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Fix simulation files (#276)
* `./Smith_BMCSystBiol2013/simulatedData_Smith_BMCSystBiol2013.tsv` was CSV, not TSV. Fixed now. * More consistent simulation file names (Armistead_CellDeathDis2024) * Also consider files named `simulations.tsv` in `get_simulation_df`
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3 files changed

+67
-66
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Benchmark-Models/Armistead_CellDeathDis2024/simulationData_Armistead_CellDeathDis2024.tsv renamed to Benchmark-Models/Armistead_CellDeathDis2024/simulatedData_Armistead_CellDeathDis2024.tsv

File renamed without changes.

‎Benchmark-Models/Smith_BMCSystBiol2013/simulatedData_Smith_BMCSystBiol2013.tsv‎

Lines changed: 63 additions & 63 deletions
Original file line numberDiff line numberDiff line change
@@ -1,63 +1,63 @@
1-
,time,observableId,simulation,simulationConditionId,datasetId
2-
2,15.0,Glucose_uptake__2B,94.91500464909144,figure2B__0_0__1_3em10,base
3-
5,15.0,PI3K_activity__2B,473.8698413793524,figure2B__0_0__1_5em08,base
4-
5,15.0,PI3K_activity__2B,230.99842698611383,figure2B__0_0__1_5em09,base
5-
5,15.0,PI3K_activity__2B,33.879716807154765,figure2B__0_0__1_5em10,base
6-
2,15.0,Glucose_uptake__2B,40.16011524433328,figure2B__0_0__1_5em11,base
7-
5,15.0,PI3K_activity__2B,514.9996159307263,figure2B__0_0__1em06,base
8-
2,15.0,Glucose_uptake__2B,228.73007399487088,figure2B__0_0__1em07,base
9-
5,15.0,PI3K_activity__2B,509.2177670470764,figure2B__0_0__1em07,base
10-
2,15.0,Glucose_uptake__2B,225.4105513021212,figure2B__0_0__1em08,base
11-
0,15.0,Cell_Bound_Ins__2B,92.47938382869233,figure2B__0_0__1em08,base
12-
2,15.0,Glucose_uptake__2B,191.91403413334686,figure2B__0_0__1em09,base
13-
0,15.0,Cell_Bound_Ins__2B,15.905461920594918,figure2B__0_0__1em09,base
14-
2,15.0,Glucose_uptake__2B,40.00086599803474,figure2B__0_0__1em14,base
15-
5,15.0,PI3K_activity__2B,0.0023534342407404603,figure2B__0_0__1em14,base
16-
0,15.0,Cell_Bound_Ins__2B,31.136798157388277,figure2B__0_0__2em09,base
17-
0,15.0,Cell_Bound_Ins__2B,3.0127939691315655,figure2B__0_0__2em10,base
18-
0,15.0,Cell_Bound_Ins__2B,0.29167254246854996,figure2B__0_0__2em11,base
19-
2,15.0,Glucose_uptake__2B,139.78740642745532,figure2B__0_0__3_1em10,base
20-
5,15.0,PI3K_activity__2B,8.240138838336627,figure2B__0_0__3_5em11,base
21-
2,15.0,Glucose_uptake__2B,229.0079457277544,figure2B__0_0__3em07,base
22-
0,15.0,Cell_Bound_Ins__2B,140.35735018974614,figure2B__0_0__3em07,base
23-
5,15.0,PI3K_activity__2B,513.5136523321487,figure2B__0_0__3em07,base
24-
2,15.0,Glucose_uptake__2B,227.88871310641113,figure2B__0_0__3em08,base
25-
0,15.0,Cell_Bound_Ins__2B,122.10832991884763,figure2B__0_0__3em08,base
26-
2,15.0,Glucose_uptake__2B,216.18829389676606,figure2B__0_0__3em09,base
27-
2,15.0,Glucose_uptake__2B,56.467568456604866,figure2B__0_0__4_5em11,base
28-
0,15.0,Cell_Bound_Ins__2B,6.17612173920017,figure2B__0_0__4em10,base
29-
5,15.0,PI3K_activity__2B,502.79918321082994,figure2B__0_0__5em08,base
30-
5,15.0,PI3K_activity__2B,394.2378709554225,figure2B__0_0__5em09,base
31-
5,15.0,PI3K_activity__2B,101.09658482036407,figure2B__0_0__5em10,base
32-
0,15.0,Cell_Bound_Ins__2B,0.7337256961847068,figure2B__0_0__5em11,base
33-
30,0.0,IRSYp__2C,0.0,figure2C__0_0__500000,fig2A
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31,1.0,IRSYp__2C,220.00007254787616,figure2C__0_0__500000,fig2A
35-
32,1.25,IRSYp__2C,209.8607916814312,figure2C__0_0__500000,fig2A
