duration for forward integration" type="unsignedFloat" value="1000000000"/>
+        <Parameter name="Maximum duration for backward integration" type="unsignedFloat" value="1000000"/>
+      </Method>
+    </Task>
+    <Task key="Task_16" name="Time-Course" type="timeCourse" scheduled="false" updateModel="false">
+      <Problem>
+        <Parameter name="AutomaticStepSize" type="bool" value="0"/>
+        <Parameter name="StepNumber" type="unsignedInteger" value="1000"/>
+        <Parameter name="StepSize" type="float" value="0.01"/>
+        <Parameter name="Duration" type="float" value="10"/>
+        <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
+        <Parameter name="OutputStartTime" type="float" value="0.10000000000000001"/>
+        <Parameter name="Output Event" type="bool" value="1"/>
+        <Parameter name="Start in Steady State" type="bool" value="0"/>
+        <Parameter name="Use Values" type="bool" value="0"/>
+        <Parameter name="Values" type="string" value=""/>
+      </Problem>
+      <Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
+        <Parameter name="Integrate Reduced Model" type="bool" value="0"/>
+        <Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-07"/>
+        <Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
+        <Parameter name="Max Internal Steps" type="unsignedInteger" value="100000"/>
+        <Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
+      </Method>
+    </Task>
+    <Task key="Task_17" name="Scan" type="scan" scheduled="false" updateModel="false">
+      <Problem>
+        <Parameter name="Subtask" type="unsignedInteger" value="0"/>
+        <ParameterGroup name="ScanItems">
+        </ParameterGroup>
+        <Parameter name="Output in subtask" type="bool" value="0"/>
+        <Parameter name="Adjust initial conditions" type="bool" value="0"/>
+        <Parameter name="Continue on Error" type="bool" value="0"/>
+      </Problem>
+      <Method name="Scan Framework" type="ScanFramework">
+      </Method>
+    </Task>
+    <Task key="Task_18" name="Elementary Flux Modes" type="fluxMode" scheduled="false" updateModel="false">
+      <Report reference="Report_11" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+      </Problem>
+      <Method name="EFM Algorithm" type="EFMAlgorithm">
+      </Method>
+    </Task>
+    <Task key="Task_19" name="Optimization" type="optimization" scheduled="false" updateModel="false">
+      <Report reference="Report_12" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="Subtask" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
+        <ParameterText name="ObjectiveExpression" type="expression">
+          
+        </ParameterText>
+        <Parameter name="Maximize" type="bool" value="0"/>
+        <Parameter name="Randomize Start Values" type="bool" value="0"/>
+        <Parameter name="Calculate Statistics" type="bool" value="1"/>
+        <ParameterGroup name="OptimizationItemList">
+        </ParameterGroup>
+        <ParameterGroup name="OptimizationConstraintList">
+        </ParameterGroup>
+      </Problem>
+      <Method name="Random Search" type="RandomSearch">
+        <Parameter name="Log Verbosity" type="unsignedInteger" value="0"/>
+        <Parameter name="Number of Iterations" type="unsignedInteger" value="100000"/>
+        <Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
+        <Parameter name="Seed" type="unsignedInteger" value="0"/>
+      </Method>
+    </Task>
+    <Task key="Task_20" name="Parameter Estimation" type="parameterFitting" scheduled="false" updateModel="false">
+      <Report reference="Report_13" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="Maximize" type="bool" value="0"/>
+        <Parameter name="Randomize Start Values" type="bool" value="0"/>
+        <Parameter name="Calculate Statistics" type="bool" value="1"/>
+        <ParameterGroup name="OptimizationItemList">
+        </ParameterGroup>
+        <ParameterGroup name="OptimizationConstraintList">
+        </ParameterGroup>
+        <Parameter name="Steady-State" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
+        <Parameter name="Time-Course" type="cn" value="CN=Root,Vector=TaskList[Time-Course]"/>
+        <Parameter name="Create Parameter Sets" type="bool" value="0"/>
+        <ParameterGroup name="Experiment Set">
+        </ParameterGroup>
+        <ParameterGroup name="Validation Set">
+          <Parameter name="Weight" type="unsignedFloat" value="1"/>
+          <Parameter name="Threshold" type="unsignedInteger" value="5"/>
+        </ParameterGroup>
+      </Problem>
+      <Method name="Current Solution Statistics" type="CurrentSolutionStatistics">
+        <Parameter name="Log Verbosity" type="unsignedInteger" value="0"/>
+      </Method>
+    </Task>
+    <Task key="Task_21" name="Metabolic Control Analysis" type="metabolicControlAnalysis" scheduled="false" updateModel="false">
+      <Report reference="Report_14" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="Steady-State" type="key" value="Task_15"/>
+      </Problem>
+      <Method name="MCA Method (Reder)" type="MCAMethod(Reder)">
+        <Parameter name="Modulation Factor" type="unsignedFloat" value="1.0000000000000001e-09"/>
+        <Parameter name="Use Reder" type="bool" value="1"/>
+        <Parameter name="Use Smallbone" type="bool" value="1"/>
+      </Method>
+    </Task>
+    <Task key="Task_22" name="Lyapunov Exponents" type="lyapunovExponents" scheduled="false" updateModel="false">
+      <Report reference="Report_15" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="ExponentNumber" type="unsignedInteger" value="3"/>
+        <Parameter name="DivergenceRequested" type="bool" value="1"/>
+        <Parameter name="TransientTime" type="float" value="0"/>
+      </Problem>
+      <Method name="Wolf Method" type="WolfMethod">
+        <Parameter name="Orthonormalization Interval" type="unsignedFloat" value="1"/>
+        <Parameter name="Overall time" type="unsignedFloat" value="1000"/>
+        <Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-07"/>
+        <Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
+        <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
+      </Method>
+    </Task>
+    <Task key="Task_23" name="Time Scale Separation Analysis" type="timeScaleSeparationAnalysis" scheduled="false" updateModel="false">
+      <Report reference="Report_16" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="StepNumber" type="unsignedInteger" value="100"/>
+        <Parameter name="StepSize" type="float" value="0.01"/>
+        <Parameter name="Duration" type="float" value="1"/>
+        <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
+        <Parameter name="OutputStartTime" type="float" value="0"/>
+      </Problem>
+      <Method name="ILDM (LSODA,Deuflhard)" type="TimeScaleSeparation(ILDM,Deuflhard)">
+        <Parameter name="Deuflhard Tolerance" type="unsignedFloat" value="0.0001"/>
+      </Method>
+    </Task>
+    <Task key="Task_24" name="Sensitivities" type="sensitivities" scheduled="false" updateModel="false">
+      <Report reference="Report_17" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="SubtaskType" type="unsignedInteger" value="1"/>
+        <ParameterGroup name="TargetFunctions">
+          <Parameter name="SingleObject" type="cn" value=""/>
+          <Parameter name="ObjectListType" type="unsignedInteger" value="7"/>
+        </ParameterGroup>
+        <ParameterGroup name="ListOfVariables">
+          <ParameterGroup name="Variables">
+            <Parameter name="SingleObject" type="cn" value=""/>
+            <Parameter name="ObjectListType" type="unsignedInteger" value="41"/>
+          </ParameterGroup>
+          <ParameterGroup name="Variables">
+            <Parameter name="SingleObject" type="cn" value=""/>
+            <Parameter name="ObjectListType" type="unsignedInteger" value="0"/>
+          </ParameterGroup>
+        </ParameterGroup>
+      </Problem>
+      <Method name="Sensitivities Method" type="SensitivitiesMethod">
+        <Parameter name="Delta factor" type="unsignedFloat" value="0.001"/>
+        <Parameter name="Delta minimum" type="unsignedFloat" value="9.9999999999999998e-13"/>
+      </Method>
+    </Task>
+    <Task key="Task_25" name="Moieties" type="moieties" scheduled="false" updateModel="false">
+      <Report reference="Report_18" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+      </Problem>
+      <Method name="Householder Reduction" type="Householder">
+      </Method>
+    </Task>
+    <Task key="Task_26" name="Cross Section" type="crosssection" scheduled="false" updateModel="false">
+      <Problem>
+        <Parameter name="AutomaticStepSize" type="bool" value="0"/>
+        <Parameter name="StepNumber" type="unsignedInteger" value="100"/>
+        <Parameter name="StepSize" type="float" value="0.01"/>
+        <Parameter name="Duration" type="float" value="1"/>
+        <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
+        <Parameter name="OutputStartTime" type="float" value="0"/>
+        <Parameter name="Output Event" type="bool" value="0"/>
+        <Parameter name="Start in Steady State" type="bool" value="0"/>
+        <Parameter name="Use Values" type="bool" value="0"/>
+        <Parameter name="Values" type="string" value=""/>
+        <Parameter name="LimitCrossings" type="bool" value="0"/>
+        <Parameter name="NumCrossingsLimit" type="unsignedInteger" value="0"/>
+        <Parameter name="LimitOutTime" type="bool" value="0"/>
+        <Parameter name="LimitOutCrossings" type="bool" value="0"/>
+        <Parameter name="PositiveDirection" type="bool" value="1"/>
+        <Parameter name="NumOutCrossingsLimit" type="unsignedInteger" value="0"/>
+        <Parameter name="LimitUntilConvergence" type="bool" value="0"/>
+        <Parameter name="ConvergenceTolerance" type="float" value="9.9999999999999995e-07"/>
+        <Parameter name="Threshold" type="float" value="0"/>
+        <Parameter name="DelayOutputUntilConvergence" type="bool" value="0"/>
+        <Parameter name="OutputConvergenceTolerance" type="float" value="9.9999999999999995e-07"/>
+        <ParameterText name="TriggerExpression" type="expression">
+          
+        </ParameterText>
+        <Parameter name="SingleVariable" type="cn" value=""/>
+      </Problem>
+      <Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
+        <Parameter name="Integrate Reduced Model" type="bool" value="0"/>
+        <Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-07"/>
+        <Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
+        <Parameter name="Max Internal Steps" type="unsignedInteger" value="100000"/>
+        <Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
+      </Method>
+    </Task>
+    <Task key="Task_27" name="Linear Noise Approximation" type="linearNoiseApproximation" scheduled="false" updateModel="false">
+      <Report reference="Report_19" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="Steady-State" type="key" value="Task_15"/>
+      </Problem>
+      <Method name="Linear Noise Approximation" type="LinearNoiseApproximation">
+      </Method>
+    </Task>
+    <Task key="Task_28" name="Time-Course Sensitivities" type="timeSensitivities" scheduled="false" updateModel="false">
+      <Problem>
+        <Parameter name="AutomaticStepSize" type="bool" value="0"/>
+        <Parameter name="StepNumber" type="unsignedInteger" value="100"/>
+        <Parameter name="StepSize" type="float" value="0.01"/>
+        <Parameter name="Duration" type="float" value="1"/>
+        <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
+        <Parameter name="OutputStartTime" type="float" value="0"/>
+        <Parameter name="Output Event" type="bool" value="0"/>
+        <Parameter name="Start in Steady State" type="bool" value="0"/>
+        <Parameter name="Use Values" type="bool" value="0"/>
+        <Parameter name="Values" type="string" value=""/>
+        <ParameterGroup name="ListOfParameters">
+        </ParameterGroup>
+        <ParameterGroup name="ListOfTargets">
+        </ParameterGroup>
+      </Problem>
+      <Method name="LSODA Sensitivities" type="Sensitivities(LSODA)">
+        <Parameter name="Integrate Reduced Model" type="bool" value="0"/>
+        <Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-07"/>
+        <Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
+        <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
+        <Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
+      </Method>
+    </Task>
+  </ListOfTasks>
+  <ListOfReports>
+    <Report key="Report_10" name="Steady-State" taskType="steadyState" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Footer>
+        <Object cn="CN=Root,Vector=TaskList[Steady-State]"/>
+      </Footer>
+    </Report>
+    <Report key="Report_11" name="Elementary Flux Modes" taskType="fluxMode" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Footer>
+        <Object cn="CN=Root,Vector=TaskList[Elementary Flux Modes],Object=Result"/>
+      </Footer>
+    </Report>
+    <Report key="Report_12" name="Optimization" taskType="optimization" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Header>
+        <Object cn="CN=Root,Vector=TaskList[Optimization],Object=Description"/>
+        <Object cn="String=\[Function Evaluations\]"/>
+        <Object cn="Separator=&#x09;"/>
+        <Object cn="String=\[Best Value\]"/>
+        <Object cn="Separator=&#x09;"/>
+        <Object cn="String=\[Best Parameters\]"/>
+      </Header>
+      <Body>
+        <Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Function Evaluations"/>
+        <Object cn="Separator=&#x09;"/>
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diff --git a/model/cps/Millard2020_Ecoli_glc_ace_kinetic_model_2.cps b/model/cps/Millard2020_Ecoli_glc_ace_kinetic_model_2.cps
new file mode 100644
index 0000000..0cb7926
--- /dev/null
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+see Millard et al., 2020 for details
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+      </ModelValue>
+      <ModelValue key="ModelValue_28" name="v_glc_uptake" simulationType="assignment" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_28">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-04-30T12:35:30Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <Expression>
+          &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt],Reference=Flux>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[volume],Reference=InitialValue>
+        </Expression>
+      </ModelValue>
+      <ModelValue key="ModelValue_29" name="v_ace_net" simulationType="assignment" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_29">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-04-30T12:35:57Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <Expression>
+          &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch],Reference=Flux>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[volume],Reference=InitialValue>
+        </Expression>
+      </ModelValue>
+      <ModelValue key="ModelValue_30" name="_dilution_rate" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_30">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-05-01T07:35:17Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <Comment>
+          dilution rate (in h-1), used to simulate chemostat experiment
+
+default value: 0
+        </Comment>
+      </ModelValue>
+      <ModelValue key="ModelValue_31" name="_feed" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_31">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-05-01T07:35:27Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <Comment>
+          feed (in mmolGlc/h-1), used to simulate chemostat experiment
+
+default value: 0
+        </Comment>
+      </ModelValue>
+      <ModelValue key="ModelValue_32" name="_X_conc_pulse" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_32">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-05-01T07:42:16Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <Comment>
+          biomass concentration at which a 30mM acetate pulse it performed
+
+default value: 10000 (i.e., no pulse)
+        </Comment>
+      </ModelValue>
+    </ListOfModelValues>
+    <ListOfReactions>
+      <Reaction key="Reaction_0" name="glc_upt" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF
+   xmlns:dcterms="http://purl.org/dc/terms/"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_0">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:27:37Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_0" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_3" stoichiometry="1.4"/>
+        </ListOfProducts>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_5" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5378" name="V" value="5631.87"/>
+          <Constant key="Parameter_5377" name="KM" value="0.02"/>
+          <Constant key="Parameter_5376" name="Ki" value="32.9126"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_41" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_265">
+              <SourceParameter reference="Parameter_5378"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_250">
+              <SourceParameter reference="Metabolite_0"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_261">
+              <SourceParameter reference="Parameter_5377"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_266">
+              <SourceParameter reference="Metabolite_5"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_267">
+              <SourceParameter reference="Parameter_5376"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_1" name="ackA" reversible="true" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_1">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:28:35Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_1" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_2" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfConstants>
+          <Constant key="Parameter_5375" name="v_ACK_Vmax" value="94935.2"/>
+          <Constant key="Parameter_5374" name="ACP" value="1"/>
+          <Constant key="Parameter_5373" name="ADP" value="0.606"/>
+          <Constant key="Parameter_5372" name="v_ACK_KmACP" value="0.16"/>
+          <Constant key="Parameter_5371" name="v_ACK_KmADP" value="0.5"/>
+          <Constant key="Parameter_5370" name="ACE" value="1"/>
+          <Constant key="Parameter_5369" name="v_ACK_KmACE" value="7"/>
+          <Constant key="Parameter_5368" name="ATP" value="2.4"/>
+          <Constant key="Parameter_5367" name="v_ACK_KmATP" value="0.07"/>
+          <Constant key="Parameter_5366" name="v_ACK_Keq" value="174"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_43" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_281">
+              <SourceParameter reference="ModelValue_10"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_280">
+              <SourceParameter reference="Metabolite_1"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_279">
+              <SourceParameter reference="ModelValue_11"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_278">
+              <SourceParameter reference="ModelValue_15"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_277">
+              <SourceParameter reference="ModelValue_12"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_276">
+              <SourceParameter reference="ModelValue_13"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_275">
+              <SourceParameter reference="Metabolite_2"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_282">
+              <SourceParameter reference="ModelValue_14"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_283">
+              <SourceParameter reference="ModelValue_16"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_284">
+              <SourceParameter reference="ModelValue_17"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_2" name="pta" reversible="true" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF
+   xmlns:dcterms="http://purl.org/dc/terms/"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_2">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:28:06Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_3" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_1" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_3" stoichiometry="1"/>
+          <Modifier metabolite="Metabolite_1" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5365" name="v_PTA_Vmax" value="7.31139e+06"/>
+          <Constant key="Parameter_5364" name="ACCOA" value="1"/>
+          <Constant key="Parameter_5363" name="P" value="10"/>
+          <Constant key="Parameter_5362" name="ACP" value="1"/>
+          <Constant key="Parameter_5361" name="COA" value="1.22"/>
+          <Constant key="Parameter_5360" name="v_PTA_KiACCOA" value="0.2"/>
+          <Constant key="Parameter_5359" name="v_PTA_KmP" value="2.6"/>
+          <Constant key="Parameter_5358" name="v_PTA_KiP" value="2.6"/>
+          <Constant key="Parameter_5357" name="v_PTA_KiACP" value="0.2"/>
