Merge branch 'master' of gitlab.liu.se:eliny61/macrophage-model

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. 
+
+First, you need to install the toolbox from https://iqmtools.intiquan.com/
+
+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 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
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+`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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+`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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