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add Armistead_CellDeathDis2024 (#249)
add new model Armistead_CellDeathDis2024 Co-authored-by: dilpath <dilan.private+github@outlook.com>
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Benchmark-Models/Armistead_CellDeathDis2024/Armistead_CellDeathDis2024.yaml
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| format_version: 1 | ||
| parameter_file: parameters_Armistead_CellDeathDis2024.tsv | ||
| problems: | ||
| - condition_files: | ||
| - experimentalConditions_Armistead_CellDeathDis2024.tsv | ||
| measurement_files: | ||
| - measurementData_Armistead_CellDeathDis2024.tsv | ||
| observable_files: | ||
| - observables_Armistead_CellDeathDis2024.tsv | ||
| sbml_files: | ||
| - model_Armistead_CellDeathDis2024.xml | ||
| visualization_files: | ||
| - visualizationSpecification_Armistead_CellDeathDis2024.tsv |
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...k-Models/Armistead_CellDeathDis2024/experimentalConditions_Armistead_CellDeathDis2024.tsv
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| conditionId conditionName S_on Cer Sphinga Sphingo S1P | ||
| wild_type wild-type 1 0.988 0.000732 0.000395 1.551 | ||
| mutant Hai1a deletion mutant 0 0.822 0.000795 0.000364 2.07 |
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Benchmark-Models/Armistead_CellDeathDis2024/measurementData_Armistead_CellDeathDis2024.tsv
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| Original file line number | Diff line number | Diff line change |
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| observableId simulationConditionId measurement time noiseParameters replicateId datasetId | ||
| Sphinga_obs wild_type 0.000806 0 sd_Sphinga_obs R1 wt_day2 | ||
| Sphinga_obs wild_type 0.000618 0 sd_Sphinga_obs R2 wt_day2 | ||
| Sphinga_obs wild_type 0.000675 0 sd_Sphinga_obs R3 wt_day2 | ||
| Sphinga_obs wild_type 0.000828 0 sd_Sphinga_obs R4 wt_day2 | ||
| Sphinga_obs wild_type 0.000176620209326007 2 sd_Sphinga_obs R1 wt_day4 | ||
| Sphinga_obs wild_type 0.000144832895774474 2 sd_Sphinga_obs R2 wt_day4 | ||
| Sphinga_obs wild_type 0.000137134901470714 2 sd_Sphinga_obs R3 wt_day4 | ||
| Sphinga_obs wild_type 0.000181912527619117 2 sd_Sphinga_obs R4 wt_day4 | ||
| Cer_obs wild_type 1.02701422984826 0 sd_Cer_obs R1 wt_day2 | ||
| Cer_obs wild_type 0.886288740504458 0 sd_Cer_obs R2 wt_day2 | ||
| Cer_obs wild_type 0.945776256657445 0 sd_Cer_obs R3 wt_day2 | ||
| Cer_obs wild_type 1.09426905460355 0 sd_Cer_obs R4 wt_day2 | ||
| Cer_obs wild_type 0.612244538629556 2 sd_Cer_obs R1 wt_day4 | ||
| Cer_obs wild_type 0.665790676225569 2 sd_Cer_obs R2 wt_day4 | ||
| Cer_obs wild_type 0.712634629073372 2 sd_Cer_obs R3 wt_day4 | ||
| Cer_obs wild_type 0.641981159099886 2 sd_Cer_obs R4 wt_day4 | ||
| Sphingo_obs wild_type 0.000384239736109822 0 sd_Sphingo_obs R1 wt_day2 | ||
| Sphingo_obs wild_type 0.000391938220558207 0 sd_Sphingo_obs R2 wt_day2 | ||
| Sphingo_obs wild_type 0.000371485514201383 0 sd_Sphingo_obs R3 wt_day2 | ||