+          <Constant key="Parameter_5356" name="v_PTA_KiCOA" value="0.029"/>
+          <Constant key="Parameter_5355" name="v_PTA_KmACP" value="0.7"/>
+          <Constant key="Parameter_5679" name="KEQ" value="0.0281"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_44" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_294">
+              <SourceParameter reference="ModelValue_0"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_293">
+              <SourceParameter reference="Metabolite_3"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_292">
+              <SourceParameter reference="ModelValue_7"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_291">
+              <SourceParameter reference="Metabolite_1"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_290">
+              <SourceParameter reference="ModelValue_8"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_289">
+              <SourceParameter reference="ModelValue_9"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_288">
+              <SourceParameter reference="ModelValue_1"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_287">
+              <SourceParameter reference="ModelValue_2"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_286">
+              <SourceParameter reference="ModelValue_3"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_285">
+              <SourceParameter reference="ModelValue_4"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_295">
+              <SourceParameter reference="ModelValue_5"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_296">
+              <SourceParameter reference="ModelValue_6"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_3" name="sink" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_3">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:28:46Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_3" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_3" stoichiometry="1"/>
+          <Modifier metabolite="Metabolite_5" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5680" name="n" value="1"/>
+          <Constant key="Parameter_5678" name="Km" value="929.178"/>
+          <Constant key="Parameter_5681" name="Ki" value="1e+10"/>
+          <Constant key="Parameter_5708" name="V" value="3.44526e+06"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_42" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_272">
+              <SourceParameter reference="Metabolite_3"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_271">
+              <SourceParameter reference="Metabolite_3"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_270">
+              <SourceParameter reference="ModelValue_18"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_269">
+              <SourceParameter reference="Parameter_5680"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_268">
+              <SourceParameter reference="ModelValue_19"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_273">
+              <SourceParameter reference="Metabolite_5"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_274">
+              <SourceParameter reference="ModelValue_23"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_4" name="growth" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_4">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T12:07:54Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_4" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfConstants>
+          <Constant key="Parameter_5709" name="Y" value="0.000101178"/>
+          <Constant key="Parameter_5707" name="sink" value="5404.98"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_40" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_264">
+              <SourceParameter reference="ModelValue_21"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_263">
+              <SourceParameter reference="Metabolite_4"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_262">
+              <SourceParameter reference="ModelValue_20"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_5" name="ace_xch" reversible="true" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_5">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-02-26T10:33:46Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_2" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_5" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfConstants>
+          <Constant key="Parameter_5710" name="Kmp" value="0.136038"/>
+          <Constant key="Parameter_5692" name="Vf" value="15231.4"/>
+          <Constant key="Parameter_5693" name="Vr" value="15231.4"/>
+          <Constant key="Parameter_5691" name="Kms" value="0.136038"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_28" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_195">
+              <SourceParameter reference="Metabolite_2"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_196">
+              <SourceParameter reference="Metabolite_5"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_197">
+              <SourceParameter reference="ModelValue_24"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_198">
+              <SourceParameter reference="ModelValue_24"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_199">
+              <SourceParameter reference="ModelValue_25"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_200">
+              <SourceParameter reference="ModelValue_25"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+    </ListOfReactions>
+    <ListOfEvents>
+      <Event key="Event_0" name="pulse_acetate" fireAtInitialTime="0" persistentTrigger="0">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Event_0">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-04-30T20:08:42Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <TriggerExpression>
+          &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[X],Reference=Concentration> >= &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_X_conc_pulse],Reference=InitialValue>
+        </TriggerExpression>
+        <ListOfAssignments>
+          <Assignment target="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace_out]" targetKey="Metabolite_5">
+            <Expression>
+              &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace_out],Reference=Concentration>+30
+            </Expression>
+          </Assignment>
+        </ListOfAssignments>
+      </Event>
+    </ListOfEvents>
+    <ListOfModelParameterSets activeSet="ModelParameterSet_1">
+      <ModelParameterSet key="ModelParameterSet_1" name="Initial State">
+        <MiriamAnnotation>
+<rdf:RDF
+xmlns:dcterms="http://purl.org/dc/terms/"
+xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+<rdf:Description rdf:about="#ModelParameterSet_1">
+<dcterms:created>
+<rdf:Description>
+<dcterms:W3CDTF>2020-12-28T16:31:25Z</dcterms:W3CDTF>
+</rdf:Description>
+</dcterms:created>
+</rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ModelParameterGroup cn="String=Initial Time" type="Group">
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism" value="0" type="Model" simulationType="time"/>
+        </ModelParameterGroup>
+        <ModelParameterGroup cn="String=Initial Compartment Sizes" type="Group">
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]" value="1" type="Compartment" simulationType="fixed"/>
+        </ModelParameterGroup>
+        <ModelParameterGroup cn="String=Initial Species Values" type="Group">
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Glc]" value="1.2044281714000001e+22" type="Species" simulationType="ode"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[AcP]" value="6.0221408570000002e+20" type="Species" simulationType="reactions"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace]" value="6.0221408570000002e+20" type="Species" simulationType="reactions"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[AcCoA]" value="8.7923256512199996e+20" type="Species" simulationType="reactions"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[X]" value="6.0221408570000007e+19" type="Species" simulationType="ode"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace_out]" value="6.0221408570000007e+19" type="Species" simulationType="ode"/>
+        </ModelParameterGroup>
+        <ModelParameterGroup cn="String=Initial Global Quantities" type="Group">
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Vmax]" value="7311390.142" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACCOA]" value="0.20000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmP]" value="2.6000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiP]" value="2.6000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACP]" value="0.20000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiCOA]" value="0.029000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmACP]" value="0.69999999999999996" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[P]" value="10" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[CoA]" value="1.22" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Keq]" value="0.0281" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Vmax]" value="94935.208010000002" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ADP]" value="0.60599999999999998" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACP]" value="0.16" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmADP]" value="0.5" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACE]" value="7" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ATP]" value="2.3999999999999999" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmATP]" value="0.070000000000000007" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Keq]" value="174" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Vmax]" value="3445256.0219999999" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Km]" value="929.17773529999999" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[v_sink]" value="5404.9751060741219" type="ModelValue" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[Y]" value="0.00010117827920000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[volume]" value="0.0017700000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Ki]" value="10000000000" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Km]" value="0.13603847150000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Vmax]" value="15231.405570000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[v_growth_rate]" value="0.54686608035141715" type="ModelValue" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Ki]" value="60" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[v_glc_uptake]" value="9.9282771781129515" type="ModelValue" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[v_ace_net]" value="19.630156853908254" type="ModelValue" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_dilution_rate]" value="0" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_feed]" value="0" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_X_conc_pulse]" value="10000" type="ModelValue" simulationType="fixed"/>
+        </ModelParameterGroup>
+        <ModelParameterGroup cn="String=Kinetic Parameters" type="Group">
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt],ParameterGroup=Parameters,Parameter=V" value="5631.8650850000004" type="ReactionParameter" simulationType="fixed"/>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt],ParameterGroup=Parameters,Parameter=KM" value="0.02" type="ReactionParameter" simulationType="fixed"/>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt],ParameterGroup=Parameters,Parameter=Ki" value="32.912602100000001" type="ReactionParameter" simulationType="fixed"/>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=v_ACK_Vmax" value="94935.208010000002" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=ADP" value="0.60599999999999998" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ADP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=v_ACK_KmACP" value="0.16" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=v_ACK_KmADP" value="0.5" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmADP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=v_ACK_KmACE" value="7" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACE],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=ATP" value="2.3999999999999999" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ATP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=v_ACK_KmATP" value="0.070000000000000007" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmATP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=v_ACK_Keq" value="174" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Keq],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_Vmax" value="7311390.142" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=P" value="10" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[P],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=COA" value="1.22" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[CoA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_KiACCOA" value="0.20000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACCOA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_KmP" value="2.6000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_KiP" value="2.6000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_KiACP" value="0.20000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_KiCOA" value="0.029000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiCOA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_KmACP" value="0.69999999999999996" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=KEQ" value="0.0281" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Keq],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink],ParameterGroup=Parameters,Parameter=n" value="1" type="ReactionParameter" simulationType="fixed"/>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink],ParameterGroup=Parameters,Parameter=Km" value="929.17773529999999" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Km],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink],ParameterGroup=Parameters,Parameter=Ki" value="10000000000" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Ki],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink],ParameterGroup=Parameters,Parameter=V" value="3445256.0219999999" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[growth]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[growth],ParameterGroup=Parameters,Parameter=Y" value="0.00010117827920000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[Y],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[growth],ParameterGroup=Parameters,Parameter=sink" value="5404.9751060741219" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[v_sink],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch],ParameterGroup=Parameters,Parameter=Kmp" value="0.13603847150000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Km],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch],ParameterGroup=Parameters,Parameter=Vf" value="15231.405570000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch],ParameterGroup=Parameters,Parameter=Vr" value="15231.405570000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch],ParameterGroup=Parameters,Parameter=Kms" value="0.13603847150000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Km],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+        </ModelParameterGroup>
+      </ModelParameterSet>
+    </ListOfModelParameterSets>
+    <StateTemplate>
+      <StateTemplateVariable objectReference="Model_1"/>
+      <StateTemplateVariable objectReference="Metabolite_0"/>
+      <StateTemplateVariable objectReference="Metabolite_4"/>
+      <StateTemplateVariable objectReference="Metabolite_5"/>
+      <StateTemplateVariable objectReference="Metabolite_3"/>
+      <StateTemplateVariable objectReference="Metabolite_2"/>
+      <StateTemplateVariable objectReference="Metabolite_1"/>
+      <StateTemplateVariable objectReference="ModelValue_20"/>
+      <StateTemplateVariable objectReference="ModelValue_26"/>
+      <StateTemplateVariable objectReference="ModelValue_28"/>
+      <StateTemplateVariable objectReference="ModelValue_29"/>
+      <StateTemplateVariable objectReference="Compartment_0"/>
+      <StateTemplateVariable objectReference="ModelValue_0"/>
+      <StateTemplateVariable objectReference="ModelValue_1"/>
+      <StateTemplateVariable objectReference="ModelValue_2"/>
+      <StateTemplateVariable objectReference="ModelValue_3"/>
+      <StateTemplateVariable objectReference="ModelValue_4"/>
+      <StateTemplateVariable objectReference="ModelValue_5"/>
+      <StateTemplateVariable objectReference="ModelValue_6"/>
+      <StateTemplateVariable objectReference="ModelValue_7"/>
+      <StateTemplateVariable objectReference="ModelValue_8"/>
+      <StateTemplateVariable objectReference="ModelValue_9"/>
+      <StateTemplateVariable objectReference="ModelValue_10"/>
+      <StateTemplateVariable objectReference="ModelValue_11"/>
+      <StateTemplateVariable objectReference="ModelValue_12"/>
+      <StateTemplateVariable objectReference="ModelValue_13"/>
+      <StateTemplateVariable objectReference="ModelValue_14"/>
+      <StateTemplateVariable objectReference="ModelValue_15"/>
+      <StateTemplateVariable objectReference="ModelValue_16"/>
+      <StateTemplateVariable objectReference="ModelValue_17"/>
+      <StateTemplateVariable objectReference="ModelValue_18"/>
+      <StateTemplateVariable objectReference="ModelValue_19"/>
+      <StateTemplateVariable objectReference="ModelValue_21"/>
+      <StateTemplateVariable objectReference="ModelValue_22"/>
+      <StateTemplateVariable objectReference="ModelValue_23"/>
+      <StateTemplateVariable objectReference="ModelValue_24"/>
+      <StateTemplateVariable objectReference="ModelValue_25"/>
+      <StateTemplateVariable objectReference="ModelValue_27"/>
+      <StateTemplateVariable objectReference="ModelValue_30"/>
+      <StateTemplateVariable objectReference="ModelValue_31"/>
+      <StateTemplateVariable objectReference="ModelValue_32"/>
+    </StateTemplate>
+    <InitialState type="initialState">
+      0 1.2044281714000001e+22 6.0221408570000007e+19 6.0221408570000007e+19 8.7923256512199996e+20 6.0221408570000002e+20 6.0221408570000002e+20 5404.9751060741219 0.54686608035141715 9.9282771781129515 19.630156853908254 1 7311390.142 0.20000000000000001 2.6000000000000001 2.6000000000000001 0.20000000000000001 0.029000000000000001 0.69999999999999996 10 1.22 0.0281 94935.208010000002 0.60599999999999998 0.16 0.5 7 2.3999999999999999 0.070000000000000007 174 3445256.0219999999 929.17773529999999 0.00010117827920000001 0.0017700000000000001 10000000000 0.13603847150000001 15231.405570000001 60 0 0 10000 
+    </InitialState>
+  </Model>
+  <ListOfTasks>
+    <Task key="Task_15" name="Steady-State" type="steadyState" scheduled="false" updateModel="false">
+      <Report reference="Report_10" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="JacobianRequested" type="bool" value="1"/>
+        <Parameter name="StabilityAnalysisRequested" type="bool" value="1"/>
+      </Problem>
+      <Method name="Enhanced Newton" type="EnhancedNewton">
+        <Parameter name="Resolution" type="unsignedFloat" value="1.0000000000000001e-09"/>
+        <Parameter name="Derivation Factor" type="unsignedFloat" value="0.001"/>
+        <Parameter name="Use Newton" type="bool" value="0"/>
+        <Parameter name="Use Integration" type="bool" value="1"/>
+        <Parameter name="Use Back Integration" type="bool" value="0"/>
+        <Parameter name="Accept Negative Concentrations" type="bool" value="0"/>
+        <Parameter name="Iteration Limit" type="unsignedInteger" value="50"/>
+        <Parameter name="Maximum duration for forward integration" type="unsignedFloat" value="1000000000"/>
+        <Parameter name="Maximum duration for backward integration" type="unsignedFloat" value="1000000"/>
+      </Method>
+    </Task>
+    <Task key="Task_16" name="Time-Course" type="timeCourse" scheduled="false" updateModel="false">
+      <Problem>
+        <Parameter name="AutomaticStepSize" type="bool" value="0"/>
+        <Parameter name="StepNumber" type="unsignedInteger" value="1000"/>
+        <Parameter name="StepSize" type="float" value="0.01"/>
+        <Parameter name="Duration" type="float" value="10"/>
+        <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
+        <Parameter name="OutputStartTime" type="float" value="0.10000000000000001"/>
+        <Parameter name="Output Event" type="bool" value="1"/>
+        <Parameter name="Start in Steady State" type="bool" value="0"/>
+        <Parameter name="Use Values" type="bool" value="0"/>
+        <Parameter name="Values" type="string" value=""/>
+      </Problem>
+      <Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
+        <Parameter name="Integrate Reduced Model" type="bool" value="0"/>
+        <Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-07"/>
+        <Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
