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New Example from Klingmüller and Timmer groups #181

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a664912
Add new Example directory
NantiaL Mar 27, 2025
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remove models
NantiaL Mar 27, 2025
3a82936
Add Models/
NantiaL Mar 27, 2025
9eb2f2e
Delete arFramework3/Examples/Zeilfelder_IL6_CellSystems2024 directory
NantiaL Mar 27, 2025
873b546
Add new Example
NantiaL Mar 27, 2025
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Delete arFramework3/Examples/Zeilfelder_IL6_CellSystems2024 directory
NantiaL Mar 27, 2025
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Add new Example
NantiaL Mar 27, 2025
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16 changes: 16 additions & 0 deletions arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/BSA/protein_conc.csv
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min,mcyto_obs,mnuc_obs,experiment
0,5.28654874771286,1.93703928647129,Anja_2016_4
0,6.16519097855432,2.06383633945531,Anja_2016_4
0,6.11938768842954,1.72477985898743,Anja_2016_4
0,5.83032385791461,2.62213454153217,Anja_2016_4
0,6.67237919049041,2.4869586856573,Anja_2016_4
0,6.01744704319496,2.26827563414223,Anja_2016_4
0,5.55131442439966,2.77378816873467,Anja_2016_4
0,5.30330585408744,1.86218981259631,Anja_2016_4
0,6.42688463560078,2.36155822467353,Anja_2016_4
0,5.70771608152423,1.2493822467353,Anja_2016_4
0,6.83883524461496,2.05713346361167,Anja_2016_4
0,5.55019708421184,2.06830503433043,Anja_2016_4
0,5.68509360503976,2.55817730332899,Anja_2016_4
0,5.78535823999261,2.30542103603277,Anja_2016_4
0,6.0104649987734,2.40847868851709,Anja_2016_4
13 changes: 13 additions & 0 deletions arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/BSA/protein_conc.def
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DESCRIPTION

PREDICTOR
t T "min" "time" 0 100

INPUTS

OBSERVABLES

ERRORS

CONDITIONS
HepG2 "1"
13 changes: 13 additions & 0 deletions arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/PHH/2017_04_BSA.def
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DESCRIPTION
"data .def file template"

PREDICTOR
t T "min" "time" 0 100

INPUTS

OBSERVABLES

ERRORS

CONDITIONS
Binary file added arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/PHH/2017_04_BSA.xlsx
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13 changes: 13 additions & 0 deletions arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/PHH/2017_04_PHH_Exp45.def
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Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
DESCRIPTION
"data .def file template"

PREDICTOR
t T "min" "time" 0 100

INPUTS

OBSERVABLES

ERRORS

CONDITIONS
Binary file added arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/PHH/2017_04_PHH_Exp45.xlsx
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16 changes: 16 additions & 0 deletions arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/PHH/2018_32_PHH_genes_raw.def
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DESCRIPTION
"Experimenter: Anja Juenger"
"Cells: PHH"
"qPCR time course data"

PREDICTOR
t T "min" "time" 0 500


INPUTS

OBSERVABLES

ERRORS

CONDITIONS
Binary file added arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/PHH/2018_32_PHH_genes_raw.xlsx
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16 changes: 16 additions & 0 deletions arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/PHH/2018_32_PHH_pSTAT3.def
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DESCRIPTION
"Experimenter: Anja Juenger"
"Cells: PHH"
"qPCR time course data"

PREDICTOR
t T "min" "time" 0 500


INPUTS

OBSERVABLES

ERRORS

CONDITIONS
Binary file added arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/PHH/2018_32_PHH_pSTAT3.xlsx
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13 changes: 13 additions & 0 deletions arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/PHH/2018_42_PHH_MpC.def
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Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
DESCRIPTION
"data .def file template"

PREDICTOR
t T "min" "time" 0 100

INPUTS

OBSERVABLES

ERRORS

CONDITIONS
Binary file added arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/PHH/2018_42_PHH_MpC.xlsx
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13 changes: 13 additions & 0 deletions arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/PHH/2018_49_SOCS3_IP_Exp137.def
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Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
DESCRIPTION
"data .def file template"

