From d988b8b93b6891f6feab997edd4a9b432b195702 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Fri, 25 Oct 2024 16:18:54 +0200 Subject: [PATCH] add PEtab model for reformulated Fiedler_BMCSystBiol2016 --- .../reformulated/Fiedler_BMCSystBiol2016.yaml | 13 ++++ ...entalCondition_Fiedler_BMCSystBiol2016.tsv | 4 + ...easurementData_Fiedler_BMCSystBiol2016.tsv | 73 +++++++++++++++++++ ....xml => model_Fiedler_BMCSystBiol2016.xml} | 4 +- .../observables_Fiedler_BMCSystBiol2016.tsv | 3 + .../parameters_Fiedler_BMCSystBiol2016.tsv | 23 ++++++ ...nSpecification_Fiedler_BMCSystBiol2016.tsv | 7 ++ 7 files changed, 125 insertions(+), 2 deletions(-) create mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016.yaml create mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/experimentalCondition_Fiedler_BMCSystBiol2016.tsv create mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016.tsv rename Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/{model.xml => model_Fiedler_BMCSystBiol2016.xml} (99%) create mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016.tsv create mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016.tsv create mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016.yaml b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016.yaml new file mode 100644 index 0000000..67687dd --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016.yaml @@ -0,0 +1,13 @@ +format_version: 1 +parameter_file: parameters_Fiedler_BMCSystBiol2016.tsv +problems: +- condition_files: + - experimentalCondition_Fiedler_BMCSystBiol2016.tsv + measurement_files: + - measurementData_Fiedler_BMCSystBiol2016.tsv + observable_files: + - observables_Fiedler_BMCSystBiol2016.tsv + sbml_files: + - model_Fiedler_BMCSystBiol2016.xml + visualization_files: + - visualizationSpecification_Fiedler_BMCSystBiol2016.tsv diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/experimentalCondition_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/experimentalCondition_Fiedler_BMCSystBiol2016.tsv new file mode 100644 index 0000000..2d18519 --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/experimentalCondition_Fiedler_BMCSystBiol2016.tsv @@ -0,0 +1,4 @@ +conditionId conditionName Sorafenib UO126 +model1_data1 0 0 +model1_data2 5 0 +model1_data3 0 30 diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016.tsv new file mode 100644 index 0000000..c2a1473 --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016.tsv @@ -0,0 +1,73 @@ +observableId preequilibrationConditionId simulationConditionId measurement time observableParameters noiseParameters datasetId +pMek_rel model1_data1 0.116721 0 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.232984 0.25 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.305171 1 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.125647 5.5 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.073706 7 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.058253 8.5 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.066667 10 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.22033 0 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 1.683107 0.25 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 1.441176 1 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.225572 5.5 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.278346 7 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.137178 8.5 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.196426 10 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data2 0.121231 0 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.086929466 1 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.054910478 5.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.048881617 7 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.052341248 8.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.052595374 10 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.155276 0 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.24 1 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.12 5.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.12 7 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.07 8.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.07 10 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data3 1.724493879 1 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.683168571 5.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.470175735 7 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.557371739 8.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.559108205 10 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 5.857600733 1 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 2.857976654 5.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 4.607660706 7 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 2.789397964 8.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.623004546 10 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pErk_rel model1_data1 0.037959 0 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.042262 0.25 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.162628 1 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.052124 5.5 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.023196 7 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.037687 8.5 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.028724 10 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.297881 0 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 3.043549 0.25 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 3.098459 1 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.224662 5.5 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.38254 7 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.123338 8.5 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.229486 10 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data2 0.039731 0 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.03303482 1 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.019296634 5.