+        <Parameter name="Max Internal Steps" type="unsignedInteger" value="100000"/>
+        <Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
+      </Method>
+    </Task>
+    <Task key="Task_17" name="Scan" type="scan" scheduled="false" updateModel="false">
+      <Problem>
+        <Parameter name="Subtask" type="unsignedInteger" value="0"/>
+        <ParameterGroup name="ScanItems">
+        </ParameterGroup>
+        <Parameter name="Output in subtask" type="bool" value="0"/>
+        <Parameter name="Adjust initial conditions" type="bool" value="0"/>
+        <Parameter name="Continue on Error" type="bool" value="0"/>
+      </Problem>
+      <Method name="Scan Framework" type="ScanFramework">
+      </Method>
+    </Task>
+    <Task key="Task_18" name="Elementary Flux Modes" type="fluxMode" scheduled="false" updateModel="false">
+      <Report reference="Report_11" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+      </Problem>
+      <Method name="EFM Algorithm" type="EFMAlgorithm">
+      </Method>
+    </Task>
+    <Task key="Task_19" name="Optimization" type="optimization" scheduled="false" updateModel="false">
+      <Report reference="Report_12" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="Subtask" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
+        <ParameterText name="ObjectiveExpression" type="expression">
+          
+        </ParameterText>
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diff --git a/model/cps/Millard2020_Ecoli_glc_ace_kinetic_model_3.cps b/model/cps/Millard2020_Ecoli_glc_ace_kinetic_model_3.cps
new file mode 100644
index 0000000..0d14f4b
--- /dev/null
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+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T12:15:09Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+      </MiriamAnnotation>
+      <Expression>
+        V*S/((KM+S)*(1+I/Ki))
+      </Expression>
+      <ListOfParameterDescriptions>
+        <ParameterDescription key="FunctionParameter_265" name="V" order="0" role="constant"/>
+        <ParameterDescription key="FunctionParameter_250" name="S" order="1" role="substrate"/>
+        <ParameterDescription key="FunctionParameter_261" name="KM" order="2" role="constant"/>
+        <ParameterDescription key="FunctionParameter_266" name="I" order="3" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_267" name="Ki" order="4" role="constant"/>
+      </ListOfParameterDescriptions>
+    </Function>
+    <Function key="Function_42" name="function_sink" type="UserDefined" reversible="unspecified">
+      <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Function_42">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T14:21:54Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+      </MiriamAnnotation>
+      <Expression>
+        A/At*V*At^n/((At^n+Km)*(1+I/Ki))
+      </Expression>
+      <ListOfParameterDescriptions>
+        <ParameterDescription key="FunctionParameter_272" name="A" order="0" role="substrate"/>
+        <ParameterDescription key="FunctionParameter_271" name="At" order="1" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_270" name="V" order="2" role="constant"/>
+        <ParameterDescription key="FunctionParameter_269" name="n" order="3" role="constant"/>
+        <ParameterDescription key="FunctionParameter_268" name="Km" order="4" role="constant"/>
+        <ParameterDescription key="FunctionParameter_273" name="I" order="5" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_274" name="Ki" order="6" role="constant"/>
+      </ListOfParameterDescriptions>
+    </Function>
+    <Function key="Function_43" name="ack" type="UserDefined" reversible="unspecified">
+      <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Function_43">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-04-30T11:17:51Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+      </MiriamAnnotation>
+      <Expression>
+        v_ACK_Vmax*(ACP*ADP-ACE*ATP/v_ACK_Keq)/ (v_ACK_KmACP*v_ACK_KmADP)/((1+ACP/ v_ACK_KmACP+ACE/v_ACK_KmACE)*(1+ADP/v_ACK_KmADP+ATP/v_ACK_KmATP))
+      </Expression>
+      <ListOfParameterDescriptions>
+        <ParameterDescription key="FunctionParameter_281" name="v_ACK_Vmax" order="0" role="constant"/>
+        <ParameterDescription key="FunctionParameter_280" name="ACP" order="1" role="substrate"/>
+        <ParameterDescription key="FunctionParameter_279" name="ADP" order="2" role="constant"/>
+        <ParameterDescription key="FunctionParameter_278" name="ATP" order="3" role="constant"/>
+        <ParameterDescription key="FunctionParameter_277" name="v_ACK_KmACP" order="4" role="constant"/>
+        <ParameterDescription key="FunctionParameter_276" name="v_ACK_KmADP" order="5" role="constant"/>
+        <ParameterDescription key="FunctionParameter_275" name="ACE" order="6" role="product"/>
+        <ParameterDescription key="FunctionParameter_282" name="v_ACK_KmACE" order="7" role="constant"/>
+        <ParameterDescription key="FunctionParameter_283" name="v_ACK_KmATP" order="8" role="constant"/>
+        <ParameterDescription key="FunctionParameter_284" name="v_ACK_Keq" order="9" role="constant"/>
+      </ListOfParameterDescriptions>
+    </Function>
+    <Function key="Function_44" name="pta" type="UserDefined" reversible="unspecified">
+      <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Function_44">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:31:22Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+      </MiriamAnnotation>
+      <Expression>
+        v_PTA_Vmax*(ACCOA*P-ACP*COA/KEQ)/ (v_PTA_KiACCOA*v_PTA_KmP)/(1+ACCOA/v_PTA_KiACCOA+P/ v_PTA_KiP+ACP/v_PTA_KiACP+COA/v_PTA_KiCOA+ACCOA*P/ (v_PTA_KiACCOA*v_PTA_KmP)+ACP*COA/(v_PTA_KmACP*v_PTA_KiCOA))
+      </Expression>
+      <ListOfParameterDescriptions>
+        <ParameterDescription key="FunctionParameter_294" name="v_PTA_Vmax" order="0" role="constant"/>
+        <ParameterDescription key="FunctionParameter_293" name="ACCOA" order="1" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_292" name="P" order="2" role="constant"/>
+        <ParameterDescription key="FunctionParameter_291" name="ACP" order="3" role="modifier"/>
+        <ParameterDescription key="FunctionParameter_290" name="COA" order="4" role="constant"/>
+        <ParameterDescription key="FunctionParameter_289" name="KEQ" order="5" role="constant"/>
+        <ParameterDescription key="FunctionParameter_288" name="v_PTA_KiACCOA" order="6" role="constant"/>
+        <ParameterDescription key="FunctionParameter_287" name="v_PTA_KmP" order="7" role="constant"/>
+        <ParameterDescription key="FunctionParameter_286" name="v_PTA_KiP" order="8" role="constant"/>
+        <ParameterDescription key="FunctionParameter_285" name="v_PTA_KiACP" order="9" role="constant"/>
+        <ParameterDescription key="FunctionParameter_295" name="v_PTA_KiCOA" order="10" role="constant"/>
+        <ParameterDescription key="FunctionParameter_296" name="v_PTA_KmACP" order="11" role="constant"/>
+      </ListOfParameterDescriptions>
+    </Function>
+  </ListOfFunctions>
+  <Model key="Model_1" name="E. coli model - Glc-Ace metabolism" simulationType="time" timeUnit="h" volumeUnit="l" areaUnit="m²" lengthUnit="m" quantityUnit="mmol" type="deterministic" avogadroConstant="6.0221408570000002e+23">
+    <MiriamAnnotation>
+<rdf:RDF
+   xmlns:dcterms="http://purl.org/dc/terms/"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Model_1">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:27:30Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+
+    </MiriamAnnotation>
+    <Comment>
+      Calibrated model of E. coli glucose and acetate metabolism
+
+see Millard et al., 2020 for details
+    </Comment>
+    <ListOfCompartments>
+      <Compartment key="Compartment_0" name="cell" simulationType="fixed" dimensionality="3" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Compartment_0">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:27:54Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </Compartment>
+    </ListOfCompartments>
+    <ListOfMetabolites>
+      <Metabolite key="Metabolite_0" name="Glc" simulationType="ode" compartment="Compartment_0" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Metabolite_0">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:27:54Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <Expression>
+          -&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[X],Reference=Concentration>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt],Reference=Flux>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[volume],Reference=InitialValue>+&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_feed],Reference=InitialValue>-&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_dilution_rate],Reference=InitialValue>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Glc],Reference=Concentration>
+        </Expression>
+      </Metabolite>
+      <Metabolite key="Metabolite_1" name="AcP" simulationType="reactions" compartment="Compartment_0" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Metabolite_1">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:46:12Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </Metabolite>
+      <Metabolite key="Metabolite_2" name="Ace" simulationType="reactions" compartment="Compartment_0" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Metabolite_2">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:46:12Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </Metabolite>
+      <Metabolite key="Metabolite_3" name="AcCoA" simulationType="reactions" compartment="Compartment_0" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Metabolite_3">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:47:47Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </Metabolite>
+      <Metabolite key="Metabolite_4" name="X" simulationType="ode" compartment="Compartment_0" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Metabolite_4">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T12:08:24Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <Expression>
+          &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[growth],Reference=Flux>-&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_dilution_rate],Reference=InitialValue>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[X],Reference=Concentration>
+        </Expression>
+      </Metabolite>
+      <Metabolite key="Metabolite_5" name="Ace_out" simulationType="ode" compartment="Compartment_0" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Metabolite_5">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-02-26T10:12:50Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <Comment>
+          calibrated with 0.009988794769
+        </Comment>
+        <Expression>
+          &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[X],Reference=Concentration>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch],Reference=Flux>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[volume],Reference=InitialValue>-&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_dilution_rate],Reference=InitialValue>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace_out],Reference=Concentration>
+        </Expression>
+      </Metabolite>
+    </ListOfMetabolites>
+    <ListOfModelValues>
+      <ModelValue key="ModelValue_0" name="r_PTA_Vmax" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF
+   xmlns:dcterms="http://purl.org/dc/terms/"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_0">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:53:52Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_1" name="r_PTA_KiACCOA" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_1">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:54:01Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_2" name="r_PTA_KmP" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_2">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:54:06Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_3" name="r_PTA_KiP" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_3">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:54:10Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_4" name="r_PTA_KiACP" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_4">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:54:14Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_5" name="r_PTA_KiCOA" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_5">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:54:18Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_6" name="r_PTA_KmACP" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_6">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:54:21Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_7" name="P" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_7">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:54:41Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_8" name="CoA" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_8">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:54:47Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_9" name="r_PTA_Keq" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_9">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:56:34Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_10" name="r_ACK_Vmax" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF
+   xmlns:dcterms="http://purl.org/dc/terms/"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_10">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:59:26Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_11" name="ADP" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_11">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:59:31Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_12" name="r_ACK_KmACP" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_12">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:59:35Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_13" name="r_ACK_KmADP" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_13">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:59:38Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_14" name="r_ACK_KmACE" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
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+    <dcterms:created>
+      <rdf:Description>
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+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_15" name="ATP" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
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+  </rdf:Description>
+</rdf:RDF>
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+      <ModelValue key="ModelValue_16" name="r_ACK_KmATP" simulationType="fixed" addNoise="false">
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+      </rdf:Description>
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+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_17" name="r_ACK_Keq" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
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+</rdf:RDF>
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_18" name="r_sink_Vmax" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF
+   xmlns:dcterms="http://purl.org/dc/terms/"
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+</rdf:RDF>
+
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_19" name="r_sink_Km" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF
+   xmlns:dcterms="http://purl.org/dc/terms/"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+</rdf:RDF>
+
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_20" name="v_sink" simulationType="assignment" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF
+   xmlns:dcterms="http://purl.org/dc/terms/"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_20">
+    <dcterms:created>
+      <rdf:Description>
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+        <Expression>
+          &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink],Reference=Flux>
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+      <ModelValue key="ModelValue_21" name="Y" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF
+   xmlns:dcterms="http://purl.org/dc/terms/"
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+  <rdf:Description rdf:about="#ModelValue_21">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T12:10:39Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_22" name="volume" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF
+   xmlns:dcterms="http://purl.org/dc/terms/"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_22">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T15:58:00Z</dcterms:W3CDTF>
+      </rdf:Description>
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+</rdf:RDF>
+
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_23" name="r_sink_Ki" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF
+   xmlns:dcterms="http://purl.org/dc/terms/"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_23">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T19:23:05Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_24" name="r_TRP_Km" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF
+   xmlns:dcterms="http://purl.org/dc/terms/"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_24">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-02-26T10:41:17Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_25" name="r_TRP_Vmax" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF
+   xmlns:dcterms="http://purl.org/dc/terms/"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_25">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-02-26T10:41:34Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_26" name="v_growth_rate" simulationType="assignment" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_26">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-02-26T13:37:18Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <Expression>
+          &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink],Reference=Flux>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[Y],Reference=InitialValue>
+        </Expression>
+      </ModelValue>
+      <ModelValue key="ModelValue_27" name="r_TRP_Ki" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF
+   xmlns:dcterms="http://purl.org/dc/terms/"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_27">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-04-29T19:12:37Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+
+        </MiriamAnnotation>
+      </ModelValue>
+      <ModelValue key="ModelValue_28" name="v_glc_uptake" simulationType="assignment" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_28">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-04-30T12:35:30Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <Expression>
+          &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt],Reference=Flux>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[volume],Reference=InitialValue>
+        </Expression>
+      </ModelValue>
+      <ModelValue key="ModelValue_29" name="v_ace_net" simulationType="assignment" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_29">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-04-30T12:35:57Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <Expression>
+          &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch],Reference=Flux>*&lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[volume],Reference=InitialValue>
+        </Expression>
+      </ModelValue>
+      <ModelValue key="ModelValue_30" name="_dilution_rate" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_30">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-05-01T07:35:17Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <Comment>
+          dilution rate (in h-1), used to simulate chemostat experiment
+
+default value: 0
+        </Comment>
+      </ModelValue>
+      <ModelValue key="ModelValue_31" name="_feed" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_31">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-05-01T07:35:27Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <Comment>
+          feed (in mmolGlc/h-1), used to simulate chemostat experiment
+
+default value: 0
+        </Comment>
+      </ModelValue>
+      <ModelValue key="ModelValue_32" name="_X_conc_pulse" simulationType="fixed" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#ModelValue_32">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-05-01T07:42:16Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <Comment>
+          biomass concentration at which a 30mM acetate pulse it performed
+
+default value: 10000 (i.e., no pulse)
+        </Comment>
+      </ModelValue>
+    </ListOfModelValues>
+    <ListOfReactions>
+      <Reaction key="Reaction_0" name="glc_upt" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF
+   xmlns:dcterms="http://purl.org/dc/terms/"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_0">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:27:37Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_0" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_3" stoichiometry="1.4"/>