36-
33,1.4,IRSYp__2C,197.06168921174046,figure2C__0_0__500000,fig2A
37-
34,2.2,IRSYp__2C,134.529271248975,figure2C__0_0__500000,fig2A
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35,3.3,IRSYp__2C,115.01746037724723,figure2C__0_0__500000,fig2A
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36,5.25,IRSYp__2C,114.18949547982302,figure2C__0_0__500000,fig2A
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37,7.2,IRSYp__2C,112.51771896456128,figure2C__0_0__500000,fig2A
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38,10.0,IRSYp__2C,109.72780416695367,figure2C__0_0__500000,fig2A
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39,15.0,IRSYp__2C,106.29788802282935,figure2C__0_0__500000,fig2A
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18,0.0,PTP_activ__2D,0.16,figure2D__0_0__500000,fig2A
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19,1.0,PTP_activ__2D,0.08837989163080154,figure2D__0_0__500000,fig2A
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20,5.0,PTP_activ__2D,0.06186331636255836,figure2D__0_0__500000,fig2A
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4,120.0,Glucose_uptake__120__3B,200.0,figure3B__0_0__0_0,Basal (time = 120)
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5,240.0,Glucose_uptake__240__3B,219.99999999999997,figure3B__0_0__0_0,Basal (time = 240)
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4,120.0,Glucose_uptake__120__3B,1082.6343477389623,figure3B__0_0__5_0,Ins (time = 120)
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5,240.0,Glucose_uptake__240__3B,1156.1218139768264,figure3B__0_0__5_0,Ins (time = 240)
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4,120.0,Glucose_uptake__120__3B,299.1418386833576,figure3B__60_0__0_0,H2O2 (time = 120)
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5,240.0,Glucose_uptake__240__3B,286.87311613351943,figure3B__60_0__0_0,H2O2 (time = 240)
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4,120.0,Glucose_uptake__120__3B,1097.7650232945,figure3B__60_0__5_0,Ins+H2O2 (time = 120)
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5,240.0,Glucose_uptake__240__3B,1126.3325581665342,figure3B__60_0__5_0,Ins+H2O2 (time = 240)
54-
1,960.0,FOXO4__3C,0.9999999999999999,figure3C__0_0__0_0,0.0
55-
4,960.0,MnSOD_fold_induction__3C,5.000000000000001,figure3C__0_0__0_0,0.0
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1,960.0,FOXO4__3C,0.9002414550750889,figure3C__10_0__0_0,10.0
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4,960.0,MnSOD_fold_induction__3C,6.621223246797953,figure3C__10_0__0_0,10.0
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1,960.0,FOXO4__3C,0.2089677871218716,figure3C__20_0__0_0,20.0
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4,960.0,MnSOD_fold_induction__3C,3.467095128988933,figure3C__20_0__0_0,20.0
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1,960.0,FOXO4__3C,0.11747686740168865,figure3C__50_0__0_0,50.0
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4,960.0,MnSOD_fold_induction__3C,2.1956596271789635,figure3C__50_0__0_0,50.0
62-
1,960.0,FOXO4__3C,1.0687059318438576,figure3C__5_0__0_0,5.0
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4,960.0,MnSOD_fold_induction__3C,6.620527063995212,figure3C__5_0__0_0,5.0
1+
time observableId simulation simulationConditionId datasetId
2+
2 15.0 Glucose_uptake__2B 94.91500464909144 figure2B__0_0__1_3em10 base
3+