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.017683446 7 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.020209467 8.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.02141076 10 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.301624 0 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.54 1 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.27 5.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.25 7 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.18 8.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.15 10 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data3 0.004107653 1 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.011631788 5.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.012694322 7 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.003687738 8.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.002426131 10 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.176167582 1 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.069008927 5.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.074311261 7 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.073151837 8.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.048102336 10 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model.xml b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model_Fiedler_BMCSystBiol2016.xml similarity index 99% rename from Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model.xml rename to Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model_Fiedler_BMCSystBiol2016.xml index 6bec097..e5e1d64 100644 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model.xml +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model_Fiedler_BMCSystBiol2016.xml @@ -196,7 +196,7 @@ - + @@ -1590,7 +1590,7 @@ K2 - sora + Sorafenib diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016.tsv new file mode 100644 index 0000000..da0359b --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016.tsv @@ -0,0 +1,3 @@ +observableId observableName observableFormula noiseFormula observableTransformation noiseDistribution +pMek_rel [pMEK]/MEK_0 x2 * observableParameter1_pMek_rel noiseParameter1_pMek_rel*noiseParameter2_pMek_rel lin normal +pErk_rel [pERK]/ERK_0 x3 * observableParameter1_pErk_rel noiseParameter1_pErk_rel*noiseParameter2_pErk_rel lin normal \ No newline at end of file diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016.tsv new file mode 100644 index 0000000..ede65e5 --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016.tsv @@ -0,0 +1,23 @@ +parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate +k11_k10 k_{1,1}/k{1,0} log10 1E-04 1E02 1 1 +tau1 \tau_{1} log10 1E-04 1E02 0.242822010781068 1 +tau2 \tau_{2} log10 1E-04 1E02 0.021140927521636 1 +K1_ERK0 K_1/[ERK]_0 log10 1E-04 1E02 1 1 +k11 k_{1,1} log10 1E-04 1E02 1 1 +k2 k_2 log10 1E-04 1E02 1 1 +K2 K_2 log10 1E-04 1E02 1 1 +k3_Raf0 k_3[Raf]_0 log10 1E-04 1E02 1 1 +k4 k_4 log10 1E-04 1E02 1 1 +K3 K_3 log10 1E-04 1E02 1 1 +k5_MEK0 k_5[MEK]_0 log10 1E-04 1E02 1 1 +k6 k_6 log10 1E-04 1E02 1 1 +s_pMek_rel_20140430_gel1 s_{pMek_rel,20140430,gel1} log10 1E-04 1E02 77.7404398920619 1 +s_pMek_rel_20140430_gel2 s_{pMek_rel,20140430,gel2} log10 1E-04 1E02 404.217160578548 1 +s_pMek_rel_20140505_gel1 s_{pMek_rel,20140505,gel1} log10 1E-04 1E02 392.45653075379 1 +s_pMek_rel_20140505_gel2 s_{pMek_rel,20140505,gel2} log10 1E-04 1E02 999.992845715073 1 +s_pErk_rel_20140430_gel1 s_{pErk_rel,20140430,gel1} log10 1E-04 1E02 0.369256805232789 1 +s_pErk_rel_20140430_gel2 s_{pErk_rel,20140430,gel2} log10 1E-04 1E02 0.250134156378628 1 +s_pErk_rel_20140505_gel1 s_{pErk_rel,20140505,gel1} log10 1E-04 1E02 8.92600078593847 1 +s_pErk_rel_20140505_gel2 s_{pErk_rel,20140505,gel2} log10 1E-04 1E02 2.85637035018243 1 +sigma_pMek_rel \sigma_{pMek_rel} log10 1E-10 1E02 0.000580451138215 1 +sigma_pErk_rel \sigma_{pErk_rel} log10 1E-10 1E02 0.045270131337451 1 diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv new file mode 100644 index 0000000..7d7378c --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv @@ -0,0 +1,7 @@ +plotId plotName plotTypeSimulation plotTypeData xLabel yValues yLabel datasetId +Fig8c_pMek_control relative pMek - control LinePlot replicate time [h] pMek_rel relative pMek [UI] control +Fig8c_pMek_Sorafenib relative pMek - 5 muM Sorafenib LinePlot replicate time [h] pMek_rel relative pMek [UI] Sorafenib +Fig8c_pMek_UO126 relative pMek - 30 muM UO126 LinePlot replicate time [h] pMek_rel relative pMek [UI] UO126 +Fig8c_pErk_control relative pErk - control LinePlot replicate time [h] pErk_rel relative pErk [UI] control +Fig8c_pErk_Sorafenib relative pMrk - 5 muM Sorafenib LinePlot replicate time [h] pErk_rel relative pErk [UI] Sorafenib +Fig8c_pErk_UO126 relative pMrk - 30 muM UO126 LinePlot replicate time [h] pErk_rel relative pErk [UI] UO126