From b154de9dec0cbad3b6e87d3fb8269421e941d61a Mon Sep 17 00:00:00 2001
From: Elin Nyman <elin.nyman@liu.se>
Date: Wed, 5 Feb 2020 14:10:02 +0100
Subject: [PATCH] Update README.md

---
 README.md | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 0a2f987..352b99c 100644
--- a/README.md
+++ b/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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-- 
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