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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
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parameter_file: parameters_Armistead_CellDeathDis2024.tsv
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problems:
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- condition_files:
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- experimentalConditions_Armistead_CellDeathDis2024.tsv
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measurement_files:
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- measurementData_Armistead_CellDeathDis2024.tsv
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observable_files:
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- observables_Armistead_CellDeathDis2024.tsv
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sbml_files:
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- model_Armistead_CellDeathDis2024.xml
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visualization_files:
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- visualizationSpecification_Armistead_CellDeathDis2024.tsv

‎Benchmark-Models/Armistead_CellDeathDis2024/experimentalConditions_Armistead_CellDeathDis2024.tsv

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conditionId conditionName S_on Cer Sphinga Sphingo S1P
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wild_type wild-type 1 0.988 0.000732 0.000395 1.551
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mutant Hai1a deletion mutant 0 0.822 0.000795 0.000364 2.07

‎Benchmark-Models/Armistead_CellDeathDis2024/measurementData_Armistead_CellDeathDis2024.tsv

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observableId simulationConditionId measurement time noiseParameters replicateId datasetId
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Sphinga_obs wild_type 0.000806 0 sd_Sphinga_obs R1 wt_day2
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Sphinga_obs wild_type 0.000618 0 sd_Sphinga_obs R2 wt_day2
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Sphinga_obs wild_type 0.000675 0 sd_Sphinga_obs R3 wt_day2
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Sphinga_obs wild_type 0.000828 0 sd_Sphinga_obs R4 wt_day2
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Sphinga_obs wild_type 0.000176620209326007 2 sd_Sphinga_obs R1 wt_day4
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Sphinga_obs wild_type 0.000144832895774474 2 sd_Sphinga_obs R2 wt_day4
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Sphinga_obs wild_type 0.000137134901470714 2 sd_Sphinga_obs R3 wt_day4
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Sphinga_obs wild_type 0.000181912527619117 2 sd_Sphinga_obs R4 wt_day4
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Cer_obs wild_type 1.02701422984826 0 sd_Cer_obs R1 wt_day2
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Cer_obs wild_type 0.886288740504458 0 sd_Cer_obs R2 wt_day2
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Cer_obs wild_type 0.945776256657445 0 sd_Cer_obs R3 wt_day2
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Cer_obs wild_type 1.09426905460355 0 sd_Cer_obs R4 wt_day2
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Cer_obs wild_type 0.612244538629556 2 sd_Cer_obs R1 wt_day4
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Cer_obs wild_type 0.665790676225569 2 sd_Cer_obs R2 wt_day4
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Cer_obs wild_type 0.712634629073372 2 sd_Cer_obs R3 wt_day4
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Cer_obs wild_type 0.641981159099886 2 sd_Cer_obs R4 wt_day4
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Sphingo_obs wild_type 0.000384239736109822 0 sd_Sphingo_obs R1 wt_day2
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Sphingo_obs wild_type 0.000391938220558207 0 sd_Sphingo_obs R2 wt_day2
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Sphingo_obs wild_type 0.000371485514201383 0 sd_Sphingo_obs R3 wt_day2
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Sphingo_obs wild_type 0.000431025477692304 0 sd_Sphingo_obs R4 wt_day2
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Sphingo_obs wild_type 0.000334877541530201 2 sd_Sphingo_obs R1 wt_day4
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Sphingo_obs wild_type 0.000231658738329562 2 sd_Sphingo_obs R2 wt_day4
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Sphingo_obs wild_type 0.000203229934963182 2 sd_Sphingo_obs R3 wt_day4
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Sphingo_obs wild_type 0.000227793942150799 2 sd_Sphingo_obs R4 wt_day4
