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dweindl merged 1 commit into from
Oct 20, 2025
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Fix simulation files #276

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0 ...lationData_Armistead_CellDeathDis2024.tsv → ...ulatedData_Armistead_CellDeathDis2024.tsv
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126 changes: 63 additions & 63 deletions Benchmark-Models/Smith_BMCSystBiol2013/simulatedData_Smith_BMCSystBiol2013.tsv
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Original file line number Diff line number Diff line change
@@ -1,63 +1,63 @@
,time,observableId,simulation,simulationConditionId,datasetId
2,15.0,Glucose_uptake__2B,94.91500464909144,figure2B__0_0__1_3em10,base
5,15.0,PI3K_activity__2B,473.8698413793524,figure2B__0_0__1_5em08,base
5,15.0,PI3K_activity__2B,230.99842698611383,figure2B__0_0__1_5em09,base
5,15.0,PI3K_activity__2B,33.879716807154765,figure2B__0_0__1_5em10,base
2,15.0,Glucose_uptake__2B,40.16011524433328,figure2B__0_0__1_5em11,base
5,15.0,PI3K_activity__2B,514.9996159307263,figure2B__0_0__1em06,base
2,15.0,Glucose_uptake__2B,228.73007399487088,figure2B__0_0__1em07,base
5,15.0,PI3K_activity__2B,509.2177670470764,figure2B__0_0__1em07,base
2,15.0,Glucose_uptake__2B,225.4105513021212,figure2B__0_0__1em08,base
0,15.0,Cell_Bound_Ins__2B,92.47938382869233,figure2B__0_0__1em08,base
2,15.0,Glucose_uptake__2B,191.91403413334686,figure2B__0_0__1em09,base
0,15.0,Cell_Bound_Ins__2B,15.905461920594918,figure2B__0_0__1em09,base
2,15.0,Glucose_uptake__2B,40.00086599803474,figure2B__0_0__1em14,base
5,15.0,PI3K_activity__2B,0.0023534342407404603,figure2B__0_0__1em14,base
0,15.0,Cell_Bound_Ins__2B,31.136798157388277,figure2B__0_0__2em09,base
0,15.0,Cell_Bound_Ins__2B,3.0127939691315655,figure2B__0_0__2em10,base
0,15.0,Cell_Bound_Ins__2B,0.29167254246854996,figure2B__0_0__2em11,base
2,15.0,Glucose_uptake__2B,139.78740642745532,figure2B__0_0__3_1em10,base
5,15.0,PI3K_activity__2B,8.240138838336627,figure2B__0_0__3_5em11,base
2,15.0,Glucose_uptake__2B,229.0079457277544,figure2B__0_0__3em07,base
0,15.0,Cell_Bound_Ins__2B,140.35735018974614,figure2B__0_0__3em07,base
5,15.0,PI3K_activity__2B,513.5136523321487,figure2B__0_0__3em07,base
2,15.0,Glucose_uptake__2B,227.88871310641113,figure2B__0_0__3em08,base
0,15.0,Cell_Bound_Ins__2B,122.10832991884763,figure2B__0_0__3em08,base
2,15.0,Glucose_uptake__2B,216.18829389676606,figure2B__0_0__3em09,base
2,15.0,Glucose_uptake__2B,56.467568456604866,figure2B__0_0__4_5em11,base
0,15.0,Cell_Bound_Ins__2B,6.17612173920017,figure2B__0_0__4em10,base
5,15.0,PI3K_activity__2B,502.79918321082994,figure2B__0_0__5em08,base
5,15.0,PI3K_activity__2B,394.2378709554225,figure2B__0_0__5em09,base
5,15.0,PI3K_activity__2B,101.09658482036407,figure2B__0_0__5em10,base
0,15.0,Cell_Bound_Ins__2B,0.7337256961847068,figure2B__0_0__5em11,base
30,0.0,IRSYp__2C,0.0,figure2C__0_0__500000,fig2A
31,1.0,IRSYp__2C,220.00007254787616,figure2C__0_0__500000,fig2A
32,1.25,IRSYp__2C,209.8607916814312,figure2C__0_0__500000,fig2A
33,1.4,IRSYp__2C,197.06168921174046,figure2C__0_0__500000,fig2A
34,2.2,IRSYp__2C,134.529271248975,figure2C__0_0__500000,fig2A
35,3.3,IRSYp__2C,115.01746037724723,figure2C__0_0__500000,fig2A
36,5.25,IRSYp__2C,114.18949547982302,figure2C__0_0__500000,fig2A
37,7.2,IRSYp__2C,112.51771896456128,figure2C__0_0__500000,fig2A
