From 5be375a257f55a1c976bb14843993d63b9dae095 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 14 Jul 2025 07:42:36 +0200 Subject: [PATCH 1/4] Convert to PEtab v2 --- v1_v2.py | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100755 v1_v2.py diff --git a/v1_v2.py b/v1_v2.py new file mode 100755 index 0000000..db65aa5 --- /dev/null +++ b/v1_v2.py @@ -0,0 +1,30 @@ +#!/usr/bin/env python3 +"""Convert benchmark problems from PEtab v1 to v2 format.""" + +import logging +import benchmark_models_petab +from petab.v2.petab1to2 import petab1to2 +from pathlib import Path + +def main(): + logging.basicConfig(level=logging.INFO) + v2_root = Path(__file__).resolve().parent / "v2" + + for problem_id in benchmark_models_petab.MODELS: + convert(problem_id, output_dir=v2_root / problem_id) + +def convert(problem_id: str, output_dir: Path): + """Convert a PEtab v1 problem to v2 format.""" + logging.info(f"Converting {problem_id}...") + yaml_path = benchmark_models_petab.get_problem_yaml_path(problem_id) + try: + petab1to2(yaml_path, output_dir) + except NotImplementedError as e: + logging.warning(f"Skipping {problem_id}: {e}") + return + + logging.info(f"Converted {problem_id}.") + + +if __name__ == "__main__": + main() From c1c319887b5963ed9fc85b47f000f173698db5e8 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Tue, 22 Jul 2025 12:45:44 +0200 Subject: [PATCH 2/4] .. --- v1_v2.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/v1_v2.py b/v1_v2.py index db65aa5..17f978a 100755 --- a/v1_v2.py +++ b/v1_v2.py @@ -11,6 +11,11 @@ def main(): v2_root = Path(__file__).resolve().parent / "v2" for problem_id in benchmark_models_petab.MODELS: + if problem_id == "Froehlich_CellSystems2018": + # naive conversion generates huge condition table + logging.warning("Skipping Froehlich_CellSystems2018 due to performance issues.") + continue + convert(problem_id, output_dir=v2_root / problem_id) def convert(problem_id: str, output_dir: Path): From 8d9d7bddfdde4926e179f2768ce3de08dc8cb995 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Tue, 22 Jul 2025 12:46:55 +0200 Subject: [PATCH 3/4] convert --- .../Alkan_SciSignal2018.yaml | 17 + ...erimentalCondition_Alkan_SciSignal2018.tsv | 220 + v2/Alkan_SciSignal2018/experiments.tsv | 74 + .../measurementData_Alkan_SciSignal2018.tsv | 1734 + .../model_Alkan_SciSignal2018.xml | 2832 ++ .../observables_Alkan_SciSignal2018.tsv | 13 + .../parameters_Alkan_SciSignal2018.tsv | 72 + .../Armistead_CellDeathDis2024.yaml | 17 + ...lConditions_Armistead_CellDeathDis2024.tsv | 11 + v2/Armistead_CellDeathDis2024/experiments.tsv | 3 + ...urementData_Armistead_CellDeathDis2024.tsv | 59 + .../model_Armistead_CellDeathDis2024.xml | 356 + ...observables_Armistead_CellDeathDis2024.tsv | 5 + .../parameters_Armistead_CellDeathDis2024.tsv | 15 + v2/Bachmann_MSB2011/Bachmann_MSB2011.yaml | 17 + ...experimentalCondition_Bachmann_MSB2011.tsv | 289 + v2/Bachmann_MSB2011/experiments.tsv | 37 + .../measurementData_Bachmann_MSB2011.tsv | 542 + .../model_Bachmann_MSB2011.xml | 1146 + .../observables_Bachmann_MSB2011.tsv | 21 + .../parameters_Bachmann_MSB2011.tsv | 116 + .../Beer_MolBioSystems2014.yaml | 17 + ...mentalCondition_Beer_MolBioSystems2014.tsv | 115 + v2/Beer_MolBioSystems2014/experiments.tsv | 20 + ...measurementData_Beer_MolBioSystems2014.tsv | 27133 ++++++++++++++ .../model_Beer_MolBioSystems2014.xml | 224 + .../observables_Beer_MolBioSystems2014.tsv | 3 + .../parameters_Beer_MolBioSystems2014.tsv | 73 + v2/Bertozzi_PNAS2020/conditions.tsv | 9 + v2/Bertozzi_PNAS2020/experiments.tsv | 3 + v2/Bertozzi_PNAS2020/measurements.tsv | 23 + v2/Bertozzi_PNAS2020/model.xml | 101 + v2/Bertozzi_PNAS2020/observables.tsv | 3 + v2/Bertozzi_PNAS2020/parameters.tsv | 9 + v2/Bertozzi_PNAS2020/problem.yaml | 17 + .../Blasi_CellSystems2016.yaml | 16 + ...imentalCondition_Blasi_CellSystems2016.tsv | 1 + .../measurementData_Blasi_CellSystems2016.tsv | 253 + .../model_Blasi_CellSystems2016.xml | 1055 + .../observables_Blasi_CellSystems2016.tsv | 17 + .../parameters_Blasi_CellSystems2016.tsv | 11 + .../Boehm_JProteomeRes2014.yaml | 16 + ...mentalCondition_Boehm_JProteomeRes2014.tsv | 1 + ...measurementData_Boehm_JProteomeRes2014.tsv | 49 + .../model_Boehm_JProteomeRes2014.xml | 290 + .../observables_Boehm_JProteomeRes2014.tsv | 4 + .../parameters_Boehm_JProteomeRes2014.tsv | 12 + .../Borghans_BiophysChem1997.yaml | 16 + ...ntalCondition_Borghans_BiophysChem1997.tsv | 1 + ...asurementData_Borghans_BiophysChem1997.tsv | 112 + .../model_Borghans_BiophysChem1997.xml | 367 + .../observables_Borghans_BiophysChem1997.tsv | 2 + .../parameters_Borghans_BiophysChem1997.tsv | 24 + v2/Brannmark_JBC2010/Brannmark_JBC2010.yaml | 17 + ...xperimentalCondition_Brannmark_JBC2010.tsv | 33 + v2/Brannmark_JBC2010/experiments.tsv | 17 + .../measurementData_Brannmark_JBC2010.tsv | 44 + .../model_Brannmark_JBC2010.xml | 400 + .../observables_Brannmark_JBC2010.tsv | 4 + .../parameters_Brannmark_JBC2010.tsv | 23 + v2/Bruno_JExpBot2016/Bruno_JExpBot2016.yaml | 17 + ...xperimentalCondition_Bruno_JExpBot2016.tsv | 67 + v2/Bruno_JExpBot2016/experiments.tsv | 7 + .../measurementData_Bruno_JExpBot2016.tsv | 78 + .../model_Bruno_JExpBot2016.xml | 222 + .../observables_Bruno_JExpBot2016.tsv | 7 + .../parameters_Bruno_JExpBot2016.tsv | 14 + v2/Chen_MSB2009/Chen_MSB2009.yaml | 17 + .../experimentalCondition_Chen_MSB2009.tsv | 9 + v2/Chen_MSB2009/experiments.tsv | 5 + .../measurementData_Chen_MSB2009.tsv | 121 + v2/Chen_MSB2009/model_Chen_MSB2009.xml | 29087 ++++++++++++++++ v2/Chen_MSB2009/observables_Chen_MSB2009.tsv | 4 + v2/Chen_MSB2009/parameters_Chen_MSB2009.tsv | 189 + .../Crauste_CellSystems2017.yaml | 16 + ...entalCondition_Crauste_CellSystems2017.tsv | 1 + ...easurementData_Crauste_CellSystems2017.tsv | 22 + .../model_Crauste_CellSystems2017.xml | 283 + .../observables_Crauste_CellSystems2017.tsv | 5 + .../parameters_Crauste_CellSystems2017.tsv | 13 + v2/Elowitz_Nature2000/Elowitz_Nature2000.yaml | 16 + ...perimentalCondition_Elowitz_Nature2000.tsv | 1 + .../measurementData_Elowitz_Nature2000.tsv | 59 + .../model_Elowitz_Nature2000.xml | 665 + .../observables_Elowitz_Nature2000.tsv | 2 + .../parameters_Elowitz_Nature2000.tsv | 22 + .../Fiedler_BMCSystBiol2016.yaml | 17 + ...entalCondition_Fiedler_BMCSystBiol2016.tsv | 7 + v2/Fiedler_BMCSystBiol2016/experiments.tsv | 4 + ...easurementData_Fiedler_BMCSystBiol2016.tsv | 73 + .../model_Fiedler_BMCSystBiol2016.xml | 3540 ++ .../observables_Fiedler_BMCSystBiol2016.tsv | 3 + .../parameters_Fiedler_BMCSystBiol2016.tsv | 26 + .../Fujita_SciSignal2010.yaml | 17 + ...rimentalCondition_Fujita_SciSignal2010.tsv | 49 + v2/Fujita_SciSignal2010/experiments.tsv | 7 + ...surementData_step_Fujita_SciSignal2010.tsv | 145 + .../model_Fujita_SciSignal2010.xml | 334 + .../observables_Fujita_SciSignal2010.tsv | 4 + .../parameters_Fujita_SciSignal2010.tsv | 20 + .../Giordano_Nature2020.yaml | 17 + 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.../Laske_PLOSComputBiol2019.yaml | 17 + ...ntalCondition_Laske_PLOSComputBiol2019.tsv | 7 + v2/Laske_PLOSComputBiol2019/experiments.tsv | 4 + ...asurementData_Laske_PLOSComputBiol2019.tsv | 43 + .../model_Laske_PLOSComputBiol2019.xml | 3271 ++ .../observables_Laske_PLOSComputBiol2019.tsv | 14 + .../parameters_Laske_PLOSComputBiol2019.tsv | 14 + .../Lucarelli_CellSystems2018.yaml | 17 + ...talCondition_Lucarelli_CellSystems2018.tsv | 65 + v2/Lucarelli_CellSystems2018/experiments.tsv | 17 + ...surementData_Lucarelli_CellSystems2018.tsv | 1756 + .../model_Lucarelli_CellSystems2018.xml | 1791 + .../observables_Lucarelli_CellSystems2018.tsv | 66 + .../parameters_Lucarelli_CellSystems2018.tsv | 118 + .../Okuonghae_ChaosSolitonsFractals2020.yaml | 17 + ...ns_Okuonghae_ChaosSolitonsFractals2020.tsv | 3 + .../experiments.tsv | 2 + ...ta_Okuonghae_ChaosSolitonsFractals2020.tsv | 93 + ...el_Okuonghae_ChaosSolitonsFractals2020.xml | 934 + ...es_Okuonghae_ChaosSolitonsFractals2020.tsv | 3 + 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sd_wip1_mRNA_fold +experiment____model1_data82 p21_mRNA_fold 2.0180692672729497 12.0 scale_p21_mRNA_fold sd_p21_mRNA_fold +experiment____model1_data82 Wip1_mRNA_fold 1.7269387245178205 12.0 scale_wip1_mRNA_fold sd_wip1_mRNA_fold +experiment____model1_data83 p21_mRNA_fold 1.0 12.0 scale_p21_mRNA_fold sd_p21_mRNA_fold +experiment____model1_data83 Wip1_mRNA_fold 1.0 12.0 scale_wip1_mRNA_fold sd_wip1_mRNA_fold +experiment____model1_data12 p21_mRNA_fold 1.0 12.0 scale_p21_mRNA_fold sd_p21_mRNA_fold +experiment____model1_data12 Wip1_mRNA_fold 1.0 12.0 scale_wip1_mRNA_fold sd_wip1_mRNA_fold +experiment____model1_data85 p21_mRNA_fold 5.26819610595703 12.0 scale_p21_mRNA_fold sd_p21_mRNA_fold +experiment____model1_data85 Wip1_mRNA_fold 1.52881181240082 12.0 scale_wip1_mRNA_fold sd_wip1_mRNA_fold +experiment____model1_data86 p21_mRNA_fold 7.14427137374878 12.0 scale_p21_mRNA_fold sd_p21_mRNA_fold +experiment____model1_data86 Wip1_mRNA_fold 1.97156536579132 12.0 scale_wip1_mRNA_fold sd_wip1_mRNA_fold +experiment____model1_data87 p21_mRNA_fold 9.27304553985596 12.0 scale_p21_mRNA_fold sd_p21_mRNA_fold +experiment____model1_data87 Wip1_mRNA_fold 2.0693666934967 12.0 scale_wip1_mRNA_fold sd_wip1_mRNA_fold +experiment____model1_data88 p21_mRNA_fold 11.739509582519501 12.0 scale_p21_mRNA_fold sd_p21_mRNA_fold +experiment____model1_data88 Wip1_mRNA_fold 3.2077572345733603 12.0 scale_wip1_mRNA_fold sd_wip1_mRNA_fold +experiment____model1_data89 p21_mRNA_fold 12.7283039093018 12.0 scale_p21_mRNA_fold sd_p21_mRNA_fold +experiment____model1_data89 Wip1_mRNA_fold 3.72004055976868 12.0 scale_wip1_mRNA_fold sd_wip1_mRNA_fold +experiment____model1_data90 p21_mRNA_fold 11.2542142868042 12.0 scale_p21_mRNA_fold sd_p21_mRNA_fold +experiment____model1_data90 Wip1_mRNA_fold 3.2235579490661603 12.0 scale_wip1_mRNA_fold sd_wip1_mRNA_fold diff --git a/v2/Alkan_SciSignal2018/model_Alkan_SciSignal2018.xml b/v2/Alkan_SciSignal2018/model_Alkan_SciSignal2018.xml new file mode 100644 index 0000000..a7bf3e7 --- /dev/null +++ b/v2/Alkan_SciSignal2018/model_Alkan_SciSignal2018.xml @@ -0,0 +1,2832 @@ + + + + + + 
PEtab implementation of the model from Alkan et al. (2018), Science Signaling  24 Jul 2018: Vol. 11, Issue 540, eaat0229
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+ + + + + Dox_level + 6 + + + + + + Dox_level + 6 + + + + p_mrna_exp_inh_dox_kd + 6 + + + + + 1 + + + + + + + + + + + + + + p21_mRNA_G2 + p_p21_mrna_turn + + + + + + + + + + + + + + + + p21_mRNA_G2 + p_p21_turn + + + + + + + + + + + + + p21_G2 + p_p21_turn + + + + + + + + + + + + + + + + + + p_wip1_mrna_turn + pp53_G2 + + + + + + p_mrna_exp_inh_dox + + + + + Dox_level + 6 + + + + + + Dox_level + 6 + + + + p_mrna_exp_inh_dox_kd + 6 + + + + + 1 + + + + + + + + + + + + + + Wip1_mRNA_G2 + p_wip1_mrna_turn + + + + + + + + + + + + + + + + Wip1_mRNA_G2 + p_wip1_turn + + + + + + + + + + + + + Wip1_G2 + p_wip1_turn + + + + + + + + + + + + + + + + + + + pATM_G2 + + p_h2ax_act_atm + + + yH2AX_G2 + 1 + + + + + + + + + + + + + + + + + + + + pATR_G2 + + p_h2ax_act_atr + + + yH2AX_G2 + 1 + + + + + + + + + + + + + + + + + + + + pDNAPK_G2 + + p_h2ax_act_dnapk + + + yH2AX_G2 + 1 + + + + + + + + + + + + + + p_h2ax_dea + yH2AX_G2 + + + + + + + diff --git a/v2/Alkan_SciSignal2018/observables_Alkan_SciSignal2018.tsv b/v2/Alkan_SciSignal2018/observables_Alkan_SciSignal2018.tsv new file mode 100644 index 0000000..8b7e787 --- /dev/null +++ b/v2/Alkan_SciSignal2018/observables_Alkan_SciSignal2018.tsv @@ -0,0 +1,13 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +CellsCasp_count Cells_Apo4 + Cells_Apo_ReOx noiseParameter1_CellsCasp_count noiseParameter1_CellsCasp_count +Cells_count Cells + Cells_Cycle_S + Cells_Cycle_G2 + Cells_SSBDamage_S + Cells_DSBDamage_S + Cells_DSBDamage_G2 + Cells_Apo + Cells_Apo1 + Cells_Apo2 + Cells_Apo3 + Cells_Apo4 + Cells_Apo_ReOx noiseParameter1_Cells_count noiseParameter1_Cells_count +Wip1_mRNA_fold observableParameter1_Wip1_mRNA_fold * (Wip1_mRNA_G2 + Wip1_mRNA_S) + 1 noiseParameter1_Wip1_mRNA_fold observableParameter1_Wip1_mRNA_fold noiseParameter1_Wip1_mRNA_fold +p21_mRNA_fold observableParameter1_p21_mRNA_fold * (p21_mRNA_S + p21_mRNA_G2) + 1 noiseParameter1_p21_mRNA_fold observableParameter1_p21_mRNA_fold noiseParameter1_p21_mRNA_fold +pATM_au observableParameter1_pATM_au * (pATM_G2 + pATM_S) noiseParameter1_pATM_au observableParameter1_pATM_au noiseParameter1_pATM_au +pChk1_au observableParameter1_pChk1_au * (pChk1_G2 + pChk1_S) noiseParameter1_pChk1_au observableParameter1_pChk1_au noiseParameter1_pChk1_au +pChk2_au observableParameter1_pChk2_au * (pChk2_S + pChk2_G2) noiseParameter1_pChk2_au observableParameter1_pChk2_au noiseParameter1_pChk2_au +pDNAPK_au observableParameter1_pDNAPK_au * (pDNAPK_G2 + pDNAPK_S) noiseParameter1_pDNAPK_au observableParameter1_pDNAPK_au noiseParameter1_pDNAPK_au +pp53_au observableParameter1_pp53_au * (pp53_S + pp53_G2) noiseParameter1_pp53_au observableParameter1_pp53_au noiseParameter1_pp53_au +tp21_au observableParameter1_tp21_au * (p21_S + p21_G2) noiseParameter1_tp21_au observableParameter1_tp21_au noiseParameter1_tp21_au +tp53_au observableParameter1_tp53_au * (pp53_S + pp53_G2) noiseParameter1_tp53_au observableParameter1_tp53_au noiseParameter1_tp53_au +yH2AX_au observableParameter1_yH2AX_au * (yH2AX_S + yH2AX_G2) noiseParameter1_yH2AX_au observableParameter1_yH2AX_au noiseParameter1_yH2AX_au diff --git a/v2/Alkan_SciSignal2018/parameters_Alkan_SciSignal2018.tsv b/v2/Alkan_SciSignal2018/parameters_Alkan_SciSignal2018.tsv new file mode 100644 index 0000000..247e39f --- /dev/null +++ b/v2/Alkan_SciSignal2018/parameters_Alkan_SciSignal2018.tsv @@ -0,0 +1,72 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorParameters +init_Cells init_Cells 0.1 1000.0 1.0 false +init_Cells_Cycle_G2_rel init_Cells_Cycle_G2_rel 0.0 1.0 0.4 false +init_Cells_Cycle_S_rel init_Cells_Cycle_S_rel 0.0 1.0 0.5 false +init_Space init_Space 1e-05 1000.0 100.0 false +k_apo_dsb_g2 k_apo_dsb_g2 1e-05 1000.0 1e-05 false +k_apo_dsb_s k_apo_dsb_s 1e-05 1000.0 1e-05 false +k_apo_ssb k_apo_ssb 1e-05 1000.0 1e-05 false +k_cyc_arr_chk1 k_cyc_arr_chk1 1.0 1000.0 999.9999999999314 false +k_cyc_arr_chk2 k_cyc_arr_chk2 1.0 1000.0 1000.0 false +k_damage_dox_dsb k_damage_dox_dsb 1.0 1000.0 214.76028158340145 true +k_damage_gem_ssb k_damage_gem_ssb 1.0 1000.0 49.87004701128138 true +k_damage_sn38_ssb k_damage_sn38_ssb 1.0 1000.0 174.43473709802518 true +k_death k_death 0.01 1.0 0.10317784266317824 false +k_death_delay k_death_delay 0.01 1.0 0.14104161220660824 false +k_death_reox k_death_reox 0.01 1.0 0.03412462375216097 true +k_dox_apo k_dox_apo 0.01 0.1 0.04880099644550196 true +k_dox_kd k_dox_kd 1e-05 1000.0 0.3564511334262443 false +k_lyse k_lyse 1e-05 1000.0 10.0 false +k_rep_hr k_rep_hr 1e-05 1.0 1.000000000000092e-05 true +k_rep_nhej k_rep_nhej 1e-05 1.0 0.32419762816439085 true +k_rep_nhej_sat k_rep_nhej_sat 1e-05 1.0 0.006867002980361337 true +k_rep_s k_rep_s 1e-05 1.0 1.000000000000092e-05 true +k_ssb_to_dsb k_ssb_to_dsb 1e-05 1.0 0.03049962682347336 true +k_ssb_to_dsb_sn38 k_ssb_to_dsb_sn38 1e-05 1000.0 999.999674332203 true +kt kt 0.1 1.0 0.18739209303744497 true +kt_apo kt_apo 0.01 1.0 0.12350156944465318 false +p_atm_act_dsb p_atm_act_dsb 0.01 1.0 0.9999999999999243 true +p_atr_act_atm p_atr_act_atm 0.01 1.0 0.09021825700580331 true +p_atr_act_ssb p_atr_act_ssb 0.01 1.0 0.07918341948722293 true +p_chk1_act p_chk1_act 0.01 10.0 8.432499250969515 true +p_chk1_dea_wip1 p_chk1_dea_wip1 0.01 10.0 9.999999988851322 true +p_chk2_act p_chk2_act 0.01 10.0 6.893081978138526 true +p_chk2_dea_wip1 p_chk2_dea_wip1 0.01 10.0 9.999999999999195 true +p_dnapk_act p_dnapk_act 0.01 10.0 9.999997649241926 true +p_dnapk_dea_wip1 p_dnapk_dea_wip1 0.01 10.0 6.588069227084837 true +p_h2ax_act_atm p_h2ax_act_atm 1e-05 1000.0 0.0013544454800986025 true +p_h2ax_act_atr p_h2ax_act_atr 1e-05 1000.0 0.005377641612290161 true +p_h2ax_act_dnapk p_h2ax_act_dnapk 1e-05 1000.0 1.0000000000096242e-05 true +p_h2ax_dea p_h2ax_dea 1e-05 1000.0 1.0000346614441236e-05 true +p_mrna_exp_inh_dox p_mrna_exp_inh_dox 1.0 1000.0 999.999999999908 true +p_mrna_exp_inh_dox_kd p_mrna_exp_inh_dox_kd 0.01 10.0 0.3564511794976623 false +p_p21_mrna_turn p_p21_mrna_turn 0.01 1.0 0.10935440467323092 true +p_p21_turn p_p21_turn 0.01 1.0 0.9999999999999213 true +p_p53_act_atm p_p53_act_atm 0.01 1.0 0.17266754231557666 true +p_p53_act_atr p_p53_act_atr 1e-05 1.0 1.000000000000092e-05 true +p_p53_act_chk1 p_p53_act_chk1 1e-05 1000.0 1.0000000000085424e-05 true +p_p53_act_chk2 p_p53_act_chk2 1e-05 1000.0 0.05123913415198176 true +p_wip1_mrna_turn p_wip1_mrna_turn 0.1 10.0 3.401016300696056 