+        </ListOfProducts>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_5" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5378" name="V" value="4853.02"/>
+          <Constant key="Parameter_5377" name="KM" value="0.02"/>
+          <Constant key="Parameter_5376" name="Ki" value="1e+10"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_41" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_265">
+              <SourceParameter reference="Parameter_5378"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_250">
+              <SourceParameter reference="Metabolite_0"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_261">
+              <SourceParameter reference="Parameter_5377"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_266">
+              <SourceParameter reference="Metabolite_5"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_267">
+              <SourceParameter reference="Parameter_5376"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_1" name="ackA" reversible="true" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_1">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:28:35Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_1" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_2" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfConstants>
+          <Constant key="Parameter_5375" name="v_ACK_Vmax" value="343271"/>
+          <Constant key="Parameter_5374" name="ACP" value="1"/>
+          <Constant key="Parameter_5373" name="ADP" value="0.606"/>
+          <Constant key="Parameter_5372" name="v_ACK_KmACP" value="0.16"/>
+          <Constant key="Parameter_5371" name="v_ACK_KmADP" value="0.5"/>
+          <Constant key="Parameter_5370" name="ACE" value="1"/>
+          <Constant key="Parameter_5369" name="v_ACK_KmACE" value="7"/>
+          <Constant key="Parameter_5368" name="ATP" value="2.4"/>
+          <Constant key="Parameter_5367" name="v_ACK_KmATP" value="0.07"/>
+          <Constant key="Parameter_5366" name="v_ACK_Keq" value="174"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_43" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_281">
+              <SourceParameter reference="ModelValue_10"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_280">
+              <SourceParameter reference="Metabolite_1"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_279">
+              <SourceParameter reference="ModelValue_11"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_278">
+              <SourceParameter reference="ModelValue_15"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_277">
+              <SourceParameter reference="ModelValue_12"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_276">
+              <SourceParameter reference="ModelValue_13"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_275">
+              <SourceParameter reference="Metabolite_2"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_282">
+              <SourceParameter reference="ModelValue_14"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_283">
+              <SourceParameter reference="ModelValue_16"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_284">
+              <SourceParameter reference="ModelValue_17"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_2" name="pta" reversible="true" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_2">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:28:06Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_3" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_1" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_3" stoichiometry="1"/>
+          <Modifier metabolite="Metabolite_1" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5365" name="v_PTA_Vmax" value="9.99975e+06"/>
+          <Constant key="Parameter_5364" name="ACCOA" value="1"/>
+          <Constant key="Parameter_5363" name="P" value="10"/>
+          <Constant key="Parameter_5362" name="ACP" value="1"/>
+          <Constant key="Parameter_5361" name="COA" value="1.22"/>
+          <Constant key="Parameter_5360" name="v_PTA_KiACCOA" value="0.2"/>
+          <Constant key="Parameter_5359" name="v_PTA_KmP" value="2.6"/>
+          <Constant key="Parameter_5358" name="v_PTA_KiP" value="2.6"/>
+          <Constant key="Parameter_5357" name="v_PTA_KiACP" value="0.2"/>
+          <Constant key="Parameter_5356" name="v_PTA_KiCOA" value="0.029"/>
+          <Constant key="Parameter_5355" name="v_PTA_KmACP" value="0.7"/>
+          <Constant key="Parameter_5679" name="KEQ" value="0.0281"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_44" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_294">
+              <SourceParameter reference="ModelValue_0"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_293">
+              <SourceParameter reference="Metabolite_3"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_292">
+              <SourceParameter reference="ModelValue_7"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_291">
+              <SourceParameter reference="Metabolite_1"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_290">
+              <SourceParameter reference="ModelValue_8"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_289">
+              <SourceParameter reference="ModelValue_9"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_288">
+              <SourceParameter reference="ModelValue_1"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_287">
+              <SourceParameter reference="ModelValue_2"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_286">
+              <SourceParameter reference="ModelValue_3"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_285">
+              <SourceParameter reference="ModelValue_4"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_295">
+              <SourceParameter reference="ModelValue_5"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_296">
+              <SourceParameter reference="ModelValue_6"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_3" name="sink" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF
+   xmlns:dcterms="http://purl.org/dc/terms/"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_3">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T11:28:46Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_3" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfModifiers>
+          <Modifier metabolite="Metabolite_3" stoichiometry="1"/>
+          <Modifier metabolite="Metabolite_5" stoichiometry="1"/>
+        </ListOfModifiers>
+        <ListOfConstants>
+          <Constant key="Parameter_5680" name="n" value="1"/>
+          <Constant key="Parameter_5678" name="Km" value="257.225"/>
+          <Constant key="Parameter_5681" name="Ki" value="1e+10"/>
+          <Constant key="Parameter_5708" name="V" value="6.92338e+06"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_42" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_272">
+              <SourceParameter reference="Metabolite_3"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_271">
+              <SourceParameter reference="Metabolite_3"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_270">
+              <SourceParameter reference="ModelValue_18"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_269">
+              <SourceParameter reference="Parameter_5680"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_268">
+              <SourceParameter reference="ModelValue_19"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_273">
+              <SourceParameter reference="Metabolite_5"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_274">
+              <SourceParameter reference="ModelValue_23"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_4" name="growth" reversible="false" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_4">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2019-09-24T12:07:54Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_4" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfConstants>
+          <Constant key="Parameter_5709" name="Y" value="8.48483e-05"/>
+          <Constant key="Parameter_5707" name="sink" value="39075.1"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_40" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_264">
+              <SourceParameter reference="ModelValue_21"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_263">
+              <SourceParameter reference="Metabolite_4"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_262">
+              <SourceParameter reference="ModelValue_20"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+      <Reaction key="Reaction_5" name="ace_xch" reversible="true" fast="false" addNoise="false">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Reaction_5">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-02-26T10:33:46Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ListOfSubstrates>
+          <Substrate metabolite="Metabolite_2" stoichiometry="1"/>
+        </ListOfSubstrates>
+        <ListOfProducts>
+          <Product metabolite="Metabolite_5" stoichiometry="1"/>
+        </ListOfProducts>
+        <ListOfConstants>
+          <Constant key="Parameter_5710" name="Kmp" value="99.9999"/>
+          <Constant key="Parameter_5692" name="Vf" value="595957"/>
+          <Constant key="Parameter_5693" name="Vr" value="595957"/>
+          <Constant key="Parameter_5691" name="Kms" value="99.9999"/>
+        </ListOfConstants>
+        <KineticLaw function="Function_28" unitType="Default" scalingCompartment="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]">
+          <ListOfCallParameters>
+            <CallParameter functionParameter="FunctionParameter_195">
+              <SourceParameter reference="Metabolite_2"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_196">
+              <SourceParameter reference="Metabolite_5"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_197">
+              <SourceParameter reference="ModelValue_24"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_198">
+              <SourceParameter reference="ModelValue_24"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_199">
+              <SourceParameter reference="ModelValue_25"/>
+            </CallParameter>
+            <CallParameter functionParameter="FunctionParameter_200">
+              <SourceParameter reference="ModelValue_25"/>
+            </CallParameter>
+          </ListOfCallParameters>
+        </KineticLaw>
+      </Reaction>
+    </ListOfReactions>
+    <ListOfEvents>
+      <Event key="Event_0" name="pulse_acetate" fireAtInitialTime="0" persistentTrigger="0">
+        <MiriamAnnotation>
+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+  <rdf:Description rdf:about="#Event_0">
+    <dcterms:created>
+      <rdf:Description>
+        <dcterms:W3CDTF>2020-04-30T20:08:42Z</dcterms:W3CDTF>
+      </rdf:Description>
+    </dcterms:created>
+  </rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <TriggerExpression>
+          &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[X],Reference=Concentration> >= &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_X_conc_pulse],Reference=InitialValue>
+        </TriggerExpression>
+        <ListOfAssignments>
+          <Assignment target="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace_out]" targetKey="Metabolite_5">
+            <Expression>
+              &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace_out],Reference=Concentration>+30
+            </Expression>
+          </Assignment>
+        </ListOfAssignments>
+      </Event>
+    </ListOfEvents>
+    <ListOfModelParameterSets activeSet="ModelParameterSet_1">
+      <ModelParameterSet key="ModelParameterSet_1" name="Initial State">
+        <MiriamAnnotation>
+<rdf:RDF
+xmlns:dcterms="http://purl.org/dc/terms/"
+xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+<rdf:Description rdf:about="#ModelParameterSet_1">
+<dcterms:created>
+<rdf:Description>
+<dcterms:W3CDTF>2020-12-28T16:35:26Z</dcterms:W3CDTF>
+</rdf:Description>
+</dcterms:created>
+</rdf:Description>
+</rdf:RDF>
+        </MiriamAnnotation>
+        <ModelParameterGroup cn="String=Initial Time" type="Group">
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism" value="0" type="Model" simulationType="time"/>
+        </ModelParameterGroup>
+        <ModelParameterGroup cn="String=Initial Compartment Sizes" type="Group">
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell]" value="1" type="Compartment" simulationType="fixed"/>
+        </ModelParameterGroup>
+        <ModelParameterGroup cn="String=Initial Species Values" type="Group">
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Glc]" value="1.2044281714000001e+22" type="Species" simulationType="ode"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[AcP]" value="6.0221408570000002e+20" type="Species" simulationType="reactions"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace]" value="6.0221408570000002e+20" type="Species" simulationType="reactions"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[AcCoA]" value="8.7923256512199996e+20" type="Species" simulationType="reactions"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[X]" value="6.0221408570000007e+19" type="Species" simulationType="ode"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Compartments[cell],Vector=Metabolites[Ace_out]" value="6.0221408570000007e+19" type="Species" simulationType="ode"/>
+        </ModelParameterGroup>
+        <ModelParameterGroup cn="String=Initial Global Quantities" type="Group">
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Vmax]" value="9999746.1950000003" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACCOA]" value="0.20000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmP]" value="2.6000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiP]" value="2.6000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACP]" value="0.20000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiCOA]" value="0.029000000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmACP]" value="0.69999999999999996" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[P]" value="10" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[CoA]" value="1.22" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Keq]" value="0.0281" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Vmax]" value="343270.58559999999" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ADP]" value="0.60599999999999998" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACP]" value="0.16" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmADP]" value="0.5" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACE]" value="7" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ATP]" value="2.3999999999999999" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmATP]" value="0.070000000000000007" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Keq]" value="174" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Vmax]" value="6923380.0420000004" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Km]" value="257.22453519999999" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[v_sink]" value="39075.141671704077" type="ModelValue" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[Y]" value="8.4848287729999994e-05" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[volume]" value="0.0017700000000000001" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Ki]" value="10000000000" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Km]" value="99.999857860000006" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Vmax]" value="595956.55830000003" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[v_growth_rate]" value="3.3154588636512603" type="ModelValue" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Ki]" value="60" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[v_glc_uptake]" value="8.5812641357783246" type="ModelValue" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[v_ace_net]" value="9.3903079338305613" type="ModelValue" simulationType="assignment"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_dilution_rate]" value="0" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_feed]" value="0" type="ModelValue" simulationType="fixed"/>
+          <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[_X_conc_pulse]" value="10000" type="ModelValue" simulationType="fixed"/>
+        </ModelParameterGroup>
+        <ModelParameterGroup cn="String=Kinetic Parameters" type="Group">
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt],ParameterGroup=Parameters,Parameter=V" value="4853.0200000000004" type="ReactionParameter" simulationType="fixed"/>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt],ParameterGroup=Parameters,Parameter=KM" value="0.02" type="ReactionParameter" simulationType="fixed"/>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[glc_upt],ParameterGroup=Parameters,Parameter=Ki" value="10000000000" type="ReactionParameter" simulationType="fixed"/>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=v_ACK_Vmax" value="343270.58559999999" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=ADP" value="0.60599999999999998" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ADP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=v_ACK_KmACP" value="0.16" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=v_ACK_KmADP" value="0.5" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmADP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=v_ACK_KmACE" value="7" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmACE],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=ATP" value="2.3999999999999999" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[ATP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=v_ACK_KmATP" value="0.070000000000000007" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_KmATP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ackA],ParameterGroup=Parameters,Parameter=v_ACK_Keq" value="174" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_ACK_Keq],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_Vmax" value="9999746.1950000003" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=P" value="10" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[P],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=COA" value="1.22" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[CoA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_KiACCOA" value="0.20000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACCOA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_KmP" value="2.6000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_KiP" value="2.6000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_KiACP" value="0.20000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_KiCOA" value="0.029000000000000001" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KiCOA],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=v_PTA_KmACP" value="0.69999999999999996" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_KmACP],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[pta],ParameterGroup=Parameters,Parameter=KEQ" value="0.0281" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_PTA_Keq],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink],ParameterGroup=Parameters,Parameter=n" value="1" type="ReactionParameter" simulationType="fixed"/>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink],ParameterGroup=Parameters,Parameter=Km" value="257.22453519999999" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Km],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink],ParameterGroup=Parameters,Parameter=Ki" value="10000000000" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Ki],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[sink],ParameterGroup=Parameters,Parameter=V" value="6923380.0420000004" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_sink_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[growth]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[growth],ParameterGroup=Parameters,Parameter=Y" value="8.4848287729999994e-05" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[Y],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[growth],ParameterGroup=Parameters,Parameter=sink" value="39075.141671704077" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[v_sink],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+          <ModelParameterGroup cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch]" type="Reaction">
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch],ParameterGroup=Parameters,Parameter=Kmp" value="99.999857860000006" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Km],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch],ParameterGroup=Parameters,Parameter=Vf" value="595956.55830000003" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch],ParameterGroup=Parameters,Parameter=Vr" value="595956.55830000003" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Vmax],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+            <ModelParameter cn="CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Reactions[ace_xch],ParameterGroup=Parameters,Parameter=Kms" value="99.999857860000006" type="ReactionParameter" simulationType="assignment">