| Sphingo_obs wild_type 0.000431025477692304 0 sd_Sphingo_obs R4 wt_day2 | ||
| Sphingo_obs wild_type 0.000334877541530201 2 sd_Sphingo_obs R1 wt_day4 | ||
| Sphingo_obs wild_type 0.000231658738329562 2 sd_Sphingo_obs R2 wt_day4 | ||
| Sphingo_obs wild_type 0.000203229934963182 2 sd_Sphingo_obs R3 wt_day4 | ||
| Sphingo_obs wild_type 0.000227793942150799 2 sd_Sphingo_obs R4 wt_day4 | ||
| S1P_obs wild_type 1.421 0 sd_S1P_obs R1 wt_day2 | ||
| S1P_obs wild_type 1.682 0 sd_S1P_obs R2 wt_day2 | ||
| S1P_obs wild_type 1.614 0 sd_S1P_obs R3 wt_day2 | ||
| S1P_obs wild_type 1.498 0 sd_S1P_obs R4 wt_day2 | ||
| S1P_obs wild_type 1.541 0 sd_S1P_obs R5 wt_day2 | ||
| Sphinga_obs mutant 0.000818 0 sd_Sphinga_obs R1 mut_day2 | ||
| Sphinga_obs mutant 0.000761 0 sd_Sphinga_obs R2 mut_day2 | ||
| Sphinga_obs mutant 0.000766 0 sd_Sphinga_obs R3 mut_day2 | ||
| Sphinga_obs mutant 0.000835 0 sd_Sphinga_obs R4 mut_day2 | ||
| Sphinga_obs mutant 0.000243420646439453 2 sd_Sphinga_obs R1 mut_day4 | ||
| Sphinga_obs mutant 0.000239502545840865 2 sd_Sphinga_obs R2 mut_day4 | ||
| Sphinga_obs mutant 0.000234873603648106 2 sd_Sphinga_obs R3 mut_day4 | ||
| Sphinga_obs mutant 0.000233253355552097 2 sd_Sphinga_obs R4 mut_day4 | ||
| Cer_obs mutant 0.892791183665478 0 sd_Cer_obs R1 mut_day2 | ||
| Cer_obs mutant 0.677804963784483 0 sd_Cer_obs R2 mut_day2 | ||
| Cer_obs mutant 0.857649492135442 0 sd_Cer_obs R3 mut_day2 | ||
| Cer_obs mutant 0.857816589043671 0 sd_Cer_obs R4 mut_day2 | ||
| Cer_obs mutant 0.877785182287324 2 sd_Cer_obs R1 mut_day4 | ||
| Cer_obs mutant 1.02057671816819 2 sd_Cer_obs R2 mut_day4 | ||
| Cer_obs mutant 0.96666151369505 2 sd_Cer_obs R3 mut_day4 | ||
| Cer_obs mutant 0.827292874601032 2 sd_Cer_obs R4 mut_day4 | ||
| Sphingo_obs mutant 0.000417035014112306 0 sd_Sphingo_obs R1 mut_day2 | ||
| Sphingo_obs mutant 0.000366195755858261 0 sd_Sphingo_obs R2 mut_day2 | ||
| Sphingo_obs mutant 0.0003291610891578 0 sd_Sphingo_obs R3 mut_day2 | ||
| Sphingo_obs mutant 0.000341631934155604 0 sd_Sphingo_obs R4 mut_day2 | ||
| Sphingo_obs mutant 0.000323262438726203 2 sd_Sphingo_obs R1 mut_day4 | ||
| Sphingo_obs mutant 0.000316663676062039 2 sd_Sphingo_obs R2 mut_day4 | ||
| Sphingo_obs mutant 0.000279704837681421 2 sd_Sphingo_obs E3 mut_day4 | ||
| Sphingo_obs mutant 0.000242795904444989 2 sd_Sphingo_obs E4 mut_day4 | ||
| S1P_obs mutant 2.128 0 sd_S1P_obs R1 mut_day2 | ||
| S1P_obs mutant 2.143 0 sd_S1P_obs R2 mut_day2 | ||
| S1P_obs mutant 1.565 0 sd_S1P_obs R3 mut_day2 | ||
| S1P_obs mutant 2.275 0 sd_S1P_obs R4 mut_day2 | ||
| S1P_obs mutant 2.238 0 sd_S1P_obs R5 mut_day2 |
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Benchmark-Models/Armistead_CellDeathDis2024/model_Armistead_CellDeathDis2024.xml
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Benchmark-Models/Armistead_CellDeathDis2024/observables_Armistead_CellDeathDis2024.tsv
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| observableId observableName observableFormula noiseFormula noiseDistribution | ||