true +p_wip1_turn p_wip1_turn 0.1 10.0 3.41164292406599 true +scale_p21_mRNA_fold scale_p21_mRNA_fold 1e-05 1000.0 19.80629123796992 true +scale_patm_au scale_patm_au 1e-05 1000.0 0.9204521777169525 true +scale_pchk1_au scale_pchk1_au 1e-05 1000.0 1.050009497949471 true +scale_pchk2_au scale_pchk2_au 1e-05 1000.0 1.5255622653671697 true +scale_pdnapk_au scale_pdnapk_au 1e-05 1000.0 0.46781331017373756 true +scale_pp53_au scale_pp53_au 1e-05 1000.0 1.1357598257673152 true +scale_tp21_au scale_tp21_au 1e-05 1000.0 3.9178550677340596 true +scale_tp53_au scale_tp53_au 1e-05 1000.0 1.4313361828755429 true +scale_wip1_mRNA_fold scale_wip1_mRNA_fold 1e-05 1000.0 2.2770003237741387 true +scale_yh2ax_au scale_yh2ax_au 1e-05 1000.0 60.50316673653378 true +sd_count_abs sd_count_abs 1e-05 1000.0 0.1 true +sd_count_casp_abs sd_count_casp_abs 1e-05 1000.0 0.1 true +sd_p21_mRNA_fold sd_p21_mRNA_fold 1e-05 1000.0 1.0 true +sd_patm_au sd_patm_au 1e-05 1000.0 0.07943282347242814 true +sd_pchk1_au sd_pchk1_au 1e-05 1000.0 0.1 true +sd_pchk2_au sd_pchk2_au 1e-05 1000.0 0.31622776601683794 true +sd_pdnapk_au sd_pdnapk_au 1e-05 1000.0 0.19952623149688797 true +sd_pp53_au sd_pp53_au 1e-05 1000.0 0.19952623149688797 true +sd_tp21_au sd_tp21_au 1e-05 1000.0 0.31622776601683794 true +sd_tp53_au sd_tp53_au 1e-05 1000.0 0.19952623149688797 true +sd_wip1_mRNA_fold sd_wip1_mRNA_fold 1e-05 1000.0 1.0 true +sd_yh2ax_au sd_yh2ax_au 1e-05 1000.0 0.12589254117941673 true diff --git a/v2/Armistead_CellDeathDis2024/Armistead_CellDeathDis2024.yaml b/v2/Armistead_CellDeathDis2024/Armistead_CellDeathDis2024.yaml new file mode 100644 index 0000000..cb45dd0 --- /dev/null +++ b/v2/Armistead_CellDeathDis2024/Armistead_CellDeathDis2024.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Armistead_CellDeathDis2024.tsv +model_files: + model_Armistead_CellDeathDis2024: + location: model_Armistead_CellDeathDis2024.xml + language: sbml +measurement_files: +- measurementData_Armistead_CellDeathDis2024.tsv +condition_files: +- experimentalConditions_Armistead_CellDeathDis2024.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Armistead_CellDeathDis2024.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Armistead_CellDeathDis2024/experimentalConditions_Armistead_CellDeathDis2024.tsv b/v2/Armistead_CellDeathDis2024/experimentalConditions_Armistead_CellDeathDis2024.tsv new file mode 100644 index 0000000..30eea79 --- /dev/null +++ b/v2/Armistead_CellDeathDis2024/experimentalConditions_Armistead_CellDeathDis2024.tsv @@ -0,0 +1,11 @@ +conditionId targetId targetValue +wild_type S_on 1.0 +mutant S_on 0.0 +wild_type Cer 0.988 +mutant Cer 0.822 +wild_type Sphinga 0.000732 +mutant Sphinga 0.000795 +wild_type Sphingo 0.000395 +mutant Sphingo 0.000364 +wild_type S1P 1.551 +mutant S1P 2.07 diff --git a/v2/Armistead_CellDeathDis2024/experiments.tsv b/v2/Armistead_CellDeathDis2024/experiments.tsv new file mode 100644 index 0000000..faff654 --- /dev/null +++ b/v2/Armistead_CellDeathDis2024/experiments.tsv @@ -0,0 +1,3 @@ +experimentId conditionId time +experiment____mutant mutant 0 +experiment____wild_type wild_type 0 diff --git a/v2/Armistead_CellDeathDis2024/measurementData_Armistead_CellDeathDis2024.tsv b/v2/Armistead_CellDeathDis2024/measurementData_Armistead_CellDeathDis2024.tsv new file mode 100644 index 0000000..613ca42 --- /dev/null +++ b/v2/Armistead_CellDeathDis2024/measurementData_Armistead_CellDeathDis2024.tsv @@ -0,0 +1,59 @@ +experimentId observableId measurement time noiseParameters replicateId datasetId +experiment____wild_type Sphinga_obs 0.000806 0 sd_Sphinga_obs R1 wt_day2 +experiment____wild_type Sphinga_obs 0.000618 0 sd_Sphinga_obs R2 wt_day2 +experiment____wild_type Sphinga_obs 0.000675 0 sd_Sphinga_obs R3 wt_day2 +experiment____wild_type Sphinga_obs 0.000828 0 sd_Sphinga_obs R4 wt_day2 +experiment____wild_type Sphinga_obs 0.000176620209326007 2 sd_Sphinga_obs R1 wt_day4 +experiment____wild_type Sphinga_obs 0.000144832895774474 2 sd_Sphinga_obs R2 wt_day4 +experiment____wild_type Sphinga_obs 0.000137134901470714 2 sd_Sphinga_obs R3 wt_day4 +experiment____wild_type Sphinga_obs 0.000181912527619117 2 sd_Sphinga_obs R4 wt_day4 +experiment____wild_type Cer_obs 1.02701422984826 0 sd_Cer_obs R1 wt_day2 +experiment____wild_type Cer_obs 0.886288740504458 0 sd_Cer_obs R2 wt_day2 +experiment____wild_type Cer_obs 0.945776256657445 0 sd_Cer_obs R3 wt_day2 +experiment____wild_type Cer_obs 1.09426905460355 0 sd_Cer_obs R4 wt_day2 +experiment____wild_type Cer_obs 0.612244538629556 2 sd_Cer_obs R1 wt_day4 +experiment____wild_type Cer_obs 0.665790676225569 2 sd_Cer_obs R2 wt_day4 +experiment____wild_type Cer_obs 0.712634629073372 2 sd_Cer_obs R3 wt_day4 +experiment____wild_type Cer_obs 0.641981159099886 2 sd_Cer_obs R4 wt_day4 +experiment____wild_type Sphingo_obs 0.000384239736109822 0 sd_Sphingo_obs R1 wt_day2 +experiment____wild_type Sphingo_obs 0.000391938220558207 0 sd_Sphingo_obs R2 wt_day2 +experiment____wild_type Sphingo_obs 0.000371485514201383 0 sd_Sphingo_obs R3 wt_day2 +experiment____wild_type Sphingo_obs 0.000431025477692304 0 sd_Sphingo_obs R4 wt_day2 +experiment____wild_type Sphingo_obs 0.000334877541530201 2 sd_Sphingo_obs R1 wt_day4 +experiment____wild_type Sphingo_obs 0.000231658738329562 2 sd_Sphingo_obs R2 wt_day4 +experiment____wild_type Sphingo_obs 0.000203229934963182 2 sd_Sphingo_obs R3 wt_day4 +experiment____wild_type Sphingo_obs 0.000227793942150799 2 sd_Sphingo_obs R4 wt_day4 +experiment____wild_type S1P_obs 1.421 0 sd_S1P_obs R1 wt_day2 +experiment____wild_type S1P_obs 1.682 