38,10.0,IRSYp__2C,109.72780416695367,figure2C__0_0__500000,fig2A
39,15.0,IRSYp__2C,106.29788802282935,figure2C__0_0__500000,fig2A
18,0.0,PTP_activ__2D,0.16,figure2D__0_0__500000,fig2A
19,1.0,PTP_activ__2D,0.08837989163080154,figure2D__0_0__500000,fig2A
20,5.0,PTP_activ__2D,0.06186331636255836,figure2D__0_0__500000,fig2A
4,120.0,Glucose_uptake__120__3B,200.0,figure3B__0_0__0_0,Basal (time = 120)
5,240.0,Glucose_uptake__240__3B,219.99999999999997,figure3B__0_0__0_0,Basal (time = 240)
4,120.0,Glucose_uptake__120__3B,1082.6343477389623,figure3B__0_0__5_0,Ins (time = 120)
5,240.0,Glucose_uptake__240__3B,1156.1218139768264,figure3B__0_0__5_0,Ins (time = 240)
4,120.0,Glucose_uptake__120__3B,299.1418386833576,figure3B__60_0__0_0,H2O2 (time = 120)
5,240.0,Glucose_uptake__240__3B,286.87311613351943,figure3B__60_0__0_0,H2O2 (time = 240)
4,120.0,Glucose_uptake__120__3B,1097.7650232945,figure3B__60_0__5_0,Ins+H2O2 (time = 120)
5,240.0,Glucose_uptake__240__3B,1126.3325581665342,figure3B__60_0__5_0,Ins+H2O2 (time = 240)
1,960.0,FOXO4__3C,0.9999999999999999,figure3C__0_0__0_0,0.0
4,960.0,MnSOD_fold_induction__3C,5.000000000000001,figure3C__0_0__0_0,0.0
1,960.0,FOXO4__3C,0.9002414550750889,figure3C__10_0__0_0,10.0
4,960.0,MnSOD_fold_induction__3C,6.621223246797953,figure3C__10_0__0_0,10.0
1,960.0,FOXO4__3C,0.2089677871218716,figure3C__20_0__0_0,20.0
4,960.0,MnSOD_fold_induction__3C,3.467095128988933,figure3C__20_0__0_0,20.0
1,960.0,FOXO4__3C,0.11747686740168865,figure3C__50_0__0_0,50.0
4,960.0,MnSOD_fold_induction__3C,2.1956596271789635,figure3C__50_0__0_0,50.0
1,960.0,FOXO4__3C,1.0687059318438576,figure3C__5_0__0_0,5.0
4,960.0,MnSOD_fold_induction__3C,6.620527063995212,figure3C__5_0__0_0,5.0
time observableId simulation simulationConditionId datasetId
2 15.0 Glucose_uptake__2B 94.91500464909144 figure2B__0_0__1_3em10 base
5 15.0 PI3K_activity__2B 473.8698413793524 figure2B__0_0__1_5em08 base
5 15.0 PI3K_activity__2B 230.99842698611383 figure2B__0_0__1_5em09 base
5 15.0 PI3K_activity__2B 33.879716807154765 figure2B__0_0__1_5em10 base
2 15.0 Glucose_uptake__2B 40.16011524433328 figure2B__0_0__1_5em11 base
5 15.0 PI3K_activity__2B 514.9996159307263 figure2B__0_0__1em06 base
2 15.0 Glucose_uptake__2B 228.73007399487088 figure2B__0_0__1em07 base
5 15.0 PI3K_activity__2B 509.2177670470764 figure2B__0_0__1em07 base
2 15.0 Glucose_uptake__2B 225.4105513021212 figure2B__0_0__1em08 base
0 15.0 Cell_Bound_Ins__2B 92.47938382869233 figure2B__0_0__1em08 base
2 15.0 Glucose_uptake__2B 191.91403413334686 figure2B__0_0__1em09 base
0 15.0 Cell_Bound_Ins__2B 15.905461920594918 figure2B__0_0__1em09 base
2 15.0 Glucose_uptake__2B 40.00086599803474 figure2B__0_0__1em14 base
5 15.0 PI3K_activity__2B 0.0023534342407404603 figure2B__0_0__1em14 base
0 15.0 Cell_Bound_Ins__2B 31.136798157388277 figure2B__0_0__2em09 base
0 15.0 Cell_Bound_Ins__2B 3.0127939691315655 figure2B__0_0__2em10 base
0 15.0 Cell_Bound_Ins__2B 0.29167254246854996 figure2B__0_0__2em11 base
2 15.0 Glucose_uptake__2B 139.78740642745532 figure2B__0_0__3_1em10 base
5 15.0 PI3K_activity__2B 8.240138838336627 figure2B__0_0__3_5em11 base
2 15.0 Glucose_uptake__2B 229.0079457277544 figure2B__0_0__3em07 base
0 15.0 Cell_Bound_Ins__2B 140.35735018974614 figure2B__0_0__3em07 base
5 15.0 PI3K_activity__2B 513.5136523321487 figure2B__0_0__3em07 base