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S1P_obs wild_type 1.421 0 sd_S1P_obs R1 wt_day2
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S1P_obs wild_type 1.682 0 sd_S1P_obs R2 wt_day2
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S1P_obs wild_type 1.614 0 sd_S1P_obs R3 wt_day2
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S1P_obs wild_type 1.498 0 sd_S1P_obs R4 wt_day2
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S1P_obs wild_type 1.541 0 sd_S1P_obs R5 wt_day2
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Sphinga_obs mutant 0.000818 0 sd_Sphinga_obs R1 mut_day2
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Sphinga_obs mutant 0.000761 0 sd_Sphinga_obs R2 mut_day2
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Sphinga_obs mutant 0.000766 0 sd_Sphinga_obs R3 mut_day2
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Sphinga_obs mutant 0.000835 0 sd_Sphinga_obs R4 mut_day2
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Sphinga_obs mutant 0.000243420646439453 2 sd_Sphinga_obs R1 mut_day4
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Sphinga_obs mutant 0.000239502545840865 2 sd_Sphinga_obs R2 mut_day4
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Sphinga_obs mutant 0.000234873603648106 2 sd_Sphinga_obs R3 mut_day4
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Sphinga_obs mutant 0.000233253355552097 2 sd_Sphinga_obs R4 mut_day4
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Cer_obs mutant 0.892791183665478 0 sd_Cer_obs R1 mut_day2
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Cer_obs mutant 0.677804963784483 0 sd_Cer_obs R2 mut_day2
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Cer_obs mutant 0.857649492135442 0 sd_Cer_obs R3 mut_day2
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Cer_obs mutant 0.857816589043671 0 sd_Cer_obs R4 mut_day2
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Cer_obs mutant 0.877785182287324 2 sd_Cer_obs R1 mut_day4
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Cer_obs mutant 1.02057671816819 2 sd_Cer_obs R2 mut_day4
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Cer_obs mutant 0.96666151369505 2 sd_Cer_obs R3 mut_day4
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Cer_obs mutant 0.827292874601032 2 sd_Cer_obs R4 mut_day4
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Sphingo_obs mutant 0.000417035014112306 0 sd_Sphingo_obs R1 mut_day2
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Sphingo_obs mutant 0.000366195755858261 0 sd_Sphingo_obs R2 mut_day2
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Sphingo_obs mutant 0.0003291610891578 0 sd_Sphingo_obs R3 mut_day2
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Sphingo_obs mutant 0.000341631934155604 0 sd_Sphingo_obs R4 mut_day2
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Sphingo_obs mutant 0.000323262438726203 2 sd_Sphingo_obs R1 mut_day4
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Sphingo_obs mutant 0.000316663676062039 2 sd_Sphingo_obs R2 mut_day4
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Sphingo_obs mutant 0.000279704837681421 2 sd_Sphingo_obs E3 mut_day4
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Sphingo_obs mutant 0.000242795904444989 2 sd_Sphingo_obs E4 mut_day4
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S1P_obs mutant 2.128 0 sd_S1P_obs R1 mut_day2
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S1P_obs mutant 2.143 0 sd_S1P_obs R2 mut_day2
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S1P_obs mutant 1.565 0 sd_S1P_obs R3 mut_day2
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S1P_obs mutant 2.275 0 sd_S1P_obs R4 mut_day2
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S1P_obs mutant 2.238 0 sd_S1P_obs R5 mut_day2

‎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
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Sphinga_obs Sphinganine concentration [area ratio/Protein] - indication of Cer de novo production Sphinga noiseParameter1_Sphinga_obs*Sphinga normal
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Cer_obs Ceramide concentration [area ratio/Protein] Cer noiseParameter1_Cer_obs*Cer normal
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Sphingo_obs Sphingosine concentration [area ratio/Protein] Sphingo noiseParameter1_Sphingo_obs*Sphingo normal
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S1P_obs Sphingosine-1-phosphate indirect measurement S1P noiseParameter1_S1P_obs*S1P normal

‎Benchmark-Models/Armistead_CellDeathDis2024/parameters_Armistead_CellDeathDis2024.tsv