0 sd_S1P_obs R2 wt_day2 +experiment____wild_type S1P_obs 1.614 0 sd_S1P_obs R3 wt_day2 +experiment____wild_type S1P_obs 1.498 0 sd_S1P_obs R4 wt_day2 +experiment____wild_type S1P_obs 1.541 0 sd_S1P_obs R5 wt_day2 +experiment____mutant Sphinga_obs 0.000818 0 sd_Sphinga_obs R1 mut_day2 +experiment____mutant Sphinga_obs 0.000761 0 sd_Sphinga_obs R2 mut_day2 +experiment____mutant Sphinga_obs 0.000766 0 sd_Sphinga_obs R3 mut_day2 +experiment____mutant Sphinga_obs 0.000835 0 sd_Sphinga_obs R4 mut_day2 +experiment____mutant Sphinga_obs 0.000243420646439453 2 sd_Sphinga_obs R1 mut_day4 +experiment____mutant Sphinga_obs 0.000239502545840865 2 sd_Sphinga_obs R2 mut_day4 +experiment____mutant Sphinga_obs 0.000234873603648106 2 sd_Sphinga_obs R3 mut_day4 +experiment____mutant Sphinga_obs 0.000233253355552097 2 sd_Sphinga_obs R4 mut_day4 +experiment____mutant Cer_obs 0.892791183665478 0 sd_Cer_obs R1 mut_day2 +experiment____mutant Cer_obs 0.677804963784483 0 sd_Cer_obs R2 mut_day2 +experiment____mutant Cer_obs 0.857649492135442 0 sd_Cer_obs R3 mut_day2 +experiment____mutant Cer_obs 0.857816589043671 0 sd_Cer_obs R4 mut_day2 +experiment____mutant Cer_obs 0.877785182287324 2 sd_Cer_obs R1 mut_day4 +experiment____mutant Cer_obs 1.02057671816819 2 sd_Cer_obs R2 mut_day4 +experiment____mutant Cer_obs 0.96666151369505 2 sd_Cer_obs R3 mut_day4 +experiment____mutant Cer_obs 0.827292874601032 2 sd_Cer_obs R4 mut_day4 +experiment____mutant Sphingo_obs 0.000417035014112306 0 sd_Sphingo_obs R1 mut_day2 +experiment____mutant Sphingo_obs 0.000366195755858261 0 sd_Sphingo_obs R2 mut_day2 +experiment____mutant Sphingo_obs 0.0003291610891578 0 sd_Sphingo_obs R3 mut_day2 +experiment____mutant Sphingo_obs 0.000341631934155604 0 sd_Sphingo_obs R4 mut_day2 +experiment____mutant Sphingo_obs 0.000323262438726203 2 sd_Sphingo_obs R1 mut_day4 +experiment____mutant Sphingo_obs 0.000316663676062039 2 sd_Sphingo_obs R2 mut_day4 +experiment____mutant Sphingo_obs 0.000279704837681421 2 sd_Sphingo_obs E3 mut_day4 +experiment____mutant Sphingo_obs 0.000242795904444989 2 sd_Sphingo_obs E4 mut_day4 +experiment____mutant S1P_obs 2.128 0 sd_S1P_obs R1 mut_day2 +experiment____mutant S1P_obs 2.143 0 sd_S1P_obs R2 mut_day2 +experiment____mutant S1P_obs 1.565 0 sd_S1P_obs R3 mut_day2 +experiment____mutant S1P_obs 2.275 0 sd_S1P_obs R4 mut_day2 +experiment____mutant S1P_obs 2.238 0 sd_S1P_obs R5 mut_day2 diff --git a/v2/Armistead_CellDeathDis2024/model_Armistead_CellDeathDis2024.xml b/v2/Armistead_CellDeathDis2024/model_Armistead_CellDeathDis2024.xml new file mode 100644 index 0000000..dc8c772 --- /dev/null +++ b/v2/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/v2/Armistead_CellDeathDis2024/observables_Armistead_CellDeathDis2024.tsv b/v2/Armistead_CellDeathDis2024/observables_Armistead_CellDeathDis2024.tsv new file mode 100644 index 0000000..dcddb19 --- /dev/null +++ b/v2/Armistead_CellDeathDis2024/observables_Armistead_CellDeathDis2024.tsv @@ -0,0 +1,5 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +Sphinga_obs Sphinganine concentration [area ratio/Protein] - indication of Cer de novo production Sphinga noiseParameter1_Sphinga_obs*Sphinga normal noiseParameter1_Sphinga_obs +Cer_obs Ceramide concentration [area ratio/Protein] Cer noiseParameter1_Cer_obs*Cer normal noiseParameter1_Cer_obs +Sphingo_obs Sphingosine concentration [area ratio/Protein] Sphingo noiseParameter1_Sphingo_obs*Sphingo normal noiseParameter1_Sphingo_obs +S1P_obs Sphingosine-1-phosphate indirect measurement S1P noiseParameter1_S1P_obs*S1P normal noiseParameter1_S1P_obs diff --git a/v2/Armistead_CellDeathDis2024/parameters_Armistead_CellDeathDis2024.tsv b/v2/Armistead_CellDeathDis2024/parameters_Armistead_CellDeathDis2024.tsv new file mode 100644 index 0000000..2bca9dd --- /dev/null +++ b/v2/Armistead_CellDeathDis2024/parameters_Armistead_CellDeathDis2024.tsv @@ -0,0 +1,15 @@ +parameterId lowerBound upperBound nominalValue estimate priorParameters +k00 0.001 1000.0 0.23808250425876593 true +k0 0.001 1000.0 999.9999277151477 true +k_d 0.001 1000.0 0.9067726310954474 true +k1 0.001 1000.0 0.30112832513704085 true +k2 0.001 1000.0 999.9972374722311 true +k3 0.001 1000.0 0.0010000471839981641 true +k4 0.001 1000.0 2.3616885412588227 true +k5 0.001 1000.0 0.0010007718402407393 true +alpha_hai1a 0.5 0.999 0.5000000538784732 true +alpha_cer -0.999 -0.001 -0.32749379807106804 true +sd_Sphinga_obs 0.001 1000.0 0.08812927862352599 true +sd_Cer_obs 0.001 1000.0 0.09173161721376666 true +sd_Sphingo_obs 0.001 1000.0 0.13184193616921516 true +sd_S1P_obs 0.001 1000.0 0.0974467251675001 true diff --git a/v2/Bachmann_MSB2011/Bachmann_MSB2011.yaml b/v2/Bachmann_MSB2011/Bachmann_MSB2011.yaml new file mode 100644 index 0000000..ea6f54e --- /dev/null +++ b/v2/Bachmann_MSB2011/Bachmann_MSB2011.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Bachmann_MSB2011.tsv +model_files: + model_Bachmann_MSB2011: + location: model_Bachmann_MSB2011.xml + language: sbml +measurement_files: +- measurementData_Bachmann_MSB2011.tsv +condition_files: +- experimentalCondition_Bachmann_MSB2011.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Bachmann_MSB2011.