5 15.0 PI3K_activity__2B 473.8698413793524 figure2B__0_0__1_5em08 base
4+
5 15.0 PI3K_activity__2B 230.99842698611383 figure2B__0_0__1_5em09 base
5+
5 15.0 PI3K_activity__2B 33.879716807154765 figure2B__0_0__1_5em10 base
6+
2 15.0 Glucose_uptake__2B 40.16011524433328 figure2B__0_0__1_5em11 base
7+
5 15.0 PI3K_activity__2B 514.9996159307263 figure2B__0_0__1em06 base
8+
2 15.0 Glucose_uptake__2B 228.73007399487088 figure2B__0_0__1em07 base
9+
5 15.0 PI3K_activity__2B 509.2177670470764 figure2B__0_0__1em07 base
10+
2 15.0 Glucose_uptake__2B 225.4105513021212 figure2B__0_0__1em08 base
11+
0 15.0 Cell_Bound_Ins__2B 92.47938382869233 figure2B__0_0__1em08 base
12+
2 15.0 Glucose_uptake__2B 191.91403413334686 figure2B__0_0__1em09 base
13+
0 15.0 Cell_Bound_Ins__2B 15.905461920594918 figure2B__0_0__1em09 base
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2 15.0 Glucose_uptake__2B 40.00086599803474 figure2B__0_0__1em14 base
15+
5 15.0 PI3K_activity__2B 0.0023534342407404603 figure2B__0_0__1em14 base
16+
0 15.0 Cell_Bound_Ins__2B 31.136798157388277 figure2B__0_0__2em09 base
17+
0 15.0 Cell_Bound_Ins__2B 3.0127939691315655 figure2B__0_0__2em10 base
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0 15.0 Cell_Bound_Ins__2B 0.29167254246854996 figure2B__0_0__2em11 base
19+
2 15.0 Glucose_uptake__2B 139.78740642745532 figure2B__0_0__3_1em10 base
20+
5 15.0 PI3K_activity__2B 8.240138838336627 figure2B__0_0__3_5em11 base
21+
2 15.0 Glucose_uptake__2B 229.0079457277544 figure2B__0_0__3em07 base
22+
0 15.0 Cell_Bound_Ins__2B 140.35735018974614 figure2B__0_0__3em07 base
23+
5 15.0 PI3K_activity__2B 513.5136523321487 figure2B__0_0__3em07 base
24+
2 15.0 Glucose_uptake__2B 227.88871310641113 figure2B__0_0__3em08 base
25+
0 15.0 Cell_Bound_Ins__2B 122.10832991884763 figure2B__0_0__3em08 base
26+
2 15.0 Glucose_uptake__2B 216.18829389676606 figure2B__0_0__3em09 base
27+
2 15.0 Glucose_uptake__2B 56.467568456604866 figure2B__0_0__4_5em11 base
28+
0 15.0 Cell_Bound_Ins__2B 6.17612173920017 figure2B__0_0__4em10 base
29+
5 15.0 PI3K_activity__2B 502.79918321082994 figure2B__0_0__5em08 base
30+
5 15.0 PI3K_activity__2B 394.2378709554225 figure2B__0_0__5em09 base
31+
5 15.0 PI3K_activity__2B 101.09658482036407 figure2B__0_0__5em10 base
32+
0 15.0 Cell_Bound_Ins__2B 0.7337256961847068 figure2B__0_0__5em11 base
33+
30 0.0 IRSYp__2C 0.0 figure2C__0_0__500000 fig2A
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31 1.0 IRSYp__2C 220.00007254787616 figure2C__0_0__500000 fig2A
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32 1.25 IRSYp__2C 209.8607916814312 figure2C__0_0__500000 fig2A
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33 1.4 IRSYp__2C 197.06168921174046 figure2C__0_0__500000 fig2A
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34 2.2 IRSYp__2C 134.529271248975 figure2C__0_0__500000 fig2A
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35 3.3 IRSYp__2C 115.01746037724723 figure2C__0_0__500000 fig2A
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36 5.25 IRSYp__2C 114.18949547982302 figure2C__0_0__500000 fig2A
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37 7.2 IRSYp__2C 112.51771896456128 figure2C__0_0__500000 fig2A
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38 10.0 IRSYp__2C 109.72780416695367 figure2C__0_0__500000 fig2A
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39 15.0 IRSYp__2C 106.29788802282935 figure2C__0_0__500000 fig2A
