Update README.md

README.md

@@ -10,14 +10,22 @@ To reproduce the results in the manuscript, run `plot_many_params.m` for each hy
 
 The included files:
 
-`macrophage_simple.txt` model text file in the format of the IQM toolbox
+`Macrophage_simple.txt` model text file used for hypothesis testing in the format of the IQM toolbox
+
+`Macrophage_treatment.txt` model text file for the model used to simulate treatment scenarios in in the format of the IQM toolbox
 
 `allGoodValuesX.dat` contains acceptable parameter values
 
 `cost_simple.m` computes the cost and need a set of parameter values as input
 
+`Optimization_simple.m` main script to use in the optimization of parameters
+
 `LoadData.m` computes mean values and standard error of the means from the raw data with only LPS stimulation and load to workspace
 
 `LoadDrugData.m` computes mean values and standard error of the means from the raw data with addition of Dexamathasone and load to workspace
 
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+`simple_plot.m` simulate the model and plot for a single set of parameter values
+
+`plot_many_params.m` simulate the model and plot for all loaded acceptable parameter values
+
+`plot_treatment.m` simulate the treatment model and plot for for all loaded acceptable parameter values
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