+              <InitialExpression>
+                &lt;CN=Root,Model=E. coli model - Glc-Ace metabolism,Vector=Values[r_TRP_Km],Reference=InitialValue>
+              </InitialExpression>
+            </ModelParameter>
+          </ModelParameterGroup>
+        </ModelParameterGroup>
+      </ModelParameterSet>
+    </ListOfModelParameterSets>
+    <StateTemplate>
+      <StateTemplateVariable objectReference="Model_1"/>
+      <StateTemplateVariable objectReference="Metabolite_0"/>
+      <StateTemplateVariable objectReference="Metabolite_4"/>
+      <StateTemplateVariable objectReference="Metabolite_5"/>
+      <StateTemplateVariable objectReference="Metabolite_3"/>
+      <StateTemplateVariable objectReference="Metabolite_2"/>
+      <StateTemplateVariable objectReference="Metabolite_1"/>
+      <StateTemplateVariable objectReference="ModelValue_20"/>
+      <StateTemplateVariable objectReference="ModelValue_26"/>
+      <StateTemplateVariable objectReference="ModelValue_28"/>
+      <StateTemplateVariable objectReference="ModelValue_29"/>
+      <StateTemplateVariable objectReference="Compartment_0"/>
+      <StateTemplateVariable objectReference="ModelValue_0"/>
+      <StateTemplateVariable objectReference="ModelValue_1"/>
+      <StateTemplateVariable objectReference="ModelValue_2"/>
+      <StateTemplateVariable objectReference="ModelValue_3"/>
+      <StateTemplateVariable objectReference="ModelValue_4"/>
+      <StateTemplateVariable objectReference="ModelValue_5"/>
+      <StateTemplateVariable objectReference="ModelValue_6"/>
+      <StateTemplateVariable objectReference="ModelValue_7"/>
+      <StateTemplateVariable objectReference="ModelValue_8"/>
+      <StateTemplateVariable objectReference="ModelValue_9"/>
+      <StateTemplateVariable objectReference="ModelValue_10"/>
+      <StateTemplateVariable objectReference="ModelValue_11"/>
+      <StateTemplateVariable objectReference="ModelValue_12"/>
+      <StateTemplateVariable objectReference="ModelValue_13"/>
+      <StateTemplateVariable objectReference="ModelValue_14"/>
+      <StateTemplateVariable objectReference="ModelValue_15"/>
+      <StateTemplateVariable objectReference="ModelValue_16"/>
+      <StateTemplateVariable objectReference="ModelValue_17"/>
+      <StateTemplateVariable objectReference="ModelValue_18"/>
+      <StateTemplateVariable objectReference="ModelValue_19"/>
+      <StateTemplateVariable objectReference="ModelValue_21"/>
+      <StateTemplateVariable objectReference="ModelValue_22"/>
+      <StateTemplateVariable objectReference="ModelValue_23"/>
+      <StateTemplateVariable objectReference="ModelValue_24"/>
+      <StateTemplateVariable objectReference="ModelValue_25"/>
+      <StateTemplateVariable objectReference="ModelValue_27"/>
+      <StateTemplateVariable objectReference="ModelValue_30"/>
+      <StateTemplateVariable objectReference="ModelValue_31"/>
+      <StateTemplateVariable objectReference="ModelValue_32"/>
+    </StateTemplate>
+    <InitialState type="initialState">
+      0 1.2044281714000001e+22 6.0221408570000007e+19 6.0221408570000007e+19 8.7923256512199996e+20 6.0221408570000002e+20 6.0221408570000002e+20 39075.141671704077 3.3154588636512603 8.5812641357783246 9.3903079338305613 1 9999746.1950000003 0.20000000000000001 2.6000000000000001 2.6000000000000001 0.20000000000000001 0.029000000000000001 0.69999999999999996 10 1.22 0.0281 343270.58559999999 0.60599999999999998 0.16 0.5 7 2.3999999999999999 0.070000000000000007 174 6923380.0420000004 257.22453519999999 8.4848287729999994e-05 0.0017700000000000001 10000000000 99.999857860000006 595956.55830000003 60 0 0 10000 
+    </InitialState>
+  </Model>
+  <ListOfTasks>
+    <Task key="Task_15" name="Steady-State" type="steadyState" scheduled="false" updateModel="false">
+      <Report reference="Report_10" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="JacobianRequested" type="bool" value="1"/>
+        <Parameter name="StabilityAnalysisRequested" type="bool" value="1"/>
+      </Problem>
+      <Method name="Enhanced Newton" type="EnhancedNewton">
+        <Parameter name="Resolution" type="unsignedFloat" value="1.0000000000000001e-09"/>
+        <Parameter name="Derivation Factor" type="unsignedFloat" value="0.001"/>
+        <Parameter name="Use Newton" type="bool" value="0"/>
+        <Parameter name="Use Integration" type="bool" value="1"/>
+        <Parameter name="Use Back Integration" type="bool" value="0"/>
+        <Parameter name="Accept Negative Concentrations" type="bool" value="0"/>
+        <Parameter name="Iteration Limit" type="unsignedInteger" value="50"/>
+        <Parameter name="Maximum duration for forward integration" type="unsignedFloat" value="1000000000"/>
+        <Parameter name="Maximum duration for backward integration" type="unsignedFloat" value="1000000"/>
+      </Method>
+    </Task>
+    <Task key="Task_16" name="Time-Course" type="timeCourse" scheduled="false" updateModel="false">
+      <Problem>
+        <Parameter name="AutomaticStepSize" type="bool" value="0"/>
+        <Parameter name="StepNumber" type="unsignedInteger" value="1000"/>
+        <Parameter name="StepSize" type="float" value="0.01"/>
+        <Parameter name="Duration" type="float" value="10"/>
+        <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
+        <Parameter name="OutputStartTime" type="float" value="0.10000000000000001"/>
+        <Parameter name="Output Event" type="bool" value="1"/>
+        <Parameter name="Start in Steady State" type="bool" value="0"/>
+        <Parameter name="Use Values" type="bool" value="0"/>
+        <Parameter name="Values" type="string" value=""/>
+      </Problem>
+      <Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
+        <Parameter name="Integrate Reduced Model" type="bool" value="0"/>
+        <Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-07"/>
+        <Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
+        <Parameter name="Max Internal Steps" type="unsignedInteger" value="100000"/>
+        <Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
+      </Method>
+    </Task>
+    <Task key="Task_17" name="Scan" type="scan" scheduled="false" updateModel="false">
+      <Problem>
+        <Parameter name="Subtask" type="unsignedInteger" value="0"/>
+        <ParameterGroup name="ScanItems">
+        </ParameterGroup>
+        <Parameter name="Output in subtask" type="bool" value="0"/>
+        <Parameter name="Adjust initial conditions" type="bool" value="0"/>
+        <Parameter name="Continue on Error" type="bool" value="0"/>
+      </Problem>
+      <Method name="Scan Framework" type="ScanFramework">
+      </Method>
+    </Task>
+    <Task key="Task_18" name="Elementary Flux Modes" type="fluxMode" scheduled="false" updateModel="false">
+      <Report reference="Report_11" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+      </Problem>
+      <Method name="EFM Algorithm" type="EFMAlgorithm">
+      </Method>
+    </Task>
+    <Task key="Task_19" name="Optimization" type="optimization" scheduled="false" updateModel="false">
+      <Report reference="Report_12" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="Subtask" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
+        <ParameterText name="ObjectiveExpression" type="expression">
+          
+        </ParameterText>
+        <Parameter name="Maximize" type="bool" value="0"/>
+        <Parameter name="Randomize Start Values" type="bool" value="0"/>
+        <Parameter name="Calculate Statistics" type="bool" value="1"/>
+        <ParameterGroup name="OptimizationItemList">
+        </ParameterGroup>
+        <ParameterGroup name="OptimizationConstraintList">
+        </ParameterGroup>
+      </Problem>
+      <Method name="Random Search" type="RandomSearch">
+        <Parameter name="Log Verbosity" type="unsignedInteger" value="0"/>
+        <Parameter name="Number of Iterations" type="unsignedInteger" value="100000"/>
+        <Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
+        <Parameter name="Seed" type="unsignedInteger" value="0"/>
+      </Method>
+    </Task>
+    <Task key="Task_20" name="Parameter Estimation" type="parameterFitting" scheduled="false" updateModel="false">
+      <Report reference="Report_13" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="Maximize" type="bool" value="0"/>
+        <Parameter name="Randomize Start Values" type="bool" value="0"/>
+        <Parameter name="Calculate Statistics" type="bool" value="1"/>
+        <ParameterGroup name="OptimizationItemList">
+        </ParameterGroup>
+        <ParameterGroup name="OptimizationConstraintList">
+        </ParameterGroup>
+        <Parameter name="Steady-State" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
+        <Parameter name="Time-Course" type="cn" value="CN=Root,Vector=TaskList[Time-Course]"/>
+        <Parameter name="Create Parameter Sets" type="bool" value="0"/>
+        <ParameterGroup name="Experiment Set">
+        </ParameterGroup>
+        <ParameterGroup name="Validation Set">
+          <Parameter name="Weight" type="unsignedFloat" value="1"/>
+          <Parameter name="Threshold" type="unsignedInteger" value="5"/>
+        </ParameterGroup>
+      </Problem>
+      <Method name="Current Solution Statistics" type="CurrentSolutionStatistics">
+        <Parameter name="Log Verbosity" type="unsignedInteger" value="0"/>
+      </Method>
+    </Task>
+    <Task key="Task_21" name="Metabolic Control Analysis" type="metabolicControlAnalysis" scheduled="false" updateModel="false">
+      <Report reference="Report_14" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="Steady-State" type="key" value="Task_15"/>
+      </Problem>
+      <Method name="MCA Method (Reder)" type="MCAMethod(Reder)">
+        <Parameter name="Modulation Factor" type="unsignedFloat" value="1.0000000000000001e-09"/>
+        <Parameter name="Use Reder" type="bool" value="1"/>
+        <Parameter name="Use Smallbone" type="bool" value="1"/>
+      </Method>
+    </Task>
+    <Task key="Task_22" name="Lyapunov Exponents" type="lyapunovExponents" scheduled="false" updateModel="false">
+      <Report reference="Report_15" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="ExponentNumber" type="unsignedInteger" value="3"/>
+        <Parameter name="DivergenceRequested" type="bool" value="1"/>
+        <Parameter name="TransientTime" type="float" value="0"/>
+      </Problem>
+      <Method name="Wolf Method" type="WolfMethod">
+        <Parameter name="Orthonormalization Interval" type="unsignedFloat" value="1"/>
+        <Parameter name="Overall time" type="unsignedFloat" value="1000"/>
+        <Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-07"/>
+        <Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
+        <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
+      </Method>
+    </Task>
+    <Task key="Task_23" name="Time Scale Separation Analysis" type="timeScaleSeparationAnalysis" scheduled="false" updateModel="false">
+      <Report reference="Report_16" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="StepNumber" type="unsignedInteger" value="100"/>
+        <Parameter name="StepSize" type="float" value="0.01"/>
+        <Parameter name="Duration" type="float" value="1"/>
+        <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
+        <Parameter name="OutputStartTime" type="float" value="0"/>
+      </Problem>
+      <Method name="ILDM (LSODA,Deuflhard)" type="TimeScaleSeparation(ILDM,Deuflhard)">
+        <Parameter name="Deuflhard Tolerance" type="unsignedFloat" value="0.0001"/>
+      </Method>
+    </Task>
+    <Task key="Task_24" name="Sensitivities" type="sensitivities" scheduled="false" updateModel="false">
+      <Report reference="Report_17" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="SubtaskType" type="unsignedInteger" value="1"/>
+        <ParameterGroup name="TargetFunctions">
+          <Parameter name="SingleObject" type="cn" value=""/>
+          <Parameter name="ObjectListType" type="unsignedInteger" value="7"/>
+        </ParameterGroup>
+        <ParameterGroup name="ListOfVariables">
+          <ParameterGroup name="Variables">
+            <Parameter name="SingleObject" type="cn" value=""/>
+            <Parameter name="ObjectListType" type="unsignedInteger" value="41"/>
+          </ParameterGroup>
+          <ParameterGroup name="Variables">
+            <Parameter name="SingleObject" type="cn" value=""/>
+            <Parameter name="ObjectListType" type="unsignedInteger" value="0"/>
+          </ParameterGroup>
+        </ParameterGroup>
+      </Problem>
+      <Method name="Sensitivities Method" type="SensitivitiesMethod">
+        <Parameter name="Delta factor" type="unsignedFloat" value="0.001"/>
+        <Parameter name="Delta minimum" type="unsignedFloat" value="9.9999999999999998e-13"/>
+      </Method>
+    </Task>
+    <Task key="Task_25" name="Moieties" type="moieties" scheduled="false" updateModel="false">
+      <Report reference="Report_18" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+      </Problem>
+      <Method name="Householder Reduction" type="Householder">
+      </Method>
+    </Task>
+    <Task key="Task_26" name="Cross Section" type="crosssection" scheduled="false" updateModel="false">
+      <Problem>
+        <Parameter name="AutomaticStepSize" type="bool" value="0"/>
+        <Parameter name="StepNumber" type="unsignedInteger" value="100"/>
+        <Parameter name="StepSize" type="float" value="0.01"/>
+        <Parameter name="Duration" type="float" value="1"/>
+        <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
+        <Parameter name="OutputStartTime" type="float" value="0"/>
+        <Parameter name="Output Event" type="bool" value="0"/>
+        <Parameter name="Start in Steady State" type="bool" value="0"/>
+        <Parameter name="Use Values" type="bool" value="0"/>
+        <Parameter name="Values" type="string" value=""/>
+        <Parameter name="LimitCrossings" type="bool" value="0"/>
+        <Parameter name="NumCrossingsLimit" type="unsignedInteger" value="0"/>
+        <Parameter name="LimitOutTime" type="bool" value="0"/>
+        <Parameter name="LimitOutCrossings" type="bool" value="0"/>
+        <Parameter name="PositiveDirection" type="bool" value="1"/>
+        <Parameter name="NumOutCrossingsLimit" type="unsignedInteger" value="0"/>
+        <Parameter name="LimitUntilConvergence" type="bool" value="0"/>
+        <Parameter name="ConvergenceTolerance" type="float" value="9.9999999999999995e-07"/>
+        <Parameter name="Threshold" type="float" value="0"/>
+        <Parameter name="DelayOutputUntilConvergence" type="bool" value="0"/>
+        <Parameter name="OutputConvergenceTolerance" type="float" value="9.9999999999999995e-07"/>
+        <ParameterText name="TriggerExpression" type="expression">
+          
+        </ParameterText>
+        <Parameter name="SingleVariable" type="cn" value=""/>
+      </Problem>
+      <Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
+        <Parameter name="Integrate Reduced Model" type="bool" value="0"/>
+        <Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-07"/>
+        <Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
+        <Parameter name="Max Internal Steps" type="unsignedInteger" value="100000"/>
+        <Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
+      </Method>
+    </Task>
+    <Task key="Task_27" name="Linear Noise Approximation" type="linearNoiseApproximation" scheduled="false" updateModel="false">
+      <Report reference="Report_19" target="" append="1" confirmOverwrite="1"/>
+      <Problem>
+        <Parameter name="Steady-State" type="key" value="Task_15"/>
+      </Problem>
+      <Method name="Linear Noise Approximation" type="LinearNoiseApproximation">
+      </Method>
+    </Task>
+    <Task key="Task_28" name="Time-Course Sensitivities" type="timeSensitivities" scheduled="false" updateModel="false">
+      <Problem>
+        <Parameter name="AutomaticStepSize" type="bool" value="0"/>
+        <Parameter name="StepNumber" type="unsignedInteger" value="100"/>
+        <Parameter name="StepSize" type="float" value="0.01"/>
+        <Parameter name="Duration" type="float" value="1"/>
+        <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
+        <Parameter name="OutputStartTime" type="float" value="0"/>
+        <Parameter name="Output Event" type="bool" value="0"/>
+        <Parameter name="Start in Steady State" type="bool" value="0"/>
+        <Parameter name="Use Values" type="bool" value="0"/>
+        <Parameter name="Values" type="string" value=""/>
+        <ParameterGroup name="ListOfParameters">
+        </ParameterGroup>
+        <ParameterGroup name="ListOfTargets">
+        </ParameterGroup>
+      </Problem>
+      <Method name="LSODA Sensitivities" type="Sensitivities(LSODA)">
+        <Parameter name="Integrate Reduced Model" type="bool" value="0"/>
+        <Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-07"/>
+        <Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
+        <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
+        <Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
+      </Method>
+    </Task>
+  </ListOfTasks>
+  <ListOfReports>
+    <Report key="Report_10" name="Steady-State" taskType="steadyState" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Footer>
+        <Object cn="CN=Root,Vector=TaskList[Steady-State]"/>
+      </Footer>
+    </Report>
+    <Report key="Report_11" name="Elementary Flux Modes" taskType="fluxMode" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Footer>
+        <Object cn="CN=Root,Vector=TaskList[Elementary Flux Modes],Object=Result"/>
+      </Footer>
+    </Report>
+    <Report key="Report_12" name="Optimization" taskType="optimization" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Header>
+        <Object cn="CN=Root,Vector=TaskList[Optimization],Object=Description"/>
+        <Object cn="String=\[Function Evaluations\]"/>
+        <Object cn="Separator=&#x09;"/>
+        <Object cn="String=\[Best Value\]"/>
+        <Object cn="Separator=&#x09;"/>
+        <Object cn="String=\[Best Parameters\]"/>
+      </Header>
+      <Body>
+        <Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Function Evaluations"/>
+        <Object cn="Separator=&#x09;"/>
+        <Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Best Value"/>
+        <Object cn="Separator=&#x09;"/>
+        <Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Best Parameters"/>
+      </Body>
+      <Footer>
+        <Object cn="String=&#x0a;"/>
+        <Object cn="CN=Root,Vector=TaskList[Optimization],Object=Result"/>
+      </Footer>
+    </Report>
+    <Report key="Report_13" name="Parameter Estimation" taskType="parameterFitting" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Header>
+        <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Object=Description"/>
+        <Object cn="String=\[Function Evaluations\]"/>
+        <Object cn="Separator=&#x09;"/>
+        <Object cn="String=\[Best Value\]"/>
+        <Object cn="Separator=&#x09;"/>
+        <Object cn="String=\[Best Parameters\]"/>
+      </Header>
+      <Body>
+        <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Function Evaluations"/>
+        <Object cn="Separator=&#x09;"/>
+        <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Best Value"/>
+        <Object cn="Separator=&#x09;"/>
+        <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Best Parameters"/>
+      </Body>
+      <Footer>
+        <Object cn="String=&#x0a;"/>
+        <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Object=Result"/>
+      </Footer>
+    </Report>
+    <Report key="Report_14" name="Metabolic Control Analysis" taskType="metabolicControlAnalysis" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Header>
+        <Object cn="CN=Root,Vector=TaskList[Metabolic Control Analysis],Object=Description"/>
+      </Header>
+      <Footer>
+        <Object cn="String=&#x0a;"/>
+        <Object cn="CN=Root,Vector=TaskList[Metabolic Control Analysis],Object=Result"/>
+      </Footer>
+    </Report>
+    <Report key="Report_15" name="Lyapunov Exponents" taskType="lyapunovExponents" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Header>
+        <Object cn="CN=Root,Vector=TaskList[Lyapunov Exponents],Object=Description"/>
+      </Header>
+      <Footer>
+        <Object cn="String=&#x0a;"/>
+        <Object cn="CN=Root,Vector=TaskList[Lyapunov Exponents],Object=Result"/>
+      </Footer>
+    </Report>
+    <Report key="Report_16" name="Time Scale Separation Analysis" taskType="timeScaleSeparationAnalysis" separator="&#x09;" precision="6">
+      <Comment>
+        Automatically generated report.
