From e19590159a086fe3b6aabcf7085868e2c8df65bf Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Fri, 17 Oct 2025 22:32:59 +0200 Subject: [PATCH] Fix simulation files * `./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` --- ...ulatedData_Armistead_CellDeathDis2024.tsv} | 0 .../simulatedData_Smith_BMCSystBiol2013.tsv | 126 +++++++++--------- src/python/benchmark_models_petab/base.py | 7 +- 3 files changed, 67 insertions(+), 66 deletions(-) rename Benchmark-Models/Armistead_CellDeathDis2024/{simulationData_Armistead_CellDeathDis2024.tsv => simulatedData_Armistead_CellDeathDis2024.tsv} (100%) diff --git a/Benchmark-Models/Armistead_CellDeathDis2024/simulationData_Armistead_CellDeathDis2024.tsv b/Benchmark-Models/Armistead_CellDeathDis2024/simulatedData_Armistead_CellDeathDis2024.tsv similarity index 100% rename from Benchmark-Models/Armistead_CellDeathDis2024/simulationData_Armistead_CellDeathDis2024.tsv rename to Benchmark-Models/Armistead_CellDeathDis2024/simulatedData_Armistead_CellDeathDis2024.tsv diff --git a/Benchmark-Models/Smith_BMCSystBiol2013/simulatedData_Smith_BMCSystBiol2013.tsv b/Benchmark-Models/Smith_BMCSystBiol2013/simulatedData_Smith_BMCSystBiol2013.tsv index 99b71aaa..c83d9c1e 100644 --- a/Benchmark-Models/Smith_BMCSystBiol2013/simulatedData_Smith_BMCSystBiol2013.tsv +++ b/Benchmark-Models/Smith_BMCSystBiol2013/simulatedData_Smith_BMCSystBiol2013.tsv @@ -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 diff --git a/src/python/benchmark_models_petab/base.py b/src/python/benchmark_models_petab/base.py index 0a4a3246..8a813295 100644 --- a/src/python/benchmark_models_petab/base.py +++ b/src/python/benchmark_models_petab/base.py @@ -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