├── .gitattributes ├── .github ├── CODEOWNERS ├── dependabot.yml ├── pull_request_template.md └── workflows │ ├── gh-pages.yml │ ├── python.yml │ ├── simulate.yml │ └── tests.yml ├── .gitignore ├── .pre-commit-config.yaml ├── Benchmark-Models ├── Alkan_SciSignal2018 │ ├── Alkan_SciSignal2018.yaml │ ├── experimentalCondition_Alkan_SciSignal2018.tsv │ ├── measurementData_Alkan_SciSignal2018.tsv │ ├── model_Alkan_SciSignal2018.xml │ ├── observables_Alkan_SciSignal2018.tsv │ ├── parameters_Alkan_SciSignal2018.tsv │ ├── simulatedData_Alkan_SciSignal2018.tsv │ └── visualizationSpecification_Alkan_SciSignal2018.tsv ├── Armistead_CellDeathDis2024 │ ├── Armistead_CellDeathDis2024.yaml │ ├── experimentalConditions_Armistead_CellDeathDis2024.tsv │ ├── measurementData_Armistead_CellDeathDis2024.tsv │ ├── model_Armistead_CellDeathDis2024.xml │ ├── observables_Armistead_CellDeathDis2024.tsv │ ├── parameters_Armistead_CellDeathDis2024.tsv │ ├── simulatedData_Armistead_CellDeathDis2024.tsv │ └── visualizationSpecification_Armistead_CellDeathDis2024.tsv ├── Bachmann_MSB2011 │ ├── Bachmann_MSB2011.yaml │ ├── experimentalCondition_Bachmann_MSB2011.tsv │ ├── measurementData_Bachmann_MSB2011.tsv │ ├── model_Bachmann_MSB2011.xml │ ├── observables_Bachmann_MSB2011.tsv │ ├── parameters_Bachmann_MSB2011.tsv │ └── simulatedData_Bachmann_MSB2011.tsv ├── Beer_MolBioSystems2014 │ ├── Beer_MolBioSystems2014.yaml │ ├── General_info.xlsx │ ├── experimentalCondition_Beer_MolBioSystems2014.tsv │ ├── measurementData_Beer_MolBioSystems2014.tsv │ ├── model_Beer_MolBioSystems2014.xml │ ├── observables_Beer_MolBioSystems2014.tsv │ ├── parameters_Beer_MolBioSystems2014.tsv │ ├── simulatedData_Beer_MolBioSystems2014.tsv │ └── visualizationSpecification_Beer_MolBioSystems2014.tsv ├── Bertozzi_PNAS2020 │ ├── conditions.tsv │ ├── measurements.tsv │ ├── model.xml │ ├── observables.tsv │ ├── parameters.tsv │ ├── problem.yaml │ ├── simulations.tsv │ └── visualizations.tsv ├── Blasi_CellSystems2016 │ ├── Blasi_CellSystems2016.yaml │ ├── experimentalCondition_Blasi_CellSystems2016.tsv │ ├── measurementData_Blasi_CellSystems2016.tsv │ ├── model_Blasi_CellSystems2016.xml │ ├── model_Blasi_CellSystems2016_allCombinations.xml │ ├── observables_Blasi_CellSystems2016.tsv │ ├── parameters_Blasi_CellSystems2016.tsv │ ├── petab_select │ │ ├── 01_create_output_dirs.sh │ │ ├── 02_create_sbml.py │ │ ├── 03_create_petab.py │ │ ├── 04_create_select.py │ │ ├── README.md │ │ ├── input │ │ │ ├── petab_problem.yaml │ │ │ └── petab_select_problem.yaml │ │ ├── model_info.py │ │ └── output │ │ │ ├── model │ │ │ └── model.xml │ │ │ ├── petab │ │ │ ├── conditions.tsv │ │ │ ├── measurements.tsv │ │ │ ├── observables.tsv │ │ │ ├── parameters.tsv │ │ │ └── petab_problem.yaml │ │ │ └── select │ │ │ ├── model_space.tsv │ │ │ └── petab_select_problem.yaml │ ├── simulatedData_Blasi_CellSystems2016.tsv │ └── visualizationSpecification_Blasi_CellSystems2016.tsv ├── Boehm_JProteomeRes2014 │ ├── Boehm_JProteomeRes2014.yaml │ ├── experimentalCondition_Boehm_JProteomeRes2014.tsv │ ├── measurementData_Boehm_JProteomeRes2014.tsv │ ├── model_Boehm_JProteomeRes2014.xml │ ├── observables_Boehm_JProteomeRes2014.tsv │ ├── parameters_Boehm_JProteomeRes2014.tsv │ ├── simulatedData_Boehm_JProteomeRes2014.tsv │ └── visualizationSpecification_Boehm_JProteomeRes2014.tsv ├── Borghans_BiophysChem1997 │ ├── Borghans_BiophysChem1997.yaml │ ├── experimentalCondition_Borghans_BiophysChem1997.tsv │ ├── measurementData_Borghans_BiophysChem1997.tsv │ ├── model_Borghans_BiophysChem1997.xml │ ├── observables_Borghans_BiophysChem1997.tsv │ ├── parameters_Borghans_BiophysChem1997.tsv │ ├── simulatedData_Borghans_BiophysChem1997.tsv │ └── visualizationSpecification_Borghans_BiophysChem1997.tsv ├── Brannmark_JBC2010 │ ├── Brannmark_JBC2010.yaml │ ├── experimentalCondition_Brannmark_JBC2010.tsv │ ├── measurementData_Brannmark_JBC2010.tsv │ ├── model_Brannmark_JBC2010.xml │ ├── observables_Brannmark_JBC2010.tsv │ ├── parameters_Brannmark_JBC2010.tsv │ ├── simulatedData_Brannmark_JBC2010.tsv │ └── visualizationSpecification_Brannmark_JBC2010.tsv ├── Bruno_JExpBot2016 │ ├── Bruno_JExpBot2016.yaml │ ├── experimentalCondition_Bruno_JExpBot2016.tsv │ ├── measurementData_Bruno_JExpBot2016.tsv │ ├── model_Bruno_JExpBot2016.xml │ ├── observables_Bruno_JExpBot2016.tsv │ ├── parameters_Bruno_JExpBot2016.tsv │ ├── simulatedData_Bruno_JExpBot2016.tsv │ └── visualizationSpecification_Bruno_JExpBot2016.tsv ├── Chen_MSB2009 │ ├── Chen_MSB2009.yaml │ ├── experimentalCondition_Chen_MSB2009.tsv │ ├── measurementData_Chen_MSB2009.tsv │ ├── model_Chen_MSB2009.xml │ ├── observables_Chen_MSB2009.tsv │ ├── parameters_Chen_MSB2009.tsv │ ├── simulatedData_Chen_MSB2009.tsv │ └── visualizationSpecification_Chen_MSB2009.tsv ├── Crauste_CellSystems2017 │ ├── Crauste_CellSystems2017.yaml │ ├── experimentalCondition_Crauste_CellSystems2017.tsv │ ├── measurementData_Crauste_CellSystems2017.tsv │ ├── model_Crauste_CellSystems2017.xml │ ├── observables_Crauste_CellSystems2017.tsv │ ├── parameters_Crauste_CellSystems2017.tsv │ ├── simulatedData_Crauste_CellSystems2017.tsv │ └── visualizationSpecification_Crauste_CellSystems2017.tsv ├── Elowitz_Nature2000 │ ├── Elowitz_Nature2000.yaml │ ├── experimentalCondition_Elowitz_Nature2000.tsv │ ├── measurementData_Elowitz_Nature2000.tsv │ ├── model_Elowitz_Nature2000.xml │ ├── observables_Elowitz_Nature2000.tsv │ ├── parameters_Elowitz_Nature2000.tsv │ ├── simulatedData_Elowitz_Nature2000.tsv │ └── visualizationSpecification_Elowitz_Nature2000.tsv ├── Fiedler_BMCSystBiol2016 │ ├── Fiedler_BMCSystBiol2016.yaml │ ├── experimentalCondition_Fiedler_BMCSystBiol2016.tsv │ ├── measurementData_Fiedler_BMCSystBiol2016.tsv │ ├── model_Fiedler_BMCSystBiol2016.xml │ ├── observables_Fiedler_BMCSystBiol2016.tsv │ ├── parameters_Fiedler_BMCSystBiol2016.tsv │ ├── reformulated │ │ ├── Fiedler_BMCSystBiol2016_rel.yaml │ │ ├── experimentalCondition_Fiedler_BMCSystBiol2016_rel.tsv │ │ ├── measurementData_Fiedler_BMCSystBiol2016_rel.tsv │ │ ├── model_Fiedler_BMCSystBiol2016_rel.xml │ │ ├── observables_Fiedler_BMCSystBiol2016_rel.tsv │ │ ├── parameters_Fiedler_BMCSystBiol2016_rel.tsv │ │ └── simulatedData_Fiedler_BMCSystBiol2016.tsv │ ├── simulatedData_Fiedler_BMCSystBiol2016.tsv │ └── visualizationSpecification_Fiedler_BMCSystBiol2016.tsv ├── Froehlich_CellSystems2018 │ ├── Froehlich_CellSystems2018.yaml │ ├── experimentalCondition_Froehlich_CellSystems2018.tsv │ ├── measurementData_Froehlich_CellSystems2018.tsv │ ├── model_Froehlich_CellSystems2018.xml │ ├── observables_Froehlich_CellSystems2018.tsv │ ├── parameters_Froehlich_CellSystems2018.tsv │ ├── simulatedData_Froehlich_CellSystems2018.tsv │ └── visualizationSpecification_Froehlich_CellSystems2018.tsv ├── Fujita_SciSignal2010 │ ├── Fujita_SciSignal2010.yaml │ ├── General_info.xlsx │ ├── experimentalCondition_Fujita_SciSignal2010.tsv │ ├── measurementData_step_Fujita_SciSignal2010.tsv │ ├── model_Fujita_SciSignal2010.xml │ ├── observables_Fujita_SciSignal2010.tsv │ ├── parameters_Fujita_SciSignal2010.tsv │ ├── simulatedData_Fujita_SciSignal2010.tsv │ ├── test_data │ │ ├── input_all_Fujita_SciSignal2010.yaml │ │ ├── input_pulse_Fujita_SciSignal2010.yaml │ │ ├── input_ramp_Fujita_SciSignal2010.yaml │ │ ├── input_test_Fujita_SciSignal2010.yaml │ │ ├── measurementData_pulse_Fujita_SciSignal2010.tsv │ │ └── measurementData_ramp_Fujita_SciSignal2010.tsv │ └── visualizationSpecification_Fujita_SciSignal2010.tsv ├── Giordano_Nature2020 │ ├── Giordano_Nature2020.yaml │ ├── experimentalCondition_Giordano_Nature2020.tsv │ ├── measurementData_Giordano_Nature2020.tsv │ ├── model_Giordano_Nature2020.xml │ ├── observables_Giordano_Nature2020.tsv │ ├── parameters_Giordano_Nature2020.tsv │ ├── simulatedData_Giordano_Nature2020.tsv │ └── visualizationSpecification_Giordano_Nature2020.tsv ├── Isensee_JCB2018 │ ├── Isensee_JCB2018.yaml │ ├── README.md │ ├── experimentalCondition_Isensee_JCB2018.tsv │ ├── measurementData_Isensee_JCB2018.tsv │ ├── model_Isensee_JCB2018.xml │ ├── observables_Isensee_JCB2018.tsv │ ├── parameters_Isensee_JCB2018.tsv │ ├── parameters_Isensee_JCB2018_model_selection.tsv │ ├── simulatedData_Isensee_JCB2018.tsv │ └── visualizationSpecification_Isensee_JCB2018.tsv ├── Lang_PLOSComputBiol2024 │ ├── Lang_PLOSComputBiol2024.yaml │ ├── experimentalCondition_Lang_PLOSComputBiol2024.tsv │ ├── measurementData_Lang_PLOSComputBiol2024.tsv │ ├── model_Lang_PLOSComputBiol2024.xml │ ├── observables_Lang_PLOSComputBiol2024.tsv │ ├── parameters_Lang_PLOSComputBiol2024.tsv │ ├── simulatedData_Lang_PLOSComputBiol2024.tsv │ └── visualizationSpecification_Lang_PLOSComputBiol2024.tsv ├── Laske_PLOSComputBiol2019 │ ├── Laske_PLOSComputBiol2019.yaml │ ├── experimentalCondition_Laske_PLOSComputBiol2019.tsv │ ├── measurementData_Laske_PLOSComputBiol2019.tsv │ ├── model_Laske_PLOSComputBiol2019.xml │ ├── observables_Laske_PLOSComputBiol2019.tsv │ ├── parameters_Laske_PLOSComputBiol2019.tsv │ ├── simulatedData_Laske_PLOSComputBiol2019.tsv │ └── visualizationSpecification_Laske_PLOSComputBiol2019.tsv ├── Lucarelli_CellSystems2018 │ ├── Lucarelli_CellSystems2018.yaml │ ├── experimentalCondition_Lucarelli_CellSystems2018.tsv │ ├── measurementData_Lucarelli_CellSystems2018.tsv │ ├── model_Lucarelli_CellSystems2018.xml │ ├── observables_Lucarelli_CellSystems2018.tsv │ ├── parameters_Lucarelli_CellSystems2018.tsv │ ├── simulatedData_Lucarelli_CellSystems2018.tsv │ ├── visualizationSpecification_Lucarelli_CellSystems2018.tsv │ ├── visualizationSpecification_Lucarelli_CellSystems2018_Figure1.tsv │ ├── visualizationSpecification_Lucarelli_CellSystems2018_Figure2.tsv │ ├── visualizationSpecification_Lucarelli_CellSystems2018_Figure3_1.tsv │ ├── visualizationSpecification_Lucarelli_CellSystems2018_Figure3_2.tsv │ ├── visualizationSpecification_Lucarelli_CellSystems2018_Figure3_3.tsv │ └── visualizationSpecification_Lucarelli_CellSystems2018_Figure3_4.tsv ├── Okuonghae_ChaosSolitonsFractals2020 │ ├── Okuonghae_ChaosSolitonsFractals2020.yaml │ ├── experimentalConditions_Okuonghae_ChaosSolitonsFractals2020.tsv │ ├── measurementData_Okuonghae_ChaosSolitonsFractals2020.tsv │ ├── model_Okuonghae_ChaosSolitonsFractals2020.xml │ ├── observables_Okuonghae_ChaosSolitonsFractals2020.tsv │ ├── parameters_Okuonghae_ChaosSolitonsFractals2020.tsv │ └── visualizationSpecification_Okuonghae_ChaosSolitonsFractals2020.tsv ├── Oliveira_NatCommun2021 │ ├── Bahia │ │ ├── Oliveira_NatCommun2021_Bahia.yaml │ │ ├── experimentalConditions_Oliveira_NatCommun2021.tsv │ │ ├── measurementData_Oliveira_NatCommun2021.tsv │ │ ├── observables_Oliveira_NatCommun2021.tsv │ │ ├── parameters_Oliveira_NatCommun2021.tsv │ │ └── visualizationSpecification_Oliveira_NatCommun2021.tsv │ ├── Oliveira_NatCommun2021.yaml │ ├── Oliveira_NatCommun2021_model.xml │ ├── experimentalConditions_Oliveira_NatCommun2021.tsv │ ├── measurementData_Oliveira_NatCommun2021.tsv │ ├── observables_Oliveira_NatCommun2021.tsv │ ├── parameters_Oliveira_NatCommun2021.tsv │ └── visualizationSpecification_Oliveira_NatCommun2021.tsv ├── Perelson_Science1996 │ ├── Perelson_Science1996.yaml │ ├── experimentalCondition_Perelson_Science1996.tsv │ ├── measurementData_Perelson_Science1996.tsv │ ├── model_Perelson_Science1996.xml │ ├── observables_Perelson_Science1996.tsv │ ├── parameters_Perelson_Science1996.tsv │ ├── simulatedData_Perelson_Science1996.tsv │ └── visualizationSpecification_Perelson_Science1996.tsv ├── Rahman_MBS2016 │ ├── Rahman_MBS2016.yaml │ ├── experimentalCondition_Rahman_MBS2016.tsv │ ├── measurementData_Rahman_MBS2016.tsv │ ├── model_Rahman_MBS2016.xml │ ├── observables_Rahman_MBS2016.tsv │ ├── parameters_Rahman_MBS2016.tsv │ ├── simulatedData_Rahman_MBS2016.tsv │ └── visualizationSpecification_Rahman_MBS2016.tsv ├── Raia_CancerResearch2011 │ ├── Raia_CancerResearch2011.yaml │ ├── experimentalCondition_Raia_CancerResearch2011.tsv │ ├── measurementData_Raia_CancerResearch2011.tsv │ ├── model_Raia_CancerResearch2011.xml │ ├── observables_Raia_CancerResearch2011.tsv │ ├── parameters_Raia_CancerResearch2011.tsv │ ├── simulatedData_Raia_CancerResearch2011.tsv │ └── visualizationSpecification_Raia_CancerResearch2011.tsv ├── Raimundez_PCB2020 │ ├── Raimundez_PCB2020.yaml │ ├── experimentalCondition_Raimundez_PCB2020.tsv │ ├── measurementData_Raimundez_PCB2020.tsv │ ├── model_Raimundez_PCB2020.xml │ ├── observables_Raimundez_PCB2020.tsv │ ├── parameters_Raimundez_PCB2020.tsv │ ├── simulatedData_Raimundez_PCB2020.tsv │ ├── visualizationSpecification_Raimundez_PCB2020.tsv │ ├── visualizationSpecification_Raimundez_PCB2020_Figure2C.tsv │ ├── visualizationSpecification_Raimundez_PCB2020_Figure2D.tsv │ ├── visualizationSpecification_Raimundez_PCB2020_Figure3C.tsv │ ├── visualizationSpecification_Raimundez_PCB2020_Figure3D.tsv │ ├── visualizationSpecification_Raimundez_PCB2020_FigureS3.tsv │ ├── visualizationSpecification_Raimundez_PCB2020_FigureS3E.tsv │ └── visualizationSpecification_Raimundez_PCB2020_FigureS4.tsv ├── SalazarCavazos_MBoC2020 │ ├── SalazarCavazos_MBoC2020.yaml │ ├── experimentalCondition_SalazarCavazos_MBoC2020.tsv │ ├── measurementData_SalazarCavazos_MBoC2020.tsv │ ├── model_SalazarCavazos_MBoC2020.xml │ ├── observables_SalazarCavazos_MBoC2020.tsv │ ├── parameters_SalazarCavazos_MBoC2020.tsv │ ├── simulatedData_SalazarCavazos_MBoC2020.tsv │ └── visualizationSpecification_SalazarCavazos_MBoC2020.tsv ├── Schwen_PONE2014 │ ├── Schwen_PONE2014.yaml │ ├── experimentalCondition_Schwen_PONE2014.tsv │ ├── measurementData_Schwen_PONE2014.tsv │ ├── model_Schwen_PONE2014.xml │ ├── observables_Schwen_PONE2014.tsv │ ├── parameters_Schwen_PONE2014.tsv │ ├── simulatedData_Schwen_PONE2014.tsv │ └── visualizationSpecification_Schwen_PONE2014.tsv ├── Smith_BMCSystBiol2013 │ ├── README.md │ ├── Smith_BMCSystBiol2013.yaml │ ├── experimentalCondition_Smith_BMCSystBiol2013.tsv │ ├── generate_petab.py │ ├── measurementData_Smith_BMCSystBiol2013.tsv │ ├── model_Smith_BMCSystBiol2013.xml │ ├── observables_Smith_BMCSystBiol2013.tsv │ ├── parameters_Smith_BMCSystBiol2013.tsv │ ├── sim_test │ │ ├── Smith_BMCSystBiol2013_test.yaml │ │ ├── experimentalCondition_Smith_BMCSystBiol2013_test.tsv │ │ ├── measurementData_Smith_BMCSystBiol2013_test.tsv │ │ ├── model_Smith_BMCSystBiol2013.xml │ │ ├── observables_Smith_BMCSystBiol2013_test.tsv │ │ └── parameters_Smith_BMCSystBiol2013.tsv │ ├── simulatedData_Smith_BMCSystBiol2013.tsv │ ├── visualization.pdf │ └── visualizationSpecification_Smith_BMCSystBiol2013.tsv ├── Sneyd_PNAS2002 │ ├── Sneyd_PNAS2002.yaml │ ├── experimentalCondition_Sneyd_PNAS2002.tsv │ ├── measurementData_Sneyd_PNAS2002.tsv │ ├── model_Sneyd_PNAS2002.xml │ ├── observables_Sneyd_PNAS2002.tsv │ ├── parameters_Sneyd_PNAS2002.tsv │ ├── simulatedData_Sneyd_PNAS2002.tsv │ ├── visualizationSpecification_Sneyd_PNAS2002.tsv │ └── visualizationSpecification_Sneyd_PNAS2002_subplots.tsv ├── Weber_BMC2015 │ ├── Weber_BMC2015.yaml │ ├── experimentalCondition_Weber_BMC2015.tsv │ ├── measurementData_Weber_BMC2015.tsv │ ├── model_Weber_BMC2015.xml │ ├── observables_Weber_BMC2015.tsv │ ├── parameters_Weber_BMC2015.tsv │ ├── simulatedData_Weber_BMC2015.tsv │ └── visualizationSpecification_Weber_BMC2015.tsv ├── Zhao_QuantBiol2020 │ ├── Zhao_QuantBiol2020.yaml │ ├── experimentalCondition_Zhao_QuantBiol2020.tsv │ ├── measurementData_test_Zhao_QuantBiol2020.tsv │ ├── measurementData_training_Zhao_QuantBiol2020.tsv │ ├── model_Zhao_QuantBiol2020.xml │ ├── observable_Zhao_QuantBiol2020.tsv │ ├── parameters_Zhao_QuantBiol2020.tsv │ ├── petab_test_Zhao_QuantBiol2020.yaml │ ├── simulatedData_Zhao_QuantBiol2020.tsv │ └── 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