| Sphinga_obs Sphinganine concentration [area ratio/Protein] - indication of Cer de novo production Sphinga noiseParameter1_Sphinga_obs*Sphinga normal | ||
| Cer_obs Ceramide concentration [area ratio/Protein] Cer noiseParameter1_Cer_obs*Cer normal | ||
| Sphingo_obs Sphingosine concentration [area ratio/Protein] Sphingo noiseParameter1_Sphingo_obs*Sphingo normal | ||
| S1P_obs Sphingosine-1-phosphate indirect measurement S1P noiseParameter1_S1P_obs*S1P normal |
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Benchmark-Models/Armistead_CellDeathDis2024/parameters_Armistead_CellDeathDis2024.tsv
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| parameterId parameterScale lowerBound upperBound nominalValue estimate initializationPriorType | ||
| k00 log10 0.001 1000.0 0.23808250425876593 1 parameterScaleUniform | ||
| k0 log10 0.001 1000.0 999.9999277151477 1 parameterScaleUniform | ||
| k_d log10 0.001 1000.0 0.9067726310954474 1 parameterScaleUniform | ||
| k1 log10 0.001 1000.0 0.30112832513704085 1 parameterScaleUniform | ||
| k2 log10 0.001 1000.0 999.9972374722311 1 parameterScaleUniform | ||
| k3 log10 0.001 1000.0 0.0010000471839981641 1 parameterScaleUniform | ||
| k4 log10 0.001 1000.0 2.3616885412588227 1 parameterScaleUniform | ||
| k5 log10 0.001 1000.0 0.0010007718402407393 1 parameterScaleUniform | ||
| alpha_hai1a lin 0.5 0.999 0.5000000538784732 1 parameterScaleUniform | ||
| alpha_cer lin -0.999 -0.001 -0.32749379807106804 1 parameterScaleUniform | ||
| sd_Sphinga_obs log10 0.001 1000.0 0.08812927862352599 1 parameterScaleUniform | ||
| sd_Cer_obs log10 0.001 1000.0 0.09173161721376666 1 parameterScaleUniform | ||
| sd_Sphingo_obs log10 0.001 1000.0 0.13184193616921516 1 parameterScaleUniform | ||
| sd_S1P_obs log10 0.001 1000.0 0.0974467251675001 1 parameterScaleUniform |
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Benchmark-Models/Armistead_CellDeathDis2024/simulationData_Armistead_CellDeathDis2024.tsv
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| Original file line number | Diff line number | Diff line change |
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| observableId simulationConditionId simulation time noiseParameters replicateId datasetId | ||
| Sphinga_obs mutant 0.000795 0 sd_Sphinga_obs R1 mut_day2 | ||
| Sphinga_obs mutant 0.000795 0 sd_Sphinga_obs R2 mut_day2 | ||
| Sphinga_obs mutant 0.000795 0 sd_Sphinga_obs R3 mut_day2 | ||
| Sphinga_obs mutant 0.000795 0 sd_Sphinga_obs R4 mut_day2 | ||
| Sphinga_obs mutant 0.00023808252146852583 2 sd_Sphinga_obs R1 mut_day4 | ||
| Sphinga_obs mutant 0.00023808252146852583 2 sd_Sphinga_obs R2 mut_day4 | ||
| Sphinga_obs mutant 0.00023808252146852583 2 sd_Sphinga_obs R3 mut_day4 | ||
| Sphinga_obs mutant 0.00023808252146852583 2 sd_Sphinga_obs R4 mut_day4 | ||
| Cer_obs mutant 0.822 0 sd_Cer_obs R1 mut_day2 | ||
| Cer_obs mutant 0.822 0 sd_Cer_obs R2 mut_day2 | ||
| Cer_obs mutant 0.822 0 sd_Cer_obs R3 mut_day2 | ||
| Cer_obs mutant 0.822 0 sd_Cer_obs R4 mut_day2 | ||
| Cer_obs mutant 0.8722233694707532 2 sd_Cer_obs R1 mut_day4 | ||
