From 57be64f0583f0a32f46f4d4f53a8fdc218866e41 Mon Sep 17 00:00:00 2001
From: Elin Nyman <elin.nyman@liu.se>
Date: Wed, 5 Feb 2020 12:26:02 +0100
Subject: [PATCH] Update README.md

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 README.md | 22 +++++++++++++++++++---
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-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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+``
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