Update README.md

README.md

-Matlab files to reproduce the results of the manuscript "Mechanisms of a sustained anti-inflammatory drug response in alveolar macrophages unraveled with mathematical modeling" by Nyman et al. The IQM toolbox is used. 
+Matlab files to reproduce the results of the manuscript **Mechanisms of a sustained anti-inflammatory drug response in alveolar macrophages unraveled with mathematical modeling** by Nyman et al.
+
+The IQM toolbox is used. 
 
 First, you need to install the toolbox from https://iqmtools.intiquan.com/
 
-Second, run the file initIQM.m
+Second, run the file `initIQM.m`
+
+To reproduce the results in the manuscript, run `plot_many_params.m` for each hypothesis
+
+The included files:
+
+`macrophage_simple.txt` model text file 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
+
+`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
 
-To reproduce the results in the manuscript, run plot_many_params.m for each hypothesis
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