| Cer_obs mutant 0.8722233694707532 2 sd_Cer_obs R2 mut_day4 | ||
| Cer_obs mutant 0.8722233694707532 2 sd_Cer_obs R3 mut_day4 | ||
| Cer_obs mutant 0.8722233694707532 2 sd_Cer_obs R4 mut_day4 | ||
| Sphingo_obs mutant 0.000364 0 sd_Sphingo_obs R1 mut_day2 | ||
| Sphingo_obs mutant 0.000364 0 sd_Sphingo_obs R2 mut_day2 | ||
| Sphingo_obs mutant 0.000364 0 sd_Sphingo_obs R3 mut_day2 | ||
| Sphingo_obs mutant 0.000364 0 sd_Sphingo_obs R4 mut_day2 | ||
| Sphingo_obs mutant 0.0003062581698170869 2 sd_Sphingo_obs R1 mut_day4 | ||
| Sphingo_obs mutant 0.0003062581698170869 2 sd_Sphingo_obs R2 mut_day4 | ||
| Sphingo_obs mutant 0.0003062581698170869 2 sd_Sphingo_obs E3 mut_day4 | ||
| Sphingo_obs mutant 0.0003062581698170869 2 sd_Sphingo_obs E4 mut_day4 | ||
| S1P_obs mutant 2.07 0 sd_S1P_obs R1 mut_day2 | ||
| S1P_obs mutant 2.07 0 sd_S1P_obs R2 mut_day2 | ||
| S1P_obs mutant 2.07 0 sd_S1P_obs R3 mut_day2 | ||
| S1P_obs mutant 2.07 0 sd_S1P_obs R4 mut_day2 | ||
| S1P_obs mutant 2.07 0 sd_S1P_obs R5 mut_day2 | ||
| Sphinga_obs wild_type 0.000732 0 sd_Sphinga_obs R1 wt_day2 | ||
| Sphinga_obs wild_type 0.000732 0 sd_Sphinga_obs R2 wt_day2 | ||
| Sphinga_obs wild_type 0.000732 0 sd_Sphinga_obs R3 wt_day2 | ||
| Sphinga_obs wild_type 0.000732 0 sd_Sphinga_obs R4 wt_day2 | ||
| Sphinga_obs wild_type 0.0001601119722584617 2 sd_Sphinga_obs R1 wt_day4 | ||
| Sphinga_obs wild_type 0.0001601119722584617 2 sd_Sphinga_obs R2 wt_day4 | ||
| Sphinga_obs wild_type 0.0001601119722584617 2 sd_Sphinga_obs R3 wt_day4 | ||
| Sphinga_obs wild_type 0.0001601119722584617 2 sd_Sphinga_obs R4 wt_day4 | ||
| Cer_obs wild_type 0.988 0 sd_Cer_obs R1 wt_day2 | ||
| Cer_obs wild_type 0.988 0 sd_Cer_obs R2 wt_day2 | ||
| Cer_obs wild_type 0.988 0 sd_Cer_obs R3 wt_day2 | ||
| Cer_obs wild_type 0.988 0 sd_Cer_obs R4 wt_day2 | ||
| Cer_obs wild_type 0.6974072504687345 2 sd_Cer_obs R1 wt_day4 | ||
| Cer_obs wild_type 0.6974072504687345 2 sd_Cer_obs R2 wt_day4 | ||
| Cer_obs wild_type 0.6974072504687345 2 sd_Cer_obs R3 wt_day4 | ||
| Cer_obs wild_type 0.6974072504687345 2 sd_Cer_obs R4 wt_day4 | ||
| Sphingo_obs wild_type 0.000395 0 sd_Sphingo_obs R1 wt_day2 | ||
| Sphingo_obs wild_type 0.000395 0 sd_Sphingo_obs R2 wt_day2 | ||
| Sphingo_obs wild_type 0.000395 0 sd_Sphingo_obs R3 wt_day2 | ||
| Sphingo_obs wild_type 0.000395 0 sd_Sphingo_obs R4 wt_day2 | ||
| Sphingo_obs wild_type 0.0002427001845696418 2 sd_Sphingo_obs R1 wt_day4 | ||
| Sphingo_obs wild_type 0.0002427001845696418 2 sd_Sphingo_obs R2 wt_day4 | ||
| Sphingo_obs wild_type 0.0002427001845696418 2 sd_Sphingo_obs R3 wt_day4 | ||
| Sphingo_obs wild_type 0.0002427001845696418 2 sd_Sphingo_obs R4 wt_day4 | ||
| S1P_obs wild_type 1.551 0 sd_S1P_obs R1 wt_day2 | ||
| S1P_obs wild_type 1.551 0 sd_S1P_obs R2 wt_day2 | ||
| S1P_obs wild_type 1.551 0 sd_S1P_obs R3 wt_day2 | ||
| S1P_obs wild_type 1.551 0 sd_S1P_obs R4 wt_day2 | ||
| S1P_obs wild_type 1.551 0 sd_S1P_obs R5 wt_day2 |