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Bachmann_MSB2011/experimentalCondition_Bachmann_MSB2011.tsv b/v2/Bachmann_MSB2011/experimentalCondition_Bachmann_MSB2011.tsv new file mode 100644 index 0000000..5a49ae9 --- /dev/null +++ b/v2/Bachmann_MSB2011/experimentalCondition_Bachmann_MSB2011.tsv @@ -0,0 +1,289 @@ +conditionId targetId targetValue +model1_data1 ActD 1.0 +model1_data2 ActD 1.0 +model1_data3 ActD 1.0 +model1_data4 ActD 1.0 +model1_data5 ActD 0.0 +model1_data6 ActD 1.0 +model1_data7 ActD 1.0 +model1_data8 ActD 1.0 +model1_data9 ActD 1.0 +model1_data10 ActD 1.0 +model1_data11 ActD 1.0 +model1_data12 ActD 1.0 +model1_data13 ActD 1.0 +model1_data14 ActD 1.0 +model1_data15 ActD 1.0 +model1_data16 ActD 1.0 +model1_data17 ActD 1.0 +model1_data18 ActD 1.0 +model1_data19 ActD 1.0 +model1_data20 ActD 1.0 +model1_data21 ActD 1.0 +model1_data22 ActD 1.0 +model1_data23 ActD 1.0 +model1_data24 ActD 1.0 +model1_data25 ActD 1.0 +model1_data26 ActD 1.0 +model1_data27 ActD 1.0 +model1_data30 ActD 1.0 +model1_data31 ActD 1.0 +model1_data32 ActD 1.0 +model1_data33 ActD 1.0 +model1_data38 ActD 1.0 +model1_data39 ActD 1.0 +model1_data40 ActD 1.0 +model1_data41 ActD 1.0 +model1_data42 ActD 1.0 +model1_data1 CISoe 0.0 +model1_data2 CISoe 0.0 +model1_data3 CISoe 0.0 +model1_data4 CISoe 0.0 +model1_data5 CISoe 0.0 +model1_data6 CISoe 0.0 +model1_data7 CISoe 0.0 +model1_data8 CISoe 1.0 +model1_data9 CISoe 0.0 +model1_data10 CISoe 1.0 +model1_data11 CISoe 0.0 +model1_data12 CISoe 0.0 +model1_data13 CISoe 0.0 +model1_data14 CISoe 0.0 +model1_data15 CISoe 0.0 +model1_data16 CISoe 0.0 +model1_data17 CISoe 0.0 +model1_data18 CISoe 0.0 +model1_data19 CISoe 0.0 +model1_data20 CISoe 0.0 +model1_data21 CISoe 0.0 +model1_data22 CISoe 0.0 +model1_data23 CISoe 0.0 +model1_data24 CISoe 0.0 +model1_data25 CISoe 0.0 +model1_data26 CISoe 0.0 +model1_data27 CISoe 0.0 +model1_data30 CISoe 0.0 +model1_data31 CISoe 0.0 +model1_data32 CISoe 0.0 +model1_data33 CISoe 0.0 +model1_data38 CISoe 0.0 +model1_data39 CISoe 0.0 +model1_data40 CISoe 0.0 +model1_data41 CISoe 0.0 +model1_data42 CISoe 0.0 +model1_data1 SOCS3oe 0.0 +model1_data2 SOCS3oe 0.0 +model1_data3 SOCS3oe 0.0 +model1_data4 SOCS3oe 0.0 +model1_data5 SOCS3oe 0.0 +model1_data6 SOCS3oe 0.0 +model1_data7 SOCS3oe 0.0 +model1_data8 SOCS3oe 0.0 +model1_data9 SOCS3oe 0.0 +model1_data10 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Epo 1.25e-07 +model1_data12 Epo 1.25e-07 +model1_data13 Epo 1.25e-07 +model1_data14 Epo 1.25e-07 +model1_data15 Epo 2.5e-05 +model1_data16 Epo 2.5e-06 +model1_data17 Epo 2.5e-07 +model1_data18 Epo 2.5e-08 +model1_data19 Epo 2.5e-09 +model1_data20 Epo 1.25e-06 +model1_data21 Epo 1.25e-07 +model1_data22 Epo 2.5e-06 +model1_data23 Epo 2.5e-07 +model1_data24 Epo 2.5e-08 +model1_data25 Epo 2.5e-09 +model1_data26 Epo 1.25e-07 +model1_data27 Epo 1.25e-08 +model1_data30 Epo 2.5e-06 +model1_data31 Epo 2.5e-07 +model1_data32 Epo 2.5e-08 +model1_data33 Epo 2.5e-09 +model1_data38 Epo 1.25e-07 +model1_data39 Epo 2.5e-06 +model1_data40 Epo 2.5e-07 +model1_data41 Epo 2.5e-08 +model1_data42 Epo 2.5e-09 +model1_data1 init_CIS_multiplier 0.0 +model1_data2 init_CIS_multiplier 0.0 +model1_data3 init_CIS_multiplier 0.0 +model1_data4 init_CIS_multiplier 0.0 +model1_data5 init_CIS_multiplier 0.0 +model1_data6 init_CIS_multiplier 0.0 +model1_data7 init_CIS_multiplier 0.0 +model1_data8 init_CIS_multiplier 1.0 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init_CIS_multiplier 0.0 +model1_data41 init_CIS_multiplier 0.0 +model1_data42 init_CIS_multiplier 0.0 +model1_data1 init_EpoRJAK2_CIS 0.0 +model1_data2 init_EpoRJAK2_CIS 0.0 +model1_data3 init_EpoRJAK2_CIS 0.0 +model1_data4 init_EpoRJAK2_CIS 0.0 +model1_data5 init_EpoRJAK2_CIS 0.0 +model1_data6 init_EpoRJAK2_CIS 0.0 +model1_data7 init_EpoRJAK2_CIS 0.0 +model1_data8 init_EpoRJAK2_CIS 1.0 +model1_data9 init_EpoRJAK2_CIS 0.0 +model1_data10 init_EpoRJAK2_CIS 1.0 +model1_data11 init_EpoRJAK2_CIS 0.0 +model1_data12 init_EpoRJAK2_CIS 0.0 +model1_data13 init_EpoRJAK2_CIS 0.0 +model1_data14 init_EpoRJAK2_CIS 0.0 +model1_data15 init_EpoRJAK2_CIS 0.0 +model1_data16 init_EpoRJAK2_CIS 0.0 +model1_data17 init_EpoRJAK2_CIS 0.0 +model1_data18 init_EpoRJAK2_CIS 0.0 +model1_data19 init_EpoRJAK2_CIS 0.0 +model1_data20 init_EpoRJAK2_CIS 0.0 +model1_data21 init_EpoRJAK2_CIS 0.0 +model1_data22 init_EpoRJAK2_CIS 0.0 +model1_data23 init_EpoRJAK2_CIS 0.0 +model1_data24 init_EpoRJAK2_CIS 0.0 +model1_data25 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init_SHP1_multiplier 0.0 +model1_data16 init_SHP1_multiplier 0.0 +model1_data17 init_SHP1_multiplier 0.0 +model1_data18 init_SHP1_multiplier 0.0 +model1_data19 init_SHP1_multiplier 0.0 +model1_data20 init_SHP1_multiplier 0.0 +model1_data21 init_SHP1_multiplier 0.0 +model1_data22 init_SHP1_multiplier 0.0 +model1_data23 init_SHP1_multiplier 0.0 +model1_data24 init_SHP1_multiplier 0.0 +model1_data25 init_SHP1_multiplier 0.0 +model1_data26 init_SHP1_multiplier 0.0 +model1_data27 init_SHP1_multiplier 0.0 +model1_data30 init_SHP1_multiplier 0.0 +model1_data31 init_SHP1_multiplier 0.0 +model1_data32 init_SHP1_multiplier 0.0 +model1_data33 init_SHP1_multiplier 0.0 +model1_data38 init_SHP1_multiplier 0.0 +model1_data39 init_SHP1_multiplier 0.0 +model1_data40 init_SHP1_multiplier 0.0 +model1_data41 init_SHP1_multiplier 0.0 +model1_data42 init_SHP1_multiplier 0.0 +model1_data1 init_SOCS3_multiplier 0.0 +model1_data2 init_SOCS3_multiplier 0.0 +model1_data3 init_SOCS3_multiplier 0.0 +model1_data4 init_SOCS3_multiplier 0.0 +model1_data5 init_SOCS3_multiplier 0.0 +model1_data6 init_SOCS3_multiplier 0.0 +model1_data7 init_SOCS3_multiplier 0.0 +model1_data8 init_SOCS3_multiplier 0.0 +model1_data9 init_SOCS3_multiplier 0.0 +model1_data10 init_SOCS3_multiplier 0.0 +model1_data11 init_SOCS3_multiplier 0.0 +model1_data12 init_SOCS3_multiplier 1.0 +model1_data13 init_SOCS3_multiplier 0.0 +model1_data14 init_SOCS3_multiplier 0.0 +model1_data15 