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add PEtab model for reformulated Fiedler_BMCSystBiol2016
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Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 |
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...ls/Fiedler_BMCSystBiol2016/reformulated/experimentalCondition_Fiedler_BMCSystBiol2016.tsv
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,4 @@ | ||
| conditionId conditionName Sorafenib UO126 | ||
| model1_data1 0 0 | ||
| model1_data2 5 0 | ||
| model1_data3 0 30 |
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...k-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| 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 |
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...hmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016.tsv
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| Original file line number | Diff line number | Diff line change |
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| 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 |
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Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016.tsv
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| 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 |
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...edler_BMCSystBiol2016/reformulated/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv
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| @@ -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 |