PREDICTOR
t T "min" "time" 0 100

INPUTS

OBSERVABLES

ERRORS

CONDITIONS
Binary file added arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/PHH/2018_49_SOCS3_IP_Exp137.xlsx
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38 changes: 38 additions & 0 deletions arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/SOCS3_wb/Anja_2018_13_SOCS3.csv
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time,input_il6,input_dcf,input_apap,SOCS3_WB,experiment,cSOCS3_wb,nExpID,,
0,10,0,0,1389560.62,Anja_2018_12,1.38956062,1,,
60,10,0,0,23567579,Anja_2018_12,23.567579,1,,
90,10,0,0,18894196.38,Anja_2018_12,18.89419638,1,SOCS3 IP,HepG2 cells
120,10,0,0,16067565.55,Anja_2018_12,16.06756555,1,,
60,10,500,0,13831762.86,Anja_2018_12,13.83176286,1,input_il6,10 ng/mL
90,10,500,0,26948877.05,Anja_2018_12,26.94887705,1,input_dcf,500 µM
120,10,500,0,22310694.89,Anja_2018_12,22.31069489,1,input_apap,10 mM
60,10,0,10,14826986.57,Anja_2018_12,14.82698657,1,,
90,10,0,10,32156575.63,Anja_2018_12,32.15657563,1,,
120,10,0,10,25558518.71,Anja_2018_12,25.55851871,1,,
0,10,0,0,1612491.43,Anja_2018_11,1.61249143,2,,
60,10,0,0,17386563.26,Anja_2018_11,17.38656326,2,,
90,10,0,0,8601748.68,Anja_2018_11,8.60174868,2,,
120,10,0,0,7186259.9,Anja_2018_11,7.1862599,2,,
60,10,500,0,8283875.97,Anja_2018_11,8.28387597,2,,
90,10,500,0,18368610,Anja_2018_11,18.36861,2,,
120,10,500,0,26303102,Anja_2018_11,26.303102,2,,
60,10,0,10,9367625.33,Anja_2018_11,9.36762533,2,,
90,10,0,10,15018717.86,Anja_2018_11,15.01871786,2,,
120,10,0,10,25055034.35,Anja_2018_11,25.05503435,2,,
0,10,0,0,648599.69,Anja_2018_10,0.64859969,3,,
60,10,0,0,15513746.73,Anja_2018_10,15.51374673,3,,
90,10,0,0,14270716.47,Anja_2018_10,14.27071647,3,,
120,10,0,0,8000426.8,Anja_2018_10,8.0004268,3,,
60,10,500,0,5749143.04,Anja_2018_10,5.74914304,3,,
90,10,500,0,22045990.74,Anja_2018_10,22.04599074,3,,
120,10,500,0,17831392.48,Anja_2018_10,17.83139248,3,,
60,10,0,10,2734579.01,Anja_2018_10,2.73457901,3,,
90,10,0,10,26498944.1,Anja_2018_10,26.4989441,3,,
120,10,0,10,19643097.87,Anja_2018_10,19.64309787,3,,
0,10,0,0,930649.03,Anja_2018_09,0.93064903,4,,
60,10,0,0,21919630.38,Anja_2018_09,21.91963038,4,,
90,10,0,0,9701394.79,Anja_2018_09,9.70139479,4,,
120,10,0,0,7491874.37,Anja_2018_09,7.49187437,4,,
60,10,500,0,14643847.43,Anja_2018_09,14.64384743,4,,
90,10,500,0,23119593.86,Anja_2018_09,23.11959386,4,,
120,10,500,0,26477699.06,Anja_2018_09,26.47769906,4,,
14 changes: 14 additions & 0 deletions arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/SOCS3_wb/Anja_2018_13_SOCS3.def
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Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
DESCRIPTION
"data .def file template"

PREDICTOR
t T "min" "time" 0 100

INPUTS

OBSERVABLES

ERRORS

CONDITIONS
HepG2 "1"
17 changes: 17 additions & 0 deletions arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/SOCS3_wb/Anja_2019_03_SOCS3.csv
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time,input_il6,input_dcf,input_apap,SOCS3_WB,cSOCS3_wb,experiment,,,
0,0,0,0,274071.53,0.27407153,Anja_2019_03,,,
20,10,0,0,1762662.47,1.76266247,Anja_2019_03,,,
40,10,0,0,18709733.26,18.70973326,Anja_2019_03,,SOCS3 IP,HepG2
60,10,0,0,31446253.6,31.4462536,Anja_2019_03,,,
90,10,0,0,20465168.36,20.46516836,Anja_2019_03,,input_il6,10 ng/mL
120,10,0,0,11981801.7,11.9818017,Anja_2019_03,,input_dcf,500 µM
20,10,500,0,918549.19,0.91854919,Anja_2019_03,,input_apap,10 mM
40,10,500,0,6727664.47,6.72766447,Anja_2019_03,,,
60,10,500,0,5307621.86,5.30762186,Anja_2019_03,,,
90,10,500,0,30067738.08,30.06773808,Anja_2019_03,,,
120,10,500,0,29844590.01,29.84459001,Anja_2019_03,,,
20,10,0,10,403867.69,0.40386769,Anja_2019_03,,,
40,10,0,10,416615.83,0.41661583,Anja_2019_03,,,
60,10,0,10,18848672.68,18.84867268,Anja_2019_03,,,
90,10,0,10,29028579.68,29.02857968,Anja_2019_03,,,
120,10,0,10,18572605.89,18.57260589,Anja_2019_03,,,
14 changes: 14 additions & 0 deletions arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/SOCS3_wb/Anja_2019_03_SOCS3.def
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Original file line number Diff line number Diff line change
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DESCRIPTION
"data .def file template"

PREDICTOR
t T "min" "time" 0 100

INPUTS

OBSERVABLES

ERRORS

CONDITIONS
HepG2 "1"
7 changes: 7 additions & 0 deletions arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/gp130/gp130_degradation.csv
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time,input_il6,input_cyclo,binding_sites,binding_sites_std,,hours
60.2484310304419,0,1,87.5784484779042,5.6248535194396,93.2033019973438,1.00414051717403
120.634358480248,0,1,68.2820759876045,3.12622067133667,71.4082966589412,2.01057264133746
179.226582641077,0,1,38.6708679461472,3.43741048410199,42.1082784302492,2.98710971068462
238.562537433921,0,1,21.8731283039504,15.6245931095544,37.4977214135048,3.97604229056535
362.859300539049,0,1,7.03497304757688,3.43610843467616,10.471081482253,6.04765500898414
481.837452149684,0,1,8.12739251581989,3.12491862191088,11.2523111377308,8.03062420249473
13 changes: 13 additions & 0 deletions arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/gp130/gp130_degradation.def
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DESCRIPTION
"data .def file template"

PREDICTOR
t T "min" "time" 0 100

INPUTS

OBSERVABLES

ERRORS

CONDITIONS
17 changes: 17 additions & 0 deletions arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/mlc/mlc.def
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@@ -0,0 +1,17 @@
DESCRIPTION
"Molecules per cell"
"Experimenter: Anja Juenger"

PREDICTOR
t T "min" "time" 0 100

INPUTS

OBSERVABLES

ERRORS

CONDITIONS
HepG2 "1"

RANDOM
Binary file added arFramework3/Examples/Zeilfelder_IL6_CellSystems2025/Data/mlc/mlc.xls
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