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parameterId parameterScale lowerBound upperBound nominalValue estimate initializationPriorType
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k00 log10 0.001 1000.0 0.23808250425876593 1 parameterScaleUniform
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k0 log10 0.001 1000.0 999.9999277151477 1 parameterScaleUniform
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k_d log10 0.001 1000.0 0.9067726310954474 1 parameterScaleUniform
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k1 log10 0.001 1000.0 0.30112832513704085 1 parameterScaleUniform
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k2 log10 0.001 1000.0 999.9972374722311 1 parameterScaleUniform
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k3 log10 0.001 1000.0 0.0010000471839981641 1 parameterScaleUniform
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k4 log10 0.001 1000.0 2.3616885412588227 1 parameterScaleUniform
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k5 log10 0.001 1000.0 0.0010007718402407393 1 parameterScaleUniform
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alpha_hai1a lin 0.5 0.999 0.5000000538784732 1 parameterScaleUniform
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alpha_cer lin -0.999 -0.001 -0.32749379807106804 1 parameterScaleUniform
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sd_Sphinga_obs log10 0.001 1000.0 0.08812927862352599 1 parameterScaleUniform
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sd_Cer_obs log10 0.001 1000.0 0.09173161721376666 1 parameterScaleUniform
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sd_Sphingo_obs log10 0.001 1000.0 0.13184193616921516 1 parameterScaleUniform
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sd_S1P_obs log10 0.001 1000.0 0.0974467251675001 1 parameterScaleUniform

‎Benchmark-Models/Armistead_CellDeathDis2024/simulationData_Armistead_CellDeathDis2024.tsv