+      </Comment>
+      <Header>
+        <Object cn="CN=Root,Vector=TaskList[Time Scale Separation Analysis],Object=Description"/>
+      </Header>
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diff --git a/model/cps/Millard2020_Ecoli_glc_ace_kinetic_model.cps b/model/cps/Millard2020_Ecoli_glc_ace_kinetic_model_4.cps
similarity index 100%
rename from model/cps/Millard2020_Ecoli_glc_ace_kinetic_model.cps
rename to model/cps/Millard2020_Ecoli_glc_ace_kinetic_model_4.cps
diff --git a/model/cps/data_1mM.txt b/model/cps/data_1mM.txt
index d987ad1..211173f 100644
--- a/model/cps/data_1mM.txt
+++ b/model/cps/data_1mM.txt
@@ -1,9 +1,9 @@
 time	Ace	X	Glc	Ace_enr
-0.00	0.958577777777778	0.06308	12.7597333333333	0.0576780415430267
-0.75	1.21777777777778	0.10374	11.7168	0.32529197080292
-1.25	1.45604444444444	0.1406	11.1826666666667	0.478160007325784
-1.58	1.71364444444444	0.17138	11.2482666666667	0.569183287081464
-1.92	1.84195555555556	0.21888	10.3389333333333	0.636714602837564
+0.00	0.958577777777778	0.06308	12.6597333333333	0.0576780415430267
+0.75	1.21777777777778	0.10374	11.9168	0.32529197080292
+1.25	1.45604444444444	0.1406	11.9826666666667	0.478160007325784
+1.58	1.61364444444444	0.17138	11.2482666666667	0.569183287081464
+1.92	1.84195555555556	0.21888	10.5389333333333	0.636714602837564
 2.25	2.09435555555556	0.26828	10.0416	0.703456910638117
 2.58	2.34062222222222	0.3268	9.09706666666667	0.762741151450707
 2.92	2.54257777777777	0.38228	7.84106666666667	0.81056845196476
diff --git a/results/Figure 1-figure supplement 1.pdf b/results/Figure 1-figure supplement 1.pdf
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rename to results/Figure 4.pdf
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diff --git a/results/mc_results_100.RData b/results/mc_results_100.RData
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diff --git a/results/model_fit.pdf b/results/model_fit.pdf
deleted file mode 100644
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deleted file mode 100644
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diff --git a/results/parameters_stats.txt b/results/parameters_stats.txt
new file mode 100644
index 0000000..17fb157
--- /dev/null
+++ b/results/parameters_stats.txt
@@ -0,0 +1,11 @@
+mean	median	ci95_lb	ci95_up	sd	rsd
+Values[r_TRP_Km].InitialValue	36.4007379950144	21.922129646888	1.45531393283028	99.7756702358994	32.8001784304189	0.901085533895256
+Values[r_TRP_Vmax].InitialValue	483026.953125768	307864.006509059	77220.3384742297	1499652.77768592	413675.959224719	0.856424173739655
+Values[Y].InitialValue	9.99300033758725e-05	9.99289861093244e-05	9.55178600980106e-05	0.000104528366199826	2.33943821488031e-06	0.0234107688967131
+Values[r_sink_Ki].InitialValue	2.38423325181301	2.31004434301217	1.74950748629267	3.43975294341899	0.44113604867468	0.185022186205663
+Values[r_sink_Km].InitialValue	143.949855963944	86.7351305125475	8.38141943177607	615.391172037193	154.009588979009	1.0698835920863
+Values[r_sink_Vmax].InitialValue	4211513.73863747	2431715.23964289	237674.449144748	16925862.8012613	4576509.87518008	1.08666625807107
+Values[r_ACK_Vmax].InitialValue	360150.866434465	344034.037265075	280999.666632541	547438.938165196	105312.089147476	0.292411039268287
+Values[r_PTA_Vmax].InitialValue	2859109.50244353	906298.769182857	49521.2750880163	9920944.93455331	3608671.21558176	1.2621661438632
+(glc_upt).Ki	38.1955686658098	38.0382183399559	30.8546672222616	46.9095411207775	4.08709220394248	0.107004355392697
+(glc_upt).V	5515.76965742576	5486.45397771465	5271.10356802468	5917.63458023499	168.507382460193	0.0305501123008891
diff --git a/results/results_control_2.pdf b/results/results_control_2.pdf
deleted file mode 100644
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deleted file mode 100644
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diff --git a/run_analysis.R b/run_analysis.R
deleted file mode 100644
index 92eda22..0000000
--- a/run_analysis.R
+++ /dev/null
@@ -1,570 +0,0 @@
-
-
-
-####################################
-# Supplementary information folder #
-####################################
-
-# We assume to be already in the working directory, otherwise update the path of the supplementary data folder
-#wd <- "C:/Users/millard/Documents/GIT/acetate_regulation/acetate_regulation/"
-wd <- getwd()
-
-model_dir <- file.path(wd, "model", "cps")
-results_dir <- file.path(wd, "results")
-
-
-###################
-# Set environment #
-###################
-
-# load libraries
-library(RColorBrewer)
-library(gplots)
-library(CoRC)
-
-test_khi2 <- function(nb_points, k_val, nb_par){
-  # Perform Khi2 statistical test.
-  #
-  # Args:
-  #   nb_points (int): number of data points
-  #   k_val (float): khi2 value (cost)
-  #   nb_par (int): number of free parameters
-  #
-  # Returns (list):
-  #   $'khi2 value' (float): khi2 value (cost)
-  #   $'data points' (int): number of data points
-  #   $'fitted parameters' (int): number of free parameters
-  #   $'degrees of freedom' (int): degrees of freedom
-  #   $'khi2 reduced value' (float): chi2 reduced value
-  #   $'p-value, i.e. P(X^2<=value)' (float): p value
-  #   $conclusion (str): message indicating whether the models fits (or not) the data at 95% confidence interval
-  #
-  df <- nb_points - nb_par
-  p_val <- pchisq(k_val, df=df)
-  khi2test <- list("khi2 value"                  = k_val,
-                   "data points"                 = nb_points,
-                   "fitted parameters"           = nb_par,
-                   "degrees of freedom"          = df,
-                   "khi2 reduced value"          = k_val/df,
-                   "p-value, i.e. P(X^2<=value)" = p_val)
-  if (p_val > 0.95){
-    khi2test$conclusion <- "At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD."
-  }else{
-    khi2test$conclusion <- "At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD."
-  }
-  return(khi2test)
-}
-
-plot_points <- function(x, y, sd, col="black", offset=1.5, mode="v", cex=1){
-  # Scatterplot with error bars.
-  #
-  # Args:
-  #   x (vector): x coordinates
-  #   y (vector): y coordinates
-  #   sd (vector): error bars
-  #   col (color code): color of points
-  #   offset (float): width (or height if mode = 'v') of error bars
-  #   mode ('v' or 'h'): errors of y (if mode='v') or x (if mode='h')
-  #
-  if (mode == "v"){
-    segments(x0=x, y0=y-sd, x1=x, y1=y+sd) 
-    segments(x0=x-offset, y0=y+sd, x1=x+offset, y1=y+sd) 
-    segments(x0=x-offset, y0=y-sd, x1=x+offset, y1=y-sd) 
-  }else if (mode == "h"){
-    segments(x0=x-sd, y0=y, x1=x+sd, y1=y) 
-    segments(x0=x+sd, y0=y-offset, x1=x+sd, y1=y+offset) 
-    segments(x0=x-sd, y0=y-offset, x1=x-sd, y1=y+offset) 
-  }
-  points(x, y, pch=21, bg=col, col="black", cex=cex)
-}
-
-lines_threshold <- function(x, y, threshold, new, ...){
-  # Split data according to a given threshold, and plot lines for
-  # each set.
-  #
-  # Args:
-  #   x (vector): x coordinates
-  #   y (vector): y coordinates
-  #   threshold (float): value of x at which lines should not
-  #                      be connected
-  #   new (bool): create a new plot if TRUE, otherwise add
-  #               lines to an existing plot
-  #
-  id_1 <- (x < threshold)
-  id_2 <- (x > threshold)
-  if (new){
-    plot(x[id_1], y[id_1], ...)
-  }else{
-    suppressWarnings(lines(x[id_1], y[id_1], ...))
-  }
-  suppressWarnings(lines(x[id_2], y[id_2], ...))
-}
-
-
-######################
-# Model construction #
-######################
-
-# Test whether the different models (1-4) fit the data accurately, based on chi2 statistics
-
-# nb_points: number of experimental data points (152)
-# nb_par: number of free parameters
-
-# Go to models directory
-setwd(model_dir)
-
-# Model 1: no inhibition by acetate
-loadModel("Millard2020_Ecoli_glc_ace_model_1.cps")
-res_PE_model1 <- runParameterEstimation(method = "Statistics", model = getCurrentModel())
-res_PE_model1$chi2 <- test_khi2(nb_points=152, k_val=res_PE_model1$main$objective_value, nb_par=8)
-
-print("chi2-test for model 1:")
-print(paste("  p-value = ", res_PE_model1$chi2$`p-value, i.e. P(X^2<=value)`, sep=""))
-print(paste("  conclusion: ", res_PE_model1$chi2$conclusion, sep=""))     
-
-# Model 2: inhibition of glycolysis
-loadModel("Millard2020_Ecoli_glc_ace_model_2.cps")
-res_PE_model2 <- runParameterEstimation(method = "Statistics", model = getCurrentModel())
-res_PE_model2$chi2 <- test_khi2(nb_points=152, k_val=res_PE_model2$main$objective_value, nb_par=9)
-
-print("chi2-test for model 2:")
-print(paste("  p-value = ", res_PE_model2$chi2$`p-value, i.e. P(X^2<=value)`, sep=""))
-print(paste("  conclusion: ", res_PE_model2$chi2$conclusion, sep=""))     
-
-# Model 3: inhibition of TCA cycle
-loadModel("Millard2020_Ecoli_glc_ace_model_3.cps")
-res_PE_model3 <- runParameterEstimation(method = "Statistics", model = getCurrentModel())
-res_PE_model3$chi2 <- test_khi2(nb_points=152, k_val=res_PE_model3$main$objective_value, nb_par=9)
-
-print("chi2-test for model 3:")
-print(paste("  p-value = ", res_PE_model3$chi2$`p-value, i.e. P(X^2<=value)`, sep=""))
-print(paste("  conclusion: ", res_PE_model3$chi2$conclusion, sep=""))     
-
-# Model 4: inhibition of TCA and glycolysis
-loadModel("Millard2020_Ecoli_glc_ace_model_4.cps")
-res_PE_model4 <- runParameterEstimation(method = "Statistics", model = getCurrentModel())
-res_PE_model4$chi2 <- test_khi2(nb_points=152, k_val=res_PE_model4$main$objective_value, nb_par=10)
-
-print("chi2-test for model 4:")
-print(paste("  p-value = ", res_PE_model4$chi2$`p-value, i.e. P(X^2<=value)`, sep=""))
-print(paste("  conclusion: ", res_PE_model4$chi2$conclusion, sep=""))     
-
-# plot model evaluation results
-setwd(results_dir)
-pdf(file="model_construction.pdf", width = 5, height = 5)
-
-barplot(c(res_PE_model1$main$objective_value,
-       res_PE_model2$main$objective_value,
-       res_PE_model3$main$objective_value,
-       res_PE_model4$main$objective_value),
-       las=1,
-       ylab="variance-weighted SSR",
-       names.arg=c("model1", "model2", "model3", "model4"))
-chi2_threshold <- 171
-abline(h=chi2_threshold)
-
-dev.off()
-
-# plot fitting results for model 4
-setwd(model_dir)
-experiments <- list("ace_1" = list("conc_ini" = c("ace"=0.92, "glc"=12.9, "X"=0.0671),
-                                   "meas" = read.table("data_1mM.txt", header=TRUE, sep="\t")),
-                    "ace_10" = list("conc_ini" = c("ace"=9, "glc"=14.192, "X"=0.07),
-                                    "meas" = read.table("data_10mM.txt", header=TRUE, sep="\t")),
-                    "ace_30" = list("conc_ini" = c("ace"=30.2448, "glc"=12.5, "X"=0.07227),
-                                    "meas" = read.table("data_30mM.txt", header=TRUE, sep="\t")))
-
-loadModel("Millard2020_Ecoli_glc_ace_model_4.cps")
-setwd(results_dir)
-deleteEvent(getEvents()$key)
-
-for (i in c("ace_1", "ace_10", "ace_30")){
-  setSpecies(key="Ace0_out", initial_concentration=experiments[[i]]$conc_ini["ace"])
-  setSpecies(key="Glc", initial_concentration=experiments[[i]]$conc_ini["glc"])
-  setSpecies(key="X", initial_concentration=experiments[[i]]$conc_ini["X"])
-  applyInitialState()
-  experiments[[i]]$simulations <- runTimeCourse(duration=max(experiments[[i]]$meas$time), suppress_output_before=0.01)$result
-}
-
-sd_exp <- c("X"=0.045, "Glc"=0.5, "Ace"=0.2, "Ace_enr"=0.03)
-
-pdf(file = "model_fit.pdf", width = 7, height = 9)
-par(mfrow=c(4,3))
-
-plot(experiments$ace_1$simulations$Time, experiments$ace_1$simulations$X, type="l", lwd=2, las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="[biomass] (gDW/L)", xlab="", col="#1F4E79", main="[acetate]=1mM")
-plot_points(experiments$ace_1$meas$time, experiments$ace_1$meas$X, sd_exp["X"], offset=0.03, col="#1F4E79", cex=1.2)
-plot(experiments$ace_10$simulations$Time, experiments$ace_10$simulations$X, type="l", lwd=2, col="#2E75B6", las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="", xlab="", main="[acetate]=10mM")
-plot_points(experiments$ace_10$meas$time, experiments$ace_10$meas$X, sd_exp["X"], offset=0.03, col="#2E75B6", cex=1.2)
-plot(experiments$ace_30$simulations$Time, experiments$ace_30$simulations$X, type="l", lwd=2, col="#9DC3E6", las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="", xlab="", main="[acetate]=30mM")
-plot_points(experiments$ace_30$meas$time, experiments$ace_30$meas$X, sd_exp["X"], offset=0.03, col="#9DC3E6", cex=1.2)
-
-plot(experiments$ace_1$simulations$Time, experiments$ace_1$simulations$Glc, type="l", lwd=2, las=1, xlim=c(0,5), ylim=c(0,15), xaxs="i", yaxs="i", ylab="[Glc] (mM)", xlab="", col="#548235")
-plot_points(experiments$ace_1$meas$time, experiments$ace_1$meas$Glc, sd_exp["Glc"], offset=0.03, col="#548235", cex=1.2)