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...dels/Armistead_CellDeathDis2024/visualizationSpecification_Armistead_CellDeathDis2024.tsv
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| plotId plotName plotTypeSimulation plotTypeData xLabel yValues yLabel datasetId | ||
| Fig4k_Sphinganine Sphinganine (with neg. feedback to $k_{00}$ (ODE)) BarPlot MeanAndSD Genotype and days past fertilization (dpf=model time + 2) Sphinga_obs Concentration [area ratio/Protein] wt_day2 | ||
| Fig4k_Sphinganine Sphinganine (with neg. feedback to $k_{00}$ (ODE)) BarPlot MeanAndSD Genotype and days past fertilization (dpf=model time + 2) Sphinga_obs Concentration [area ratio/Protein] mut_day2 | ||
| Fig4k_Sphinganine Sphinganine (with neg. feedback to $k_{00}$ (ODE)) BarPlot MeanAndSD Genotype and days past fertilization (dpf=model time + 2) Sphinga_obs Concentration [area ratio/Protein] wt_day4 | ||
| Fig4k_Sphinganine Sphinganine (with neg. feedback to $k_{00}$ (ODE)) BarPlot MeanAndSD Genotype and days past fertilization (dpf=model time + 2) Sphinga_obs Concentration [area ratio/Protein] mut_day4 | ||
| Fig4k_Ceramide Ceramide (with neg. feedback to $k_{00}$ (ODE)) BarPlot MeanAndSD Genotype and days past fertilization (dpf=model time + 2) Cer_obs Concentration [area ratio/Protein] wt_day2 | ||
| Fig4k_Ceramide Ceramide (with neg. feedback to $k_{00}$ (ODE)) BarPlot MeanAndSD Genotype and days past fertilization (dpf=model time + 2) Cer_obs Concentration [area ratio/Protein] mut_day2 | ||
| Fig4k_Ceramide Ceramide (with neg. feedback to $k_{00}$ (ODE)) BarPlot MeanAndSD Genotype and days past fertilization (dpf=model time + 2) Cer_obs Concentration [area ratio/Protein] wt_day4 | ||
| Fig4k_Ceramide Ceramide (with neg. feedback to $k_{00}$ (ODE)) BarPlot MeanAndSD Genotype and days past fertilization (dpf=model time + 2) Cer_obs Concentration [area ratio/Protein] mut_day4 | ||
| Sphingo Sphingosine (with neg. feedback to $k_{00}$ (ODE)) BarPlot MeanAndSD Genotype and days past fertilization (dpf=model time + 2) Sphingo_obs Concentration [area ratio/Protein] wt_day2 | ||
| Sphingo Sphingosine (with neg. feedback to $k_{00}$ (ODE)) BarPlot MeanAndSD Genotype and days past fertilization (dpf=model time + 2) Sphingo_obs Concentration [area ratio/Protein] mut_day2 | ||
| Sphingo Sphingosine (with neg. feedback to $k_{00}$ (ODE)) BarPlot MeanAndSD Genotype and days past fertilization (dpf=model time + 2) Sphingo_obs Concentration [area ratio/Protein] wt_day4 | ||
| Sphingo Sphingosine (with neg. feedback to $k_{00}$ (ODE)) BarPlot MeanAndSD Genotype and days past fertilization (dpf=model time + 2) Sphingo_obs Concentration [area ratio/Protein] mut_day4 | ||
| S1P S1P (with neg. feedback to $k_{00}$ (ODE)) BarPlot MeanAndSD Genotype and days past fertilization (dpf=model time + 2) S1P_obs Concentration [area ratio/Protein] wt_day2 | ||
| S1P S1P (with neg. feedback to $k_{00}$ (ODE)) BarPlot MeanAndSD Genotype and days past fertilization (dpf=model time + 2) S1P_obs Concentration [area ratio/Protein] mut_day2 |
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