init_SOCS3_multiplier 0.0 +model1_data16 init_SOCS3_multiplier 0.0 +model1_data17 init_SOCS3_multiplier 0.0 +model1_data18 init_SOCS3_multiplier 0.0 +model1_data19 init_SOCS3_multiplier 0.0 +model1_data20 init_SOCS3_multiplier 0.0 +model1_data21 init_SOCS3_multiplier 0.0 +model1_data22 init_SOCS3_multiplier 0.0 +model1_data23 init_SOCS3_multiplier 0.0 +model1_data24 init_SOCS3_multiplier 0.0 +model1_data25 init_SOCS3_multiplier 0.0 +model1_data26 init_SOCS3_multiplier 0.0 +model1_data27 init_SOCS3_multiplier 0.0 +model1_data30 init_SOCS3_multiplier 0.0 +model1_data31 init_SOCS3_multiplier 0.0 +model1_data32 init_SOCS3_multiplier 0.0 +model1_data33 init_SOCS3_multiplier 0.0 +model1_data38 init_SOCS3_multiplier 0.0 +model1_data39 init_SOCS3_multiplier 0.0 +model1_data40 init_SOCS3_multiplier 0.0 +model1_data41 init_SOCS3_multiplier 0.0 +model1_data42 init_SOCS3_multiplier 0.0 diff --git a/v2/Bachmann_MSB2011/experiments.tsv b/v2/Bachmann_MSB2011/experiments.tsv new file mode 100644 index 0000000..2f2272e --- /dev/null +++ b/v2/Bachmann_MSB2011/experiments.tsv @@ -0,0 +1,37 @@ +experimentId conditionId time +experiment____model1_data1 model1_data1 0 +experiment____model1_data10 model1_data10 0 +experiment____model1_data11 model1_data11 0 +experiment____model1_data12 model1_data12 0 +experiment____model1_data13 model1_data13 0 +experiment____model1_data14 model1_data14 0 +experiment____model1_data15 model1_data15 0 +experiment____model1_data16 model1_data16 0 +experiment____model1_data17 model1_data17 0 +experiment____model1_data18 model1_data18 0 +experiment____model1_data19 model1_data19 0 +experiment____model1_data2 model1_data2 0 +experiment____model1_data20 model1_data20 0 +experiment____model1_data21 model1_data21 0 +experiment____model1_data22 model1_data22 0 +experiment____model1_data23 model1_data23 0 +experiment____model1_data24 model1_data24 0 +experiment____model1_data25 model1_data25 0 +experiment____model1_data26 model1_data26 0 +experiment____model1_data27 model1_data27 0 +experiment____model1_data3 model1_data3 0 +experiment____model1_data30 model1_data30 0 +experiment____model1_data31 model1_data31 0 +experiment____model1_data32 model1_data32 0 +experiment____model1_data33 model1_data33 0 +experiment____model1_data38 model1_data38 0 +experiment____model1_data39 model1_data39 0 +experiment____model1_data4 model1_data4 0 +experiment____model1_data40 model1_data40 0 +experiment____model1_data41 model1_data41 0 +experiment____model1_data42 model1_data42 0 +experiment____model1_data5 model1_data5 0 +experiment____model1_data6 model1_data6 0 +experiment____model1_data7 model1_data7 0 +experiment____model1_data8 model1_data8 0 +experiment____model1_data9 model1_data9 0 diff --git a/v2/Bachmann_MSB2011/measurementData_Bachmann_MSB2011.tsv b/v2/Bachmann_MSB2011/measurementData_Bachmann_MSB2011.tsv new file mode 100644 index 0000000..00727c2 --- /dev/null +++ b/v2/Bachmann_MSB2011/measurementData_Bachmann_MSB2011.tsv @@ -0,0 +1,542 @@ +experimentId observableId measurement time observableParameters noiseParameters +experiment____model1_data2 observable_CIS_abs 29.061794973113646 120.0 sd_CIS_abs +experiment____model1_data2 observable_CIS_abs 26.097567191289983 120.0 sd_CIS_abs +experiment____model1_data2 observable_CIS_abs 19.65239347179184 120.0 sd_CIS_abs +experiment____model1_data1 observable_CIS_au 0.017007483828788285 0.0 offset_CIS_long;scale_CIS_long sd_CIS_au +experiment____model1_data1 observable_CIS_au 0.038819328188923134 5.0 offset_CIS_long;scale_CIS_long sd_CIS_au +experiment____model1_data1 observable_CIS_au 0.021343795504749925 10.0 offset_CIS_long;scale_CIS_long sd_CIS_au +experiment____model1_data1 observable_CIS_au 0.03708581390971887 20.0 offset_CIS_long;scale_CIS_long sd_CIS_au +experiment____model1_data1 observable_CIS_au 0.12873027508395155 40.0 offset_CIS_long;scale_CIS_long sd_CIS_au +experiment____model1_data1 observable_CIS_au 0.28249348693920795 60.0 offset_CIS_long;scale_CIS_long sd_CIS_au +experiment____model1_data1 observable_CIS_au 0.8208313934483058 80.0 offset_CIS_long;scale_CIS_long sd_CIS_au +experiment____model1_data1 observable_CIS_au 0.9222593139245774 100.0 offset_CIS_long;scale_CIS_long sd_CIS_au +experiment____model1_data1 observable_CIS_au 0.7730953630969482 140.0 offset_CIS_long;scale_CIS_long sd_CIS_au +experiment____model1_data1 observable_CIS_au 0.7515576864023135 160.0 offset_CIS_long;scale_CIS_long sd_CIS_au +experiment____model1_data1 observable_CIS_au 0.9511272795712759 180.0 offset_CIS_long;scale_CIS_long 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observable_tSTAT5_au 0.7814814814814808 30.0 scale_tSTAT5_shp1oe sd_STAT5_au +experiment____model1_data14 observable_tSTAT5_au 0.6231481481481479 60.0 scale_tSTAT5_shp1oe sd_STAT5_au +experiment____model1_data4 observable_tSTAT5_au 0.8324324324324319 0.0 scale_tSTAT5_actd sd_STAT5_au +experiment____model1_data4 observable_tSTAT5_au 0.8972972972972967 5.0 scale_tSTAT5_actd sd_STAT5_au +experiment____model1_data4 observable_tSTAT5_au 0.8594594594594601 10.0 scale_tSTAT5_actd sd_STAT5_au +experiment____model1_data4 observable_tSTAT5_au 0.6702702702702699 30.0 scale_tSTAT5_actd sd_STAT5_au +experiment____model1_data4 observable_tSTAT5_au 0.7351351351351356 60.0 scale_tSTAT5_actd sd_STAT5_au +experiment____model1_data4 observable_tSTAT5_au 0.5837837837837839 90.0 scale_tSTAT5_actd sd_STAT5_au +experiment____model1_data4 observable_tSTAT5_au 0.8864864864864863 120.0 scale_tSTAT5_actd sd_STAT5_au +experiment____model1_data4 observable_tSTAT5_au 0.6810810810810809 