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observableId simulationConditionId simulation time noiseParameters replicateId datasetId
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Sphinga_obs mutant 0.000795 0 sd_Sphinga_obs R1 mut_day2
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Sphinga_obs mutant 0.000795 0 sd_Sphinga_obs R2 mut_day2
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Sphinga_obs mutant 0.000795 0 sd_Sphinga_obs R3 mut_day2
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Sphinga_obs mutant 0.000795 0 sd_Sphinga_obs R4 mut_day2
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Sphinga_obs mutant 0.00023808252146852583 2 sd_Sphinga_obs R1 mut_day4
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Sphinga_obs mutant 0.00023808252146852583 2 sd_Sphinga_obs R2 mut_day4
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Sphinga_obs mutant 0.00023808252146852583 2 sd_Sphinga_obs R3 mut_day4
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Sphinga_obs mutant 0.00023808252146852583 2 sd_Sphinga_obs R4 mut_day4
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Cer_obs mutant 0.822 0 sd_Cer_obs R1 mut_day2
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Cer_obs mutant 0.822 0 sd_Cer_obs R2 mut_day2
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Cer_obs mutant 0.822 0 sd_Cer_obs R3 mut_day2
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Cer_obs mutant 0.822 0 sd_Cer_obs R4 mut_day2
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Cer_obs mutant 0.8722233694707532 2 sd_Cer_obs R1 mut_day4
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Cer_obs mutant 0.8722233694707532 2 sd_Cer_obs R2 mut_day4
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Cer_obs mutant 0.8722233694707532 2 sd_Cer_obs R3 mut_day4
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Cer_obs mutant 0.8722233694707532 2 sd_Cer_obs R4 mut_day4
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Sphingo_obs mutant 0.000364 0 sd_Sphingo_obs R1 mut_day2
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Sphingo_obs mutant 0.000364 0 sd_Sphingo_obs R2 mut_day2
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Sphingo_obs mutant 0.000364 0 sd_Sphingo_obs R3 mut_day2
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Sphingo_obs mutant 0.000364 0 sd_Sphingo_obs R4 mut_day2
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Sphingo_obs mutant 0.0003062581698170869 2 sd_Sphingo_obs R1 mut_day4
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Sphingo_obs mutant 0.0003062581698170869 2 sd_Sphingo_obs R2 mut_day4
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Sphingo_obs mutant 0.0003062581698170869 2 sd_Sphingo_obs E3 mut_day4
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Sphingo_obs mutant 0.0003062581698170869 2 sd_Sphingo_obs E4 mut_day4
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S1P_obs mutant 2.07 0 sd_S1P_obs R1 mut_day2
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S1P_obs mutant 2.07 0 sd_S1P_obs R2 mut_day2
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S1P_obs mutant 2.07 0 sd_S1P_obs R3 mut_day2
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S1P_obs mutant 2.07 0 sd_S1P_obs R4 mut_day2
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S1P_obs mutant 2.07 0 sd_S1P_obs R5 mut_day2
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Sphinga_obs wild_type 0.000732 0 sd_Sphinga_obs R1 wt_day2
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Sphinga_obs wild_type 0.000732 0 sd_Sphinga_obs R2 wt_day2
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Sphinga_obs wild_type 0.000732 0 sd_Sphinga_obs R3 wt_day2
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Sphinga_obs wild_type 0.000732 0 sd_Sphinga_obs R4 wt_day2
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Sphinga_obs wild_type 0.0001601119722584617 2 sd_Sphinga_obs R1 wt_day4
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Sphinga_obs wild_type 0.0001601119722584617 2 sd_Sphinga_obs R2 wt_day4
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Sphinga_obs wild_type 0.0001601119722584617 2 sd_Sphinga_obs R3 wt_day4
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Sphinga_obs wild_type 0.0001601119722584617 2 sd_Sphinga_obs R4 wt_day4
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Cer_obs wild_type 0.988 0 sd_Cer_obs R1 wt_day2
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Cer_obs wild_type 0.988 0 sd_Cer_obs R2 wt_day2
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Cer_obs wild_type 0.988 0 sd_Cer_obs R3 wt_day2
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Cer_obs wild_type 0.988 0 sd_Cer_obs R4 wt_day2
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Cer_obs wild_type 0.6974072504687345 2 sd_Cer_obs R1 wt_day4
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Cer_obs wild_type 0.6974072504687345 2 sd_Cer_obs R2 wt_day4
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Cer_obs wild_type 0.6974072504687345 2 sd_Cer_obs R3 wt_day4
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Cer_obs wild_type 0.6974072504687345 2 sd_Cer_obs R4 wt_day4
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Sphingo_obs wild_type 0.000395 0 sd_Sphingo_obs R1 wt_day2
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Sphingo_obs wild_type 0.000395 0 sd_Sphingo_obs R2 wt_day2
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Sphingo_obs wild_type 0.000395 0 sd_Sphingo_obs R3 wt_day2
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Sphingo_obs wild_type 0.000395 0 sd_Sphingo_obs R4 wt_day2
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Sphingo_obs wild_type 0.0002427001845696418 2 sd_Sphingo_obs R1 wt_day4
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Sphingo_obs wild_type 0.0002427001845696418 2 sd_Sphingo_obs R2 wt_day4
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Sphingo_obs wild_type 0.0002427001845696418 2 sd_Sphingo_obs R3 wt_day4
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Sphingo_obs wild_type 0.0002427001845696418 2 sd_Sphingo_obs R4 wt_day4
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S1P_obs wild_type 1.551 0 sd_S1P_obs R1 wt_day2
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S1P_obs wild_type 1.551 0 sd_S1P_obs R2 wt_day2
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S1P_obs wild_type 1.551 0 sd_S1P_obs R3 wt_day2
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S1P_obs wild_type 1.551 0 sd_S1P_obs R4 wt_day2
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S1P_obs wild_type 1.551 0 sd_S1P_obs R5 wt_day2

‎Benchmark-Models/Armistead_CellDeathDis2024/visualizationSpecification_Armistead_CellDeathDis2024.tsv

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plotId plotName plotTypeSimulation plotTypeData xLabel yValues yLabel datasetId
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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

‎README.md

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| PEtab Problem ID | Conditions | Estimated Parameters | Events | Possible Discontinuities | Preequilibration | Postequilibration | Measurements | Observables | Noise distribution(s) | Objective prior distribution(s) | Species | References | SBML4Humans |
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|:---------------------------------------------------------------------------------------------|-------------:|-----------------------:|---------:|:---------------------------|-------------------:|--------------------:|---------------:|--------------:|:------------------------|:----------------------------------|----------:|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| [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) |
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| [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) |
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| [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) |
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| [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) |
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| [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) |

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