From e1cec4af1f674db99acd4548ff3c0768b1ae0f70 Mon Sep 17 00:00:00 2001 From: Maren Philipps <55318391+m-philipps@users.noreply.github.com> Date: Tue, 22 Oct 2024 23:14:15 +0200 Subject: [PATCH] add Armistead_CellDeathDis2024 (#249) add new model Armistead_CellDeathDis2024 Co-authored-by: dilpath --- .../Armistead_CellDeathDis2024.yaml | 13 + ...lConditions_Armistead_CellDeathDis2024.tsv | 3 + ...urementData_Armistead_CellDeathDis2024.tsv | 59 +++ .../model_Armistead_CellDeathDis2024.xml | 356 ++++++++++++++++++ ...observables_Armistead_CellDeathDis2024.tsv | 5 + .../parameters_Armistead_CellDeathDis2024.tsv | 15 + ...ulationData_Armistead_CellDeathDis2024.tsv | 59 +++ ...ecification_Armistead_CellDeathDis2024.tsv | 15 + README.md | 1 + 9 files changed, 526 insertions(+) create mode 100644 Benchmark-Models/Armistead_CellDeathDis2024/Armistead_CellDeathDis2024.yaml create mode 100644 Benchmark-Models/Armistead_CellDeathDis2024/experimentalConditions_Armistead_CellDeathDis2024.tsv create mode 100644 Benchmark-Models/Armistead_CellDeathDis2024/measurementData_Armistead_CellDeathDis2024.tsv create mode 100644 Benchmark-Models/Armistead_CellDeathDis2024/model_Armistead_CellDeathDis2024.xml create mode 100644 Benchmark-Models/Armistead_CellDeathDis2024/observables_Armistead_CellDeathDis2024.tsv create mode 100644 Benchmark-Models/Armistead_CellDeathDis2024/parameters_Armistead_CellDeathDis2024.tsv create mode 100644 Benchmark-Models/Armistead_CellDeathDis2024/simulationData_Armistead_CellDeathDis2024.tsv create mode 100644 Benchmark-Models/Armistead_CellDeathDis2024/visualizationSpecification_Armistead_CellDeathDis2024.tsv diff --git a/Benchmark-Models/Armistead_CellDeathDis2024/Armistead_CellDeathDis2024.yaml b/Benchmark-Models/Armistead_CellDeathDis2024/Armistead_CellDeathDis2024.yaml new file mode 100644 index 0000000..bed552d --- /dev/null +++ b/Benchmark-Models/Armistead_CellDeathDis2024/Armistead_CellDeathDis2024.yaml @@ -0,0 +1,13 @@ +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 \ No newline at end of file diff --git a/Benchmark-Models/Armistead_CellDeathDis2024/experimentalConditions_Armistead_CellDeathDis2024.tsv b/Benchmark-Models/Armistead_CellDeathDis2024/experimentalConditions_Armistead_CellDeathDis2024.tsv new file mode 100644 index 0000000..4b89388 --- /dev/null +++ b/Benchmark-Models/Armistead_CellDeathDis2024/experimentalConditions_Armistead_CellDeathDis2024.tsv @@ -0,0 +1,3 @@ +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 \ No newline at end of file diff --git a/Benchmark-Models/Armistead_CellDeathDis2024/measurementData_Armistead_CellDeathDis2024.tsv b/Benchmark-Models/Armistead_CellDeathDis2024/measurementData_Armistead_CellDeathDis2024.tsv new file mode 100644 index 0000000..234c792 --- /dev/null +++ b/Benchmark-Models/Armistead_CellDeathDis2024/measurementData_Armistead_CellDeathDis2024.tsv @@ -0,0 +1,59 @@ +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 diff --git a/Benchmark-Models/Armistead_CellDeathDis2024/model_Armistead_CellDeathDis2024.xml b/Benchmark-Models/Armistead_CellDeathDis2024/model_Armistead_CellDeathDis2024.xml new file mode 100644 index 0000000..dc8c772 --- /dev/null +++ b/Benchmark-Models/Armistead_CellDeathDis2024/model_Armistead_CellDeathDis2024.xml @@ -0,0 +1,356 @@ + + + + +

Created with https://github.com/matthiaskoenig/sbmlutils. + + DOI

+ + + + + +

+ SBML format.

