diff --git a/README.md b/README.md deleted file mode 100644 index c2fad015a85d6fe79a806176cb705b2ec43a8be5..0000000000000000000000000000000000000000 --- a/README.md +++ /dev/null @@ -1,29 +0,0 @@ -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 - -`LoadDrugData.m` computes mean values and standard error of the means from the raw data with addition of Dexamathasone and load to workspace - -`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 \ No newline at end of file