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18 0.0 PTP_activ__2D 0.16 figure2D__0_0__500000 fig2A
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19 1.0 PTP_activ__2D 0.08837989163080154 figure2D__0_0__500000 fig2A
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20 5.0 PTP_activ__2D 0.06186331636255836 figure2D__0_0__500000 fig2A
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4 120.0 Glucose_uptake__120__3B 200.0 figure3B__0_0__0_0 Basal (time = 120)
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5 240.0 Glucose_uptake__240__3B 219.99999999999997 figure3B__0_0__0_0 Basal (time = 240)
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4 120.0 Glucose_uptake__120__3B 1082.6343477389623 figure3B__0_0__5_0 Ins (time = 120)
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5 240.0 Glucose_uptake__240__3B 1156.1218139768264 figure3B__0_0__5_0 Ins (time = 240)
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4 120.0 Glucose_uptake__120__3B 299.1418386833576 figure3B__60_0__0_0 H2O2 (time = 120)
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5 240.0 Glucose_uptake__240__3B 286.87311613351943 figure3B__60_0__0_0 H2O2 (time = 240)
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4 120.0 Glucose_uptake__120__3B 1097.7650232945 figure3B__60_0__5_0 Ins+H2O2 (time = 120)
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5 240.0 Glucose_uptake__240__3B 1126.3325581665342 figure3B__60_0__5_0 Ins+H2O2 (time = 240)
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1 960.0 FOXO4__3C 0.9999999999999999 figure3C__0_0__0_0 0.0
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4 960.0 MnSOD_fold_induction__3C 5.000000000000001 figure3C__0_0__0_0 0.0
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1 960.0 FOXO4__3C 0.9002414550750889 figure3C__10_0__0_0 10.0
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4 960.0 MnSOD_fold_induction__3C 6.621223246797953 figure3C__10_0__0_0 10.0
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1 960.0 FOXO4__3C 0.2089677871218716 figure3C__20_0__0_0 20.0
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4 960.0 MnSOD_fold_induction__3C 3.467095128988933 figure3C__20_0__0_0 20.0
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1 960.0 FOXO4__3C 0.11747686740168865 figure3C__50_0__0_0 50.0
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4 960.0 MnSOD_fold_induction__3C 2.1956596271789635 figure3C__50_0__0_0 50.0
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1 960.0 FOXO4__3C 1.0687059318438576 figure3C__5_0__0_0 5.0
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4 960.0 MnSOD_fold_induction__3C 6.620527063995212 figure3C__5_0__0_0 5.0

‎src/python/benchmark_models_petab/base.py‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -56,7 +56,8 @@ def get_simulation_df(id_: str) -> pd.DataFrame | None:
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-------
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The simulation dataframe if it exists, else None.
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"""
59-
path = Path(MODELS_DIR, id_, f"simulatedData_{id_}.tsv")
60-
if path.is_file():
61-
return petab.get_simulation_df(path)
59+
for filename in (f"simulatedData_{id_}.tsv", "simulations.tsv"):
60+
if (path := Path(MODELS_DIR, id_, filename)).is_file():
61+
return petab.get_simulation_df(path)
62+
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return None

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