Merge pull request #183 from NantiaL/master

Update Example Zeilfelder_IL6_CellSystems2025

Author: timo-rachel

arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/Fig3E_HepG2_Depletion_BMP2_DCF.csv

@@ -0,0 +1,13 @@
+DCF [mM],time,obs conc (pg/mL),Experiment,mean control,norm conc (% to mean DMSO control
+0,0,,1,4.74,
+0,0,4.17,1,4.74,87.97468354
+0,0,5.32,1,4.74,112.2362869
+500,0,3.8,1,4.74,80.16877637
+500,0,2.57,1,4.74,54.21940928
+500,0,2.71,1,4.74,57.17299578
+0,0,2.65,2,2.59,102.3166023
+0,0,2.29,2,2.59,88.41698842
+0,0,2.84,2,2.59,109.6525097
+250,0,2.13,2,2.59,82.23938224
+250,0,2.18,2,2.59,84.16988417
+250,0,2.13,2,2.59,82.23938224

arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/Fig6D_PHH_IL6_BMP2_DCF_APAP_HAMPmRNA.csv

@@ -0,0 +1,58 @@
+time,IL6,BMP2,DCF,rep,HAMP_FC_to_0min
+0,Ctrl,Ctrl,Ctrl,1,0.974994051
+0,Ctrl,Ctrl,Ctrl,2,1.022848221
+0,Ctrl,Ctrl,Ctrl,3,1.002157728
+0,Ctrl,Ctrl,DCF,1,1.078521283
+0,Ctrl,Ctrl,DCF,2,0.996935172
+0,Ctrl,Ctrl,DCF,3,0.947032659
+120,Ctrl,Ctrl,Ctrl,1,0.542993344
+120,Ctrl,Ctrl,Ctrl,2,0.549477502
+120,Ctrl,Ctrl,Ctrl,3,0.562495561
+120,IL6,Ctrl,Ctrl,1,3.597994782
+120,IL6,Ctrl,Ctrl,2,3.822833876
+120,IL6,Ctrl,Ctrl,3,3.820589524
+120,Ctrl,BMP2,Ctrl,1,3.735806213
+120,Ctrl,BMP2,Ctrl,2,4.42544834
+120,Ctrl,BMP2,Ctrl,3,5.523334678
+120,IL6,BMP2,Ctrl,1,10.04526492
+120,IL6,BMP2,Ctrl,2,9.557732507
+120,IL6,BMP2,Ctrl,3,10.92290698
+120,IL6,Ctrl,DCF,1,2.423596313
+120,IL6,Ctrl,DCF,2,2.436104949
+120,IL6,Ctrl,DCF,3,2.552313476
+120,IL6,BMP2,DCF,1,2.684617158
+120,IL6,BMP2,DCF,2,2.90121803
+120,IL6,BMP2,DCF,3,3.143906578
+240,Ctrl,Ctrl,Ctrl,1,0.391490449
+240,Ctrl,Ctrl,Ctrl,2,0.381877612
+240,Ctrl,Ctrl,Ctrl,3,0.410667681
+240,IL6,Ctrl,Ctrl,1,14.02375992
+240,IL6,Ctrl,Ctrl,2,13.73523511
+240,IL6,Ctrl,Ctrl,3,14.45505145
+240,Ctrl,BMP2,Ctrl,1,14.16375937
+240,Ctrl,BMP2,Ctrl,2,14.14022847
+240,Ctrl,BMP2,Ctrl,3,14.10282553
+240,IL6,BMP2,Ctrl,1,51.68570914
+240,IL6,BMP2,Ctrl,2,57.19849265
+240,IL6,BMP2,Ctrl,3,61.24779524
+240,IL6,Ctrl,DCF,1,3.383717658
+240,IL6,Ctrl,DCF,2,3.163807469
+240,IL6,Ctrl,DCF,3,3.245136807
+240,IL6,BMP2,DCF,1,5.012690447
+240,IL6,BMP2,DCF,2,6.006726721
+240,IL6,BMP2,DCF,3,3.969293574
+0,IL6,Ctrl,Ctrl,1,0.974994051
+0,IL6,Ctrl,Ctrl,2,1.022848221
+0,IL6,Ctrl,Ctrl,3,1.002157728
+0,Ctrl,BMP2,Ctrl,1,0.974994051
+0,Ctrl,BMP2,Ctrl,2,1.022848221
+0,Ctrl,BMP2,Ctrl,3,1.002157728
+0,IL6,BMP2,Ctrl,1,0.974994051
+0,IL6,BMP2,Ctrl,2,1.022848221
+0,IL6,BMP2,Ctrl,3,1.002157728
+0,IL6,Ctrl,DCF,1,1.078521283
+0,IL6,Ctrl,DCF,2,0.996935172
+0,IL6,Ctrl,DCF,3,0.947032659
+0,IL6,BMP2,DCF,1,1.078521283
+0,IL6,BMP2,DCF,2,0.996935172
+0,IL6,BMP2,DCF,3,0.947032659

arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/FigS3BC_HepG2_DR_DCF_APAP_HAMPmRNA.csv

@@ -0,0 +1,46 @@
+Dose DCF [mM],Dose APAP [mM],Dose IL-6 [ng/mL],Time [min],Replicate,HAMP FC to t0
+0,0,0,0,1,1.224600533
+0,0,0,0,2,0.816985847
+0,0,0,120,1,0.677014437
+0,0,0,120,2,0.837734667
+0,0,10,120,1,4.754223773
+0,0,10,120,2,4.125090982
+15.625,0,10,120,1,3.964788371
+15.625,0,10,120,2,3.875642764
+31.25,0,10,120,1,4.126594576
+31.25,0,10,120,2,3.804604759
+62.5,0,10,120,1,4.999511941
+62.5,0,10,120,2,5.534672081
+125,0,10,120,1,11.60095809
+125,0,10,120,2,8.782298778
+250,0,10,120,1,20.35181936
+250,0,10,120,2,11.3088384
+500,0,10,120,1,49.58098313
+500,0,10,120,2,18.24574776
+0,0.3125,10,120,1,7.553031703
+0,0.3125,10,120,2,4.809564082
+0,0.625,10,120,1,3.799880284
+0,0.625,10,120,2,4.509331123
+0,1.25,10,120,1,6.033596784
+0,1.25,10,120,2,5.257069863
+0,2.5,10,120,1,8.51297313
+0,2.5,10,120,2,10.05594157
+0,5,10,120,1,7.531832873
+0,5,10,120,2,10.96048058
+0,10,10,120,1,7.077433152
+0,10,10,120,2,7.16301929
+0,0,0,0,3,0.95841362
+0,0,0,120,3,1.394347903
+0,0,10,120,3,4.979788044
+15.625,0,10,120,3,5.767665284
+31.25,0,10,120,3,10.0727463
+62.5,0,10,120,3,17.26320471
+125,0,10,120,3,19.92974948
+250,0,10,120,3,37.86511765
+500,0,10,120,3,43.3576133
+0,0.3125,10,120,3,14.87004975
+0,0.625,10,120,3,9.806250902
+0,1.25,10,120,3,11.07938594
+0,2.5,10,120,3,20.92711768
+0,5,10,120,3,18.18793641
+0,10,10,120,3,11.27697151

arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/README.md

@@ -44,8 +44,6 @@ A primary human hepatocyte model (PMM) which includes drug effects identified fr
 L1 regularization in HepG2 cells and included parameters reflecting differences between primary
 human hepatocytes and HepG2 cells. This model has the same structure as the integrative mondel (`combined_model.def`)
 
-All model equations, parameters as well as results from uncertainty analysis are detauled described in `Mathematical_modeling_documentation.pdf`. 
-
 ## Prerequisites
 The following installations are required for successful use of the scripts:
 - MATLAB (version 2019 or higher)
@@ -60,13 +58,10 @@ To simulate and generate figures, run the following scripts one after the other:
 
 To specify the filename and save generated figures use: `arPaperFigures(1, 0, 0, 0, 'FigureName');` 
 
-## License
-GPL-3.0 license
-
 ## Citation
 If you use the models, data, or scripts from this repository in your research, please cite the original paper:
 
 XXXXX
 
 ## Contact
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+XXXX