2 15.0 Glucose_uptake__2B 227.88871310641113 figure2B__0_0__3em08 base
0 15.0 Cell_Bound_Ins__2B 122.10832991884763 figure2B__0_0__3em08 base
2 15.0 Glucose_uptake__2B 216.18829389676606 figure2B__0_0__3em09 base
2 15.0 Glucose_uptake__2B 56.467568456604866 figure2B__0_0__4_5em11 base
0 15.0 Cell_Bound_Ins__2B 6.17612173920017 figure2B__0_0__4em10 base
5 15.0 PI3K_activity__2B 502.79918321082994 figure2B__0_0__5em08 base
5 15.0 PI3K_activity__2B 394.2378709554225 figure2B__0_0__5em09 base
5 15.0 PI3K_activity__2B 101.09658482036407 figure2B__0_0__5em10 base
0 15.0 Cell_Bound_Ins__2B 0.7337256961847068 figure2B__0_0__5em11 base
30 0.0 IRSYp__2C 0.0 figure2C__0_0__500000 fig2A
31 1.0 IRSYp__2C 220.00007254787616 figure2C__0_0__500000 fig2A
32 1.25 IRSYp__2C 209.8607916814312 figure2C__0_0__500000 fig2A
33 1.4 IRSYp__2C 197.06168921174046 figure2C__0_0__500000 fig2A
34 2.2 IRSYp__2C 134.529271248975 figure2C__0_0__500000 fig2A
35 3.3 IRSYp__2C 115.01746037724723 figure2C__0_0__500000 fig2A
36 5.25 IRSYp__2C 114.18949547982302 figure2C__0_0__500000 fig2A
37 7.2 IRSYp__2C 112.51771896456128 figure2C__0_0__500000 fig2A
38 10.0 IRSYp__2C 109.72780416695367 figure2C__0_0__500000 fig2A
39 15.0 IRSYp__2C 106.29788802282935 figure2C__0_0__500000 fig2A
18 0.0 PTP_activ__2D 0.16 figure2D__0_0__500000 fig2A
19 1.0 PTP_activ__2D 0.08837989163080154 figure2D__0_0__500000 fig2A
20 5.0 PTP_activ__2D 0.06186331636255836 figure2D__0_0__500000 fig2A
4 120.0 Glucose_uptake__120__3B 200.0 figure3B__0_0__0_0 Basal (time = 120)
5 240.0 Glucose_uptake__240__3B 219.99999999999997 figure3B__0_0__0_0 Basal (time = 240)
4 120.0 Glucose_uptake__120__3B 1082.6343477389623 figure3B__0_0__5_0 Ins (time = 120)
5 240.0 Glucose_uptake__240__3B 1156.1218139768264 figure3B__0_0__5_0 Ins (time = 240)
4 120.0 Glucose_uptake__120__3B 299.1418386833576 figure3B__60_0__0_0 H2O2 (time = 120)
5 240.0 Glucose_uptake__240__3B 286.87311613351943 figure3B__60_0__0_0 H2O2 (time = 240)
4 120.0 Glucose_uptake__120__3B 1097.7650232945 figure3B__60_0__5_0 Ins+H2O2 (time = 120)
5 240.0 Glucose_uptake__240__3B 1126.3325581665342 figure3B__60_0__5_0 Ins+H2O2 (time = 240)
1 960.0 FOXO4__3C 0.9999999999999999 figure3C__0_0__0_0 0.0
4 960.0 MnSOD_fold_induction__3C 5.000000000000001 figure3C__0_0__0_0 0.0
1 960.0 FOXO4__3C 0.9002414550750889 figure3C__10_0__0_0 10.0
4 960.0 MnSOD_fold_induction__3C 6.621223246797953 figure3C__10_0__0_0 10.0
1 960.0 FOXO4__3C 0.2089677871218716 figure3C__20_0__0_0 20.0
4 960.0 MnSOD_fold_induction__3C 3.467095128988933 figure3C__20_0__0_0 20.0
1 960.0 FOXO4__3C 0.11747686740168865 figure3C__50_0__0_0 50.0
4 960.0 MnSOD_fold_induction__3C 2.1956596271789635 figure3C__50_0__0_0 50.0
1 960.0 FOXO4__3C 1.0687059318438576 figure3C__5_0__0_0 5.0
4 960.0 MnSOD_fold_induction__3C 6.620527063995212 figure3C__5_0__0_0 5.0
7 changes: 4 additions & 3 deletions src/python/benchmark_models_petab/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,8 @@ def get_simulation_df(id_: str) -> pd.DataFrame | None:
-------
The simulation dataframe if it exists, else None.
"""
path = Path(MODELS_DIR, id_, f"simulatedData_{id_}.tsv")
if path.is_file():
return petab.get_simulation_df(path)
for filename in (f"simulatedData_{id_}.tsv", "simulations.tsv"):
if (path := Path(MODELS_DIR, id_, filename)).is_file():
return petab.get_simulation_df(path)

return None