-plot(experiments$ace_10$simulations$Time, experiments$ace_10$simulations$Glc, type="l", lwd=2, col="#70AD47", las=1, xlim=c(0,5), ylim=c(0,15), xaxs="i", yaxs="i", ylab="", xlab="")
-plot_points(experiments$ace_10$meas$time, experiments$ace_10$meas$Glc, sd_exp["Glc"], offset=0.03, col="#70AD47", cex=1.2)
-plot(experiments$ace_30$simulations$Time, experiments$ace_30$simulations$Glc, type="l", lwd=2, col="#A9D18E", las=1, xlim=c(0,5), ylim=c(0,15), xaxs="i", yaxs="i", ylab="", xlab="")
-plot_points(experiments$ace_30$meas$time, experiments$ace_30$meas$Glc, sd_exp["Glc"], offset=0.03, col="#A9D18E", cex=1.2)
-
-plot(experiments$ace_1$simulations$Time, experiments$ace_1$simulations$Acet_out, type="l", lwd=2, las=1, xlim=c(0,5), ylim=c(0,5), xaxs="i", yaxs="i", ylab="[Ace] (mM)", xlab="", col="#B63A2D")
-plot_points(experiments$ace_1$meas$time, experiments$ace_1$meas$Ace, sd_exp["Ace"], offset=0.03, col="#B63A2D", cex=1.2)
-plot(experiments$ace_10$simulations$Time, experiments$ace_10$simulations$Acet_out, type="l", lwd=2, col="#D6685C", las=1, xlim=c(0,5), ylim=c(8,11), xaxs="i", yaxs="i", ylab="", xlab="")
-plot_points(experiments$ace_10$meas$time, experiments$ace_10$meas$Ace, sd_exp["Ace"], offset=0.03, col="#D6685C", cex=1.2)
-plot(experiments$ace_30$simulations$Time, experiments$ace_30$simulations$Acet_out, type="l", lwd=2, col="#E49890", las=1, xlim=c(0,5), ylim=c(27,32), xaxs="i", yaxs="i", ylab="", xlab="")
-plot_points(experiments$ace_30$meas$time, experiments$ace_30$meas$Ace, sd_exp["Ace"], offset=0.03, col="#E49890", cex=1.2)
-
-plot(experiments$ace_1$simulations$Time, experiments$ace_1$simulations$`Values[Ace_enr]`, type="l", lwd=2, las=1, xlim=c(0,5), ylim=c(0,1), xaxs="i", yaxs="i", ylab="acetate labeling (%)", xlab="time (h)", col="#BF9000")
-plot_points(experiments$ace_1$meas$time, experiments$ace_1$meas$Ace_enr, sd_exp["Ace_enr"], offset=0.03, col="#BF9000", cex=1.2)
-plot(experiments$ace_10$simulations$Time, experiments$ace_10$simulations$`Values[Ace_enr]`, type="l", lwd=2, col="#FFD966", las=1, xlim=c(0,5), ylim=c(0,0.7), xaxs="i", yaxs="i", ylab="", xlab="time (h)")
-plot_points(experiments$ace_10$meas$time, experiments$ace_10$meas$Ace_enr, sd_exp["Ace_enr"], offset=0.03, col="#FFD966", cex=1.2)
-plot(experiments$ace_30$simulations$Time, experiments$ace_30$simulations$`Values[Ace_enr]`, type="l", lwd=2, col="#FFE699", las=1, xlim=c(0,5), ylim=c(0,0.3), xaxs="i", yaxs="i", ylab="", xlab="time (h)")
-plot_points(experiments$ace_30$meas$time, experiments$ace_30$meas$Ace_enr, sd_exp["Ace_enr"], offset=0.03, col="#FFE699", cex=1.2)
-
-dev.off()
-
-
-#####################
-# Testing the model #
-#####################
-
-pdf(file="model_validation.pdf", width = 7, height = 9)
-par(mfrow=c(4,3))
-
-# Pulse experiment (Enjalbert et al., 2017)
-###########################################
-
-setwd(model_dir)
-loadModel("Millard2020_Ecoli_glc_ace_kinetic_model.cps")
-setwd(results_dir)
-
-# set biomass concentration at which the pulse is performed
-setGlobalQuantities(key = "_X_conc_pulse", initial_value = 0.9)
-
-# simulate response to acetate pulse
-res_pulse <- runTimeCourse()
-
-# get simulation results
-id_start <- which(res_pulse$result$Ace_out >= 30)[1]+1
-id_end <- which(res_pulse$result$Time >= (res_pulse$result$Time[id_start]+8/60))[1]+1
-
-t_pulse <- (res_pulse$result$Time[seq(id_start, id_end)] - res_pulse$result$Time[id_start])
-ace_conc_pulse <- res_pulse$result$Ace_out[seq(id_start, id_end)] - res_pulse$result$Ace_out[id_start]
-glc_conc_pulse <- res_pulse$result$Glc[seq(id_start, id_end)] - res_pulse$result$Glc[id_start]
-
-# measurements
-time_meas <- seq(0,8)/60
-glc <- c(0, -0.06931183, -0.151415145, -0.189227994, -0.269451057, -0.290764495, -0.230785281, -0.464084162, -0.551878527)
-sd_glc <- c(0, 0.032476344, 0.073133915, 0.113018846, 0.049485284, 0.005325541, 0.163377704, 0.034786419, 0.048477157)
-ace <- c(0, -0.027907926, -0.078000853, -0.155334163, -0.165031608, -0.111098424, -0.182877548, -0.237262298, -0.276903255)
-sd_ace <- c(0, 0.002740145, 0.025693594, 0.053641876, 0.089975321, 0.005875669, 0.085604161, 0.061930626, 0.099140975)
-
-# plot simulations vs measurements
-plot(t_pulse, ace_conc_pulse, type="l", ylim=c(-0.4,0), las=1, main="Enjalbert_2017 (pulse 30mM ace)", ylab="change of [Ace]", xlab="time (h)", col="#D6685C", lwd=2)
-plot_points(time_meas, ace, sd_ace, offset=0.002, col="#D6685C")
-plot(t_pulse, glc_conc_pulse, type="l", main="Enjalbert_2017 (pulse 30mM ace)", las=1, ylab="change of [Glc]", xlab="time (h)", col="#70AD47", lwd=2)
-plot_points(time_meas, glc, sd_glc, offset=0.002, col="#70AD47")
-
-# simulate control experiment (i.e. no acetate pulse)
-deleteEvent(getEvents()$key)
-
-res_nopulse <- runTimeCourse()
-
-# get simulation results
-ace_conc_nopulse <- res_nopulse$result$Ace_out[seq(id_start, id_end)] - res_nopulse$result$Ace_out[id_start]
-glc_conc_nopulse <- res_nopulse$result$Glc[seq(id_start, id_end)] - res_nopulse$result$Glc[id_start]
-
-# measurements
-glc_nopulse <- c(0, -0.195637774, -0.325512845, -0.433785334, -0.628518958, -0.726913548, -0.892908748, -1.071230579, -1.16285575)
-sd_glc_nopulse <- c(0, 0.058023617, 0.109115511, 0.047090371, 0.052331837, 0.065619906, 0.133896355, 0.16828754, 0.03515465)
-ace_nopulse <- c(0, 0.01012067, 0.05974009, 0.086787283, 0.086690257, 0.104329693, 0.128507087, 0.130026354, 0.187336965)
-sd_ace_nopulse <- c(0, 0.005117257, 0.022507218, 0.040319045, 0.037548873, 0.037235285, 0.044494365, 0.045029023, 0.023982374)
-
-# plot simulations vs measurements
-plot(t_pulse, ace_conc_nopulse, type="l", ylim=c(0,0.3), main="Enjalbert_2017 (control)", las=1, ylab="change of [Ace]", xlab="time (h)", col="#D6685C", lwd=2)
-plot_points(time_meas, ace_nopulse, sd_ace_nopulse, offset=0.002, col="#D6685C")
-plot(t_pulse, glc_conc_nopulse, type="l", ylim=c(-1.4,0), main="Enjalbert_2017 (control)", las=1, ylab="change of [Glc]", xlab="time (h)", col="#70AD47", lwd=2)
-plot_points(time_meas, glc_nopulse, sd_glc_nopulse, offset=0.002, col="#70AD47")
-
-
-# Chemostat experiment (Renilla et al., 2012)
-#############################################
-
-setwd(model_dir)
-loadModel("Millard2020_Ecoli_glc_ace_kinetic_model.cps")
-setwd(results_dir)
-
-# delete events and set glc feed to 1
-deleteEvent(getEvents()$key)
-setGlobalQuantities(key = "_feed", initial_value = 1)
-
-
-n_step <- 50
-dilution_rates <- seq(0.1, 0.5, length.out = n_step)
-fluxes <- c("Values[v_growth_rate]", "Values[v_glc_uptake]", "Values[v_ace_net]")
-res_chemostat <- matrix(NA, nrow=n_step, ncol=length(fluxes)+1, dimnames=list(r=NULL, c=c("dilution_rate", fluxes)))
-for (i in seq(n_step)){
-  setGlobalQuantities(key = "_dilution_rate", initial_value = dilution_rates[i])
-  res_ss <- runSteadyState()
-  res_chemostat[i,] <- c(dilution_rates[i], unlist(res_ss$global_quantities[res_ss$global_quantities$key %in% fluxes, "value"]))
-}
-
-# acetate flux as function of dilution rate
-dilution_rate <- c(0.09586056644880175, 0.20043572984749464, 0.2997821350762528, 0.3468409586056645, 0.39912854030501094, 0.44618736383442276, 0.5002178649237474)
-q_ace <- c(0.40472342596168076, 0.7396156614846294, 1.477019302736899, 1.2154669794005626, 1.96934635755591, 2.0929143843289824, 2.006569318707304)
-q_ace_sd <- c(0.120440687823878, 0.15316333195082, 0.04595662724122, 0.0274214232252601, 0.28885933172199, 0.0777639526513201, 0.28664731148963)
-
-plot(res_chemostat[,"dilution_rate"], res_chemostat[,"Values[v_ace_net]"], type="l", las=1, xlim=c(0,0.6), ylim=c(0,4), main="Renilla_2012", lwd=2, xlab="dilution rate (h-1)", ylab="ace flux (mmol/gDW/h)", col="#D6685C")
-plot_points(dilution_rate, q_ace, q_ace_sd, offset=0.01, col="#D6685C")
-
-# acetate flux as function of glc uptake
-q_glc <- c(1.43478260869565, 2.7391304347826, 4.59130434782608, 4.69565217391304, 5.7391304347826, 5.92173913043478, 6.10434782608695, 7.12173913043477, 8.34782608695652)
-q_ace <- c(0.381358340437624, 0.762906128635029, 1.40509614473808, 1.17836506583309, 1.99602159704461, 2.08290233967983, 2.01292033721701, 2.44717249218528, 2.5848252344416)
-q_ace_sd <- c(0.139547219854126, 0.139471440750213, 0.15697641375391, 0.1045751633987, 0.19179691200152, 0.0174291938997801, 0.24397082504499, 0.52295159609737, 0.33130624230368)
-q_glc_sd <- c(0.20234760540444, 0.58899555210581, 0.36827270271402, 0.14607356337583, 0.630432119199, 0.13069807968161, 0.47630364392495, 0.99361847036576, 0.66185122193432)
-
-plot(res_chemostat[,"Values[v_glc_uptake]"], res_chemostat[,"Values[v_ace_net]"], type="l", las=1, xlim=c(0,10), ylim=c(0,4), main="Renilla_2012", lwd=2, xlab="glc uptake (mmol/gDW/h)", ylab="ace flux (mmol/gDW/h)", col="#D6685C")
-plot_points(q_glc, q_ace, q_ace_sd, offset=0.2, col="#D6685C")
-plot_points(q_glc, q_ace, q_glc_sd, offset=0.08, mode="h", col="#D6685C")
-
-
-# Steady-state fluxes for acetate concentration between 0.1 and 100mM (Enjalbert et al., 2017; Pinhal et al., 2019)
-###################################################################################################################
-
-setwd(model_dir)
-loadModel("Millard2020_Ecoli_glc_ace_kinetic_model.cps")
-setwd(results_dir)
-
-# remove events and fix concentrations of actate, glucose and biomass
-deleteEvent(getEvents()$key)
-setSpecies(key="Ace_out", type="fixed")
-setSpecies(key="Glc", type="fixed")
-setSpecies(key="X", type="fixed")
-
-# run simulations
-n_step <- 50
-ace_concentration <- 10**seq(-1, 2, length.out = n_step)
-fluxes <- c("Values[v_growth_rate]", "Values[v_glc_uptake]", "Values[v_ace_net]")
-res_ace_range <- matrix(NA, nrow=n_step, ncol=length(fluxes)+1, dimnames=list(r=NULL, c=c("ace_concentration", fluxes)))
-for (i in seq(n_step)){
-  setSpecies(key="Ace_out", initial_concentration=ace_concentration[i])
-  applyInitialState()
-  res_ss <- runSteadyState()
-  res_ace_range[i,] <- c(ace_concentration[i], unlist(res_ss$global_quantities[res_ss$global_quantities$key %in% fluxes, "value"]))
-}
-
-xlab_main <- c(0.1, 1, 10, 100)
-xlab_sec <- c(seq(0.2, 0.9, by=0.1), seq(2, 9, by=1), seq(20, 90, by=10))
-
-# growth rate as function of acetate concentration
-growth_rates <- c(0.521128511, 0.611148842625582, 0.613161998174498, 0.502533817, 0.496290415, 0.488201506, 0.547635665, 0.499830448, 0.474554197, 0.425356578, 0.377534684, 0.645724326, 0.618475601, 0.554887936, 0.564811523, 0.527571192, 0.434972836, 0.3824734, 0.583623355, 0.620905534, 0.564259247, 0.532148135, 0.483885215, 0.557074418, 0.630654409249223)
-sd_growth_rates <- c(0.001793104, 0.00204807928657914, 0.00219396182484705, 0.001709207, 0.001846205, 0.001757403, 0.001821375, 0.001025702, 0.001940912, 0.001204707, 0.001999188, 0.001418374, 0.001932601, 0.001455791, 0.001574234, 0.001206265, 0.001292476, 0.001068259, 0.001804648, 0.001643459, 0.001598405, 0.001121218, 0.000912408, 0.00194896, 0.00203369597574686)
-ace_conc <- c(0.451964624, 1.11600286648471, 2.04718732931708, 2.86252145, 5.285907977, 9.106164204, 16.67476528, 16.76626787, 17.00218707, 30.8667961, 57.92292091, 0.478352574, 4.55673229, 8.10163028, 8.22100734, 7.829591756, 33.53244905, 66.20361403, 0.436956014, 1.28468189, 1.555875222, 12.02564968, 30.24566673, 0.548011282, 2.29562227069566)
-sd_ace_conc <- c(0.262318006, 0.281361538208953, 0.289527601555302, 0.302351163, 0.327705513, 0.330782201, 0.277259011, 0.233956798, 0.31883929, 0.300578057, 0.313371784, 0.231202155, 0.264687437, 0.243480317, 0.289821733, 0.263808862, 0.289478134, 0.264861034, 0.22461248, 0.229031308, 0.241718918, 0.254111384, 0.187394292, 0.011107606, 0.290519090995892)
-plot(res_ace_range[,"ace_concentration"], xaxt='n', res_ace_range[,"Values[v_growth_rate]"], las=1, col="#2E75B6", lwd=2, type="l", xlim=c(0.1,100), ylim=c(0,0.8), log="x", main="Enjalbert_2017", xlab="[acetate] (mM)", ylab="growth rate (h-1)")
-axis(side = 1, at = xlab_main, labels = TRUE)
-axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
-plot_points(ace_conc, growth_rates, sd_growth_rates, offset=0.01, col="#2E75B6")
-plot_points(ace_conc, growth_rates, sd_ace_conc, offset=0.02, mode="h", col="#2E75B6")
-
-# glc uptake as function of acetate concentration
-glc_upt <- c(8.654860167, 8.36127542981722, 7.98010111285252, 9.236935826, 8.274418986, 7.560431219, 7.339194455, 5.775312502, 6.423391263, 5.1544758, 3.938631573, 8.115447647, 9.28067031, 6.737153424, 7.172748804, 5.884186033, 5.684201497, 4.811576974, 9.632702365, 8.055042777, 9.708342814, 7.100081588, 5.505759496, 9.242859752, 8.18621623190759)