+

+ version: 1

+

Changelog

+

+ version 1 +

+
    +
  • initial model
    • +
+ + + + + + + + + + Höpfl + Sebastian + + sebastian.hoepfl@isa.uni-stuttgart.de + University of Stuttgart, Institute for Stochastics and Applications + + + + + 1900-01-01T00:00:00Z + + + 1900-01-01T00:00:00Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k00 + + + 1 + + + S_on + alpha_cer + + + + + + + + + + + + + + + + + + k0 + Sphinga + + + + + + + + + + + + + + + + k1 + Cer + + + + + + + + + + + + + + + + k2 + Sphingo + + + + + + + + + + + + + k_d + Cer + + + + + + + + + + + + + + + + k3 + + + 1 + + + S_on + alpha_hai1a + + + Sphingo + + + + + + + + + + + + + + + + k4 + S1P + + + + + + + + + + + + + k5 + S1P + + + + + + + diff --git a/Benchmark-Models/Armistead_CellDeathDis2024/observables_Armistead_CellDeathDis2024.tsv b/Benchmark-Models/Armistead_CellDeathDis2024/observables_Armistead_CellDeathDis2024.tsv new file mode 100644 index 0000000..4cb243a --- /dev/null +++ b/Benchmark-Models/Armistead_CellDeathDis2024/observables_Armistead_CellDeathDis2024.tsv @@ -0,0 +1,5 @@ +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 diff --git a/Benchmark-Models/Armistead_CellDeathDis2024/parameters_Armistead_CellDeathDis2024.tsv b/Benchmark-Models/Armistead_CellDeathDis2024/parameters_Armistead_CellDeathDis2024.tsv new file mode 100644 index 0000000..da9028d --- /dev/null +++ b/Benchmark-Models/Armistead_CellDeathDis2024/parameters_Armistead_CellDeathDis2024.tsv @@ -0,0 +1,15 @@ +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 diff --git a/Benchmark-Models/Armistead_CellDeathDis2024/simulationData_Armistead_CellDeathDis2024.tsv b/Benchmark-Models/Armistead_CellDeathDis2024/simulationData_Armistead_CellDeathDis2024.tsv new file mode 100644 index 0000000..f5d441d --- /dev/null +++ b/Benchmark-Models/Armistead_CellDeathDis2024/simulationData_Armistead_CellDeathDis2024.tsv @@ -0,0 +1,59 @@ +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 diff --git a/Benchmark-Models/Armistead_CellDeathDis2024/visualizationSpecification_Armistead_CellDeathDis2024.tsv b/Benchmark-Models/Armistead_CellDeathDis2024/visualizationSpecification_Armistead_CellDeathDis2024.tsv new file mode 100644 index 0000000..26b21d9 --- /dev/null +++ b/Benchmark-Models/Armistead_CellDeathDis2024/visualizationSpecification_Armistead_CellDeathDis2024.tsv @@ -0,0 +1,15 @@ +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 diff --git a/README.md b/README.md index cfaa11b..db9cd64 100644 --- a/README.md +++ b/README.md @@ -9,6 +9,7 @@ Contributions to the collection are very welcome. Please see [CONTRIBUTING.md](C | PEtab Problem ID | Conditions | Estimated Parameters | Events | Possible Discontinuities | Preequilibration | Postequilibration | Measurements | Observables | Noise distribution(s) | Objective prior distribution(s) | Species | References | SBML4Humans | |:---------------------------------------------------------------------------------------------|-------------:|-----------------------:|---------:|:---------------------------|-------------------:|--------------------:|---------------:|--------------:|:------------------------|:----------------------------------|----------:|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | [Alkan_SciSignal2018](Benchmark-Models/Alkan_SciSignal2018/) | 73 | 56 | 0 | ✓ | 0 | 0 | 1733 | 12 | normal | | 36 | [\[1\]](http://identifiers.org/doi/10.1126/scisignal.aat0229) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Alkan_SciSignal2018/model_Alkan_SciSignal2018.xml) | +| [Armistead_CellDeathDis2024](Benchmark-Models/Armistead_CellDeathDis2024/) | 2 | 14 | 0 | | 0 | 0 | 58 | 4 | normal | | 4 | [\[1\]](https://doi.org/10.1038/s41419-024-07134-2) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Armistead_CellDeathDis2024/model_Armistead_CellDeathDis2024.xml) | | [Bachmann_MSB2011](Benchmark-Models/Bachmann_MSB2011/) | 36 | 113 | 0 | | 0 | 0 | 541 | 20 | normal; log10-normal | parameterScaleNormal | 25 | [\[1\]](http://identifiers.org/doi/10.1038/msb.2011.50) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Bachmann_MSB2011/model_Bachmann_MSB2011.xml) | | [Beer_MolBioSystems2014](Benchmark-Models/Beer_MolBioSystems2014/) | 19 | 72 | 0 | ✓ | 0 | 0 | 27132 | 2 | normal | | 4 | [\[1\]](http://identifiers.org/doi/10.1039/c3mb70594c) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Beer_MolBioSystems2014/model_Beer_MolBioSystems2014.xml) | | [Bertozzi_PNAS2020](Benchmark-Models/Bertozzi_PNAS2020/) | 2 | 8 | 0 | | 0 | 0 | 22 | 2 | normal | | 3 | [\[1\]](http://identifiers.org/doi/10.1073/pnas.2006520117) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Bertozzi_PNAS2020/model.xml) |