-sd_glc_upt <- c(0.337812425, 0.38531328268303, 0.373770045721031, 0.356787032, 0.334672954, 0.317509322, 0.288025925, 0.16053276, 0.375934255, 0.293148172, 0.359225607, 0.197331684, 0.360984112, 0.229372278, 0.241820396, 0.20450532, 0.260869273, 0.216134352, 0.34289286, 0.350305744, 0.293144783, 0.220135755, 0.153471508, 0.25245346, 0.396815184905029)
-ace_conc <- c(0.451964624, 1.11600286648471, 2.04718732931708, 2.86252145, 5.285907977, 9.106164204, 16.67476528, 16.76626787, 17.00218707, 30.8667961, 57.92292091, 0.478352574, 4.55673229, 8.10163028, 8.22100734, 7.829591756, 33.53244905, 66.20361403, 0.436956014, 1.28468189, 1.555875222, 12.02564968, 30.24566673, 0.548011282, 2.29562227069566)
-sd_ace_conc <- c(0.262318006, 0.281361538208953, 0.289527601555302, 0.302351163, 0.327705513, 0.330782201, 0.277259011, 0.233956798, 0.31883929, 0.300578057, 0.313371784, 0.231202155, 0.264687437, 0.243480317, 0.289821733, 0.263808862, 0.289478134, 0.264861034, 0.22461248, 0.229031308, 0.241718918, 0.254111384, 0.187394292, 0.011107606, 0.290519090995892)
-plot(res_ace_range[,"ace_concentration"], res_ace_range[,"Values[v_glc_uptake]"], xaxt='n', las=1, type="l", lwd=2, xlim=c(0.1,100), col="#70AD47", ylim=c(0,10), log="x", main="Enjalbert_2017", xlab="[acetate] (mM)", ylab="glc uptake (mmol/gDW/h)")
-axis(side = 1, at = xlab_main, labels = TRUE)
-axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
-plot_points(ace_conc, glc_upt, sd_glc_upt, offset=0.02, col="#70AD47")
-plot_points(ace_conc, glc_upt, sd_ace_conc, offset=0.2, mode="h", col="#70AD47")
-
-# ace flux as function of acetate concentration
-ace_flx <- c(3.5, -2.7, 1.516999356, 1.26845123082679, 0.775821380507016, 0.678877137, 0.017366464, -0.991478151, -1.286687213, -2.078474994, -1.530841439, -1.525342269, -1.253581266, 1.984679487, 0.546462624, -0.136780389, -0.393883917, -0.610240984, -1.120767885, -1.277455315, 2.574285211, 2.051935093, 1.828415596, -1.262442483, -1.317987733, 2.333568565, 1.85234639824858)
-sd_ace_flx <- c(0.35, 0.27, 0.316118066, 0.388752117258161, 0.40715278851436, 0.33357638, 0.37333751, 0.347029894, 0.280501612, 0.195031303, 0.376252463, 0.226182385, 0.303661317, 0.253610517, 0.385450715, 0.243880325, 0.30665695, 0.257983739, 0.23844407, 0.198458448, 0.299832036, 0.334956504, 0.317134334, 0.263807154, 0.195219648, 0.016120887, 0.386174129654754)
-ace_conc <- c(0.2, 100, 0.451964624, 1.11600286648471, 2.04718732931708, 2.86252145, 5.285907977, 9.106164204, 16.67476528, 16.76626787, 17.00218707, 30.8667961, 57.92292091, 0.478352574, 4.55673229, 8.10163028, 8.22100734, 7.829591756, 33.53244905, 66.20361403, 0.436956014, 1.28468189, 1.555875222, 12.02564968, 30.24566673, 0.548011282, 2.29562227069566)
-sd_ace_conc <- c(0.05, 10, 0.262318006, 0.281361538208953, 0.289527601555302, 0.302351163, 0.327705513, 0.330782201, 0.277259011, 0.233956798, 0.31883929, 0.300578057, 0.313371784, 0.231202155, 0.264687437, 0.243480317, 0.289821733, 0.263808862, 0.289478134, 0.264861034, 0.22461248, 0.229031308, 0.241718918, 0.254111384, 0.187394292, 0.011107606, 0.290519090995892)
-plot(res_ace_range[,"ace_concentration"], res_ace_range[,"Values[v_ace_net]"], xaxt='n', las=1, type="l", lwd=2, xlim=c(0.1,100), ylim=c(-4,4), log="x", main="Enjalbert_2017, Pinhal_2019", col="#D6685C", xlab="[acetate] (mM)", ylab="ace flux (mmol/gDW/h)")
-abline(h=0)
-axis(side = 1, at = xlab_main, labels = TRUE)
-axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
-plot_points(ace_conc, ace_flx, sd_ace_flx, offset=0.04, col="#D6685C")
-plot_points(ace_conc, ace_flx, sd_ace_conc, offset=0.2, mode="h", col="#D6685C")
-
-dev.off()
-
-
-##############################
-# Metabolic control analyses #
-##############################
-
-setwd(model_dir)
-loadModel("Millard2020_Ecoli_glc_ace_kinetic_model.cps")
-setwd(results_dir)
-
-# delete events and fix concentrations of biomass and extracellular glc and acetate
-deleteEvent(getEvents()$key)
-setSpecies(key="Ace_out", type="fixed")
-setSpecies(key="Glc", type="fixed")
-setSpecies(key="X", type="fixed")
-
-# calculate flux control coefficients
-n_step <- 50
-ace_range <- 10**(seq(-1,2,length.out = n_step))
-res_ace_MCA <- matrix(NA, nrow=length(ace_range), ncol=7)
-res_ace_MCA[,1] <- ace_range
-for (i in seq(n_step)){
-  setSpecies(key="Ace_out{cell}", initial_concentration = ace_range[i], model = getCurrentModel())
-  applyInitialState(model = getCurrentModel())
-  res_MCA <- runMetabolicControlAnalysis(model = getCurrentModel())
-  if (res_MCA$result_ss != "found"){
-    print("error")
-  }else{
-    fcc <- res_MCA$flux_control_coefficients_scaled
-    res_ace_MCA[i,seq(2,7)] <- fcc["(ackA)", colnames(fcc) != "'Summation Error'"]
-  }
-}
-colnames(res_ace_MCA) <- c("ace_conc", colnames(fcc)[colnames(fcc) != "'Summation Error'"])
-
-# plot results
-pdf(file = "results_control_1.pdf", height = 4, width = 5)
-
-setSpecies(key="Ace_out{cell}", initial_concentration = 0.1, model = getCurrentModel())
-applyInitialState(model = getCurrentModel())
-res_MCA <- runMetabolicControlAnalysis(model = getCurrentModel())
-
-hmc <- res_MCA$flux_control_coefficients_scaled[c("(glc_upt)", "(ackA)", "(sink)"), c("(glc_upt)", "(sink)", "(pta)", "(ackA)", "(ace_xch)")]
-colnames(hmc) <- c("glycolysis", "TCA", "Pta", "AckA", "Ace_xch")
-rownames(hmc) <- c("glycolysis", "acetate", "TCA")
-rgb.palette <- colorRampPalette(brewer.pal(n = 11, name = "RdBu"))
-breaks <- c(-1, -0.5, -0.2, -0.1, -0.05, -0.01, 0.01, 0.05, 0.1, 0.2, 0.5, 1, 1.5)
-col_scale <- rgb.palette(length(breaks)-1)
-col_scale[6] <- "#DDDDDD"
-heatmap.2(hmc, Rowv=FALSE, Colv=FALSE, dendrogram="none", col=col_scale, breaks=breaks,
-          scale="none", trace="none", colsep=seq(0,ncol(hmc)), rowsep=seq(0,nrow(hmc)), sepwidth=c(0.04,0.02))
-
-dev.off()
-
-pdf(file="results_control_2.pdf", width = 7, height = 9)
-par(mfrow=c(4,3))
-
-xlab_main <- c(0.1, 1, 10, 100)
-xlab_sec <- c(seq(0.2, 0.9, by=0.1), seq(2, 9, by=1), seq(20, 90, by=10))
-conc_threshold <- 14.27174
-
-ctrl_by_acetate_pathway <- apply(res_ace_MCA[,c("(ackA)", "(pta)", "(ace_xch)")], 1, sum)
-ctrl_by_glc_upt <- res_ace_MCA[,"(glc_upt)"]
-ctrl_by_TCA <- res_ace_MCA[,"(sink)"]
-
-plot(x=ace_range, y=ctrl_by_acetate_pathway, type="l", xaxt="n", las=1, ylim=c(0,1), log="x", xaxs="i", yaxs="i", xlab="[acetate] (mM)", ylab="control by acetate pathway", lwd=2)
-axis(side = 1, at = xlab_main, labels = TRUE)
-axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
-
-lines_threshold(x=ace_range, y=ctrl_by_glc_upt, threshold=conc_threshold, new=TRUE, xaxt="n", xaxs="i", yaxs="i", las=1, xlim=c(0.1,100), type="l", ylim=c(-3,3), log="x", xlab="[acetate] (mM)", ylab="control by glycolysis", lwd=2)
-axis(side = 1, at = xlab_main, labels = TRUE)
-axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
-abline(h=0)
-
-lines_threshold(x=ace_range, y=ctrl_by_TCA, threshold=conc_threshold, new=TRUE, xaxt="n", xaxs="i", yaxs="i", las=1, xlim=c(0.1,100), type="l", ylim=c(-3,3), log="x", xlab="[acetate] (mM)", ylab="control by TCA", lwd=2)
-axis(side = 1, at = xlab_main, labels = TRUE)
-axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
-abline(h=0)
-
-plot(x=ace_range, y=ctrl_by_TCA+ctrl_by_glc_upt, type="l", ylim=c(0,1), xaxt="n", xaxs="i", yaxs="i", las=1, log="x", xlab="[acetate] (mM)", ylab="control by TCA+glycolysis", lwd=2)
-axis(side = 1, at = xlab_main, labels = TRUE)
-axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
-
-plot(x=ace_range, y=-ctrl_by_TCA/ctrl_by_glc_upt, type="l", ylim=c(0,2), xaxt="n", xaxs="i", yaxs="i", las=1, log="x", xlab="[acetate] (mM)", ylab="control by TCA/glycolysis", lwd=2)
-axis(side = 1, at = xlab_main, labels = TRUE)
-axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
-abline(h=1)
-
-dev.off()
-
-
-#################################
-# Metabolic regulation analyses #
-#################################
-
-n_step <- 300
-delta_p <- 0.001
-conc_threshold <- 14.27174
-ace_range <- 10**(seq(-1, 2, length.out = n_step))
-ace_range <- ace_range[abs(ace_range - conc_threshold) > 0.1]
-res_ace_regulation <- matrix(NA, nrow=length(ace_range), ncol=4, dimnames=list(r=NULL, c=c("ace_conc", "via_acetate_pathway", "via_glc_upt", "via_tca")))
-
-for (i in seq(length(ace_range))){
-  
-  # set ace concentration
-  setSpecies(key="Ace_out{cell}", initial_concentration = ace_range[i])
-  applyInitialState()
-  
-  # get steady-state
-  res_ss_i <- runSteadyState(update_model=TRUE)$global_quantities
-  
-  # calculate control coefficients
-  res_MCA_R <- runMCA()$flux_control_coefficients_scaled
-  
-  # calculate elasticities
-  
-  # fix acetylCoA concentration to calculate elasticity of each pathway wrt acetate
-  setSpecies(key="AcCoA", type="fixed")
-  
-  # change acetate concentration
-  setSpecies(key="Ace_out{cell}", initial_concentration = ace_range[i]*(1+delta_p))
-  applyInitialState()
-  
-  # get steady-state
-  res_ss_i_eps <- runSteadyState()$global_quantities
-  
-  # calculate elasticities (using the more stable numerical method, both being equivalent)
-  #elasticities <- (log(abs(res_ss_i_eps$value)) - log(abs(res_ss_i$value))) / log(1+delta_p)
-  #print(elasticities)
-  elasticities <- (res_ss_i_eps$value - res_ss_i$value) / delta_p / res_ss_i_eps$value
-  #print(elasticities)
-  
-  # reset balance on accoa
-  setSpecies(key="AcCoA", type="reactions")
-  
-  # calculate response coefficient
-  # acetate via Pta-AckA
-  res_reg_ace_ace <- sum(res_MCA_R["(ackA)", c("(ackA)", "(pta)", "(ace_xch)")]) * elasticities[res_ss_i_eps$key == "Values[v_ace_net]"]
-  # acetate via glc uptake
-  res_reg_ace_glc <- res_MCA_R["(ackA)", "(glc_upt)"] * elasticities[res_ss_i_eps$key == "Values[v_glc_uptake]"]
-  # acetate via sink
-  res_reg_ace_tca <- res_MCA_R["(ackA)", "(sink)"] * elasticities[res_ss_i_eps$key == "Values[v_growth_rate]"]
-  
-  res_ace_regulation[i,] <- c(ace_range[i], res_reg_ace_ace, res_reg_ace_glc, res_reg_ace_tca)
-}
-
-
-pdf(file="results_regulation.pdf", width = 7, height = 9)
-par(mfrow=c(4,3))
-
-xlab_main <- c(0.1, 1, 10, 100)
-xlab_sec <- c(seq(0.2, 0.9, by=0.1), seq(2, 9, by=1), seq(20, 90, by=10))
-conc_threshold <- 14.27174
-
-# plot partitioned response coefficients
-lines_threshold(ace_range, res_ace_regulation[,"via_acetate_pathway"], threshold=conc_threshold, new=TRUE, xaxt="n", las=1, xaxs="i", yaxs="i", col="#2E75B6", xlim=c(0.1,100), type="l", log="x", ylim=c(-5, 5), xlab="[acetate] (mM)", ylab="R_ace_pathway", lwd=2)
-axis(side = 1, at = xlab_main, labels = TRUE)
-axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
-abline(h=0)
-lines_threshold(ace_range, res_ace_regulation[,"via_glc_upt"], threshold=conc_threshold, new=TRUE, xaxt="n", las=1, xaxs="i", yaxs="i", col="#D6685C", xlim=c(0.1,100), type="l", log="x", ylim=c(-5, 5), xlab="[acetate] (mM)", ylab="R_Glc_uptake", lwd=2)
-axis(side = 1, at = xlab_main, labels = TRUE)
-axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
-abline(h=0)
-lines_threshold(ace_range, res_ace_regulation[,"via_tca"], threshold=conc_threshold, new=TRUE, xaxt="n", las=1, xaxs="i", yaxs="i", col="#70AD47", xlim=c(0.1,100), type="l", log="x", ylim=c(-5, 5), xlab="[acetate] (mM)", ylab="R_TCA", lwd=2)
-axis(side = 1, at = xlab_main, labels = TRUE)
-axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
-abline(h=0)
-
-# plot contribution of each pathway
-contribution <- apply(res_ace_regulation[,2:4], 1, FUN=function(x) sum(abs(x)))
-lines_threshold(ace_range, res_ace_regulation[,"via_acetate_pathway"]/contribution, threshold=conc_threshold, new=TRUE, xaxt="n", las=1, xaxs="i", yaxs="i", xlim=c(0.1,100), type="l", log="x", xlab="[acetate] (mM)", ylab="relative_R", ylim=c(-0.7, 0.7), lwd=2, col="#2E75B6")
-axis(side = 1, at = xlab_main, labels = TRUE)
-axis(side = 1, at = xlab_sec, labels = FALSE, tcl=-0.3)
-abline(h=0)
-lines_threshold(ace_range, res_ace_regulation[,"via_glc_upt"]/contribution, threshold=conc_threshold, new=FALSE, type="l", col="#D6685C", lwd=2)
-lines_threshold(ace_range, res_ace_regulation[,"via_tca"]/contribution, threshold=conc_threshold, new=FALSE, type="l", col="#70AD47", lwd=2)
-
-dev.off()
-
-
diff --git a/set_env.R b/set_env.R
new file mode 100644
index 0000000..e46dba0
--- /dev/null
+++ b/set_env.R
@@ -0,0 +1,23 @@
+####################################
+# Supplementary information folder #
+####################################
+
+# We assume to be already in the working directory, otherwise update the path of the supplementary data folder
+wd <- getwd()
+#wd <- "C:/Users/millard/Documents/GIT/acetate_regulation/acetate_regulation/"
+
+model_dir <- file.path(wd, "model", "cps")
+results_dir <- file.path(wd, "results")
+
+###################
+# Set environment #
+###################
+
+# load libraries
+library(RColorBrewer)
+library(gplots)
+library(CoRC)
+library(stringr)
+
+setwd(wd)
+source("misc.R")