150.0 scale_tSTAT5_actd sd_STAT5_au +experiment____model1_data4 observable_tSTAT5_au 0.4713513513513509 180.0 scale_tSTAT5_actd sd_STAT5_au +experiment____model1_data5 observable_tSTAT5_au 0.9027027027027016 0.0 scale_tSTAT5_actd sd_STAT5_au +experiment____model1_data5 observable_tSTAT5_au 1.0 5.0 scale_tSTAT5_actd sd_STAT5_au +experiment____model1_data5 observable_tSTAT5_au 0.9243243243243242 10.0 scale_tSTAT5_actd sd_STAT5_au +experiment____model1_data5 observable_tSTAT5_au 0.5837837837837839 30.0 scale_tSTAT5_actd sd_STAT5_au +experiment____model1_data5 observable_tSTAT5_au 0.7945945945945941 60.0 scale_tSTAT5_actd sd_STAT5_au +experiment____model1_data5 observable_tSTAT5_au 0.772972972972973 90.0 scale_tSTAT5_actd sd_STAT5_au +experiment____model1_data5 observable_tSTAT5_au 0.7567567567567564 120.0 scale_tSTAT5_actd sd_STAT5_au +experiment____model1_data5 observable_tSTAT5_au 0.7459459459459464 150.0 scale_tSTAT5_actd sd_STAT5_au +experiment____model1_data5 observable_tSTAT5_au 0.5145945945945951 180.0 scale_tSTAT5_actd sd_STAT5_au diff --git a/v2/Bachmann_MSB2011/model_Bachmann_MSB2011.xml b/v2/Bachmann_MSB2011/model_Bachmann_MSB2011.xml new file mode 100644 index 0000000..1dd7672 --- /dev/null +++ b/v2/Bachmann_MSB2011/model_Bachmann_MSB2011.xml @@ -0,0 +1,1146 @@ + + + + + + 
PEtab implementation of the model from Bachmann et al. (2011), Mol Syst Biol. ; 7: 516.
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nuc + CISnRNA4 + CISRNADelay + + + + + + + + + + + + + + + + nuc + CISnRNA5 + CISRNADelay + + + + + + + + + + + + + cyt + CISRNA + CISRNATurn + + + + + + + + + + + + + + + + cyt + + + + + CISRNA + CISEqc + CISTurn + + CISRNAEqc + + + + + + + + + + + + + + cyt + CIS + CISTurn + + + + + + + + + + + + + cyt + CISEqc + CISTurn + CISEqcOE + CISoe + + + + + + + + + + + + + + + + nuc + + + + + SOCS3RNAEqc + SOCS3RNATurn + npSTAT5 + ActD + + init_STAT5 + + + + + + + + + + + + + + + + + nuc + SOCS3nRNA1 + SOCS3RNADelay + + + + + + + + + + + + + + + + nuc + SOCS3nRNA2 + SOCS3RNADelay + + + + + + + + + + + + + + + + nuc + SOCS3nRNA3 + SOCS3RNADelay + + + + + + + + + + + + + + + + nuc + SOCS3nRNA4 + SOCS3RNADelay + + + + + + + + + + + + + + + + nuc + SOCS3nRNA5 + SOCS3RNADelay + + + + + + + + + + + + + cyt + SOCS3RNA + SOCS3RNATurn + + + + + + + + + + + + + + + + cyt + + + + + SOCS3RNA + SOCS3Eqc + SOCS3Turn + + SOCS3RNAEqc + + + + + + + + + + + + + + cyt + SOCS3 + SOCS3Turn + + + + + + + + + + + + + cyt + SOCS3oe + SOCS3Eqc + SOCS3Turn + SOCS3EqcOE + + + + + + + diff --git a/v2/Bachmann_MSB2011/observables_Bachmann_MSB2011.tsv b/v2/Bachmann_MSB2011/observables_Bachmann_MSB2011.tsv new file mode 100644 index 0000000..a80cdfa --- /dev/null +++ b/v2/Bachmann_MSB2011/observables_Bachmann_MSB2011.tsv @@ -0,0 +1,21 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +observable_CISRNA_foldA CISRNA * observableParameter1_observable_CISRNA_foldA / CISRNAEqc + 1 noiseParameter1_observable_CISRNA_foldA observableParameter1_observable_CISRNA_foldA noiseParameter1_observable_CISRNA_foldA +observable_CISRNA_foldB CISRNA * observableParameter1_observable_CISRNA_foldB / CISRNAEqc + 1 noiseParameter1_observable_CISRNA_foldB observableParameter1_observable_CISRNA_foldB noiseParameter1_observable_CISRNA_foldB +observable_CISRNA_foldC CISRNA * observableParameter1_observable_CISRNA_foldC / CISRNAEqc + 1 noiseParameter1_observable_CISRNA_foldC observableParameter1_observable_CISRNA_foldC noiseParameter1_observable_CISRNA_foldC +observable_CIS_abs CIS noiseParameter1_observable_CIS_abs noiseParameter1_observable_CIS_abs +observable_CIS_au observableParameter1_observable_CIS_au + CIS * observableParameter2_observable_CIS_au / CISEqc noiseParameter1_observable_CIS_au observableParameter1_observable_CIS_au;observableParameter2_observable_CIS_au noiseParameter1_observable_CIS_au +observable_CIS_au1 CIS * observableParameter1_observable_CIS_au1 / CISEqc noiseParameter1_observable_CIS_au1 observableParameter1_observable_CIS_au1 noiseParameter1_observable_CIS_au1 +observable_CIS_au2 CIS * observableParameter1_observable_CIS_au2 / CISEqc noiseParameter1_observable_CIS_au2 observableParameter1_observable_CIS_au2 noiseParameter1_observable_CIS_au2 +observable_SHP1_abs SHP1 + SHP1Act noiseParameter1_observable_SHP1_abs noiseParameter1_observable_SHP1_abs +observable_SOCS3RNA_foldA SOCS3RNA * observableParameter1_observable_SOCS3RNA_foldA / SOCS3RNAEqc + 1 noiseParameter1_observable_SOCS3RNA_foldA observableParameter1_observable_SOCS3RNA_foldA noiseParameter1_observable_SOCS3RNA_foldA +observable_SOCS3RNA_foldB SOCS3RNA * observableParameter1_observable_SOCS3RNA_foldB / SOCS3RNAEqc + 1 noiseParameter1_observable_SOCS3RNA_foldB observableParameter1_observable_SOCS3RNA_foldB noiseParameter1_observable_SOCS3RNA_foldB +observable_SOCS3RNA_foldC SOCS3RNA * observableParameter1_observable_SOCS3RNA_foldC / SOCS3RNAEqc + 1 noiseParameter1_observable_SOCS3RNA_foldC observableParameter1_observable_SOCS3RNA_foldC noiseParameter1_observable_SOCS3RNA_foldC +observable_SOCS3_abs SOCS3 noiseParameter1_observable_SOCS3_abs noiseParameter1_observable_SOCS3_abs +observable_SOCS3_au observableParameter1_observable_SOCS3_au + SOCS3 * observableParameter2_observable_SOCS3_au / SOCS3Eqc noiseParameter1_observable_SOCS3_au observableParameter1_observable_SOCS3_au;observableParameter2_observable_SOCS3_au noiseParameter1_observable_SOCS3_au +observable_STAT5_abs STAT5 noiseParameter1_observable_STAT5_abs noiseParameter1_observable_STAT5_abs +observable_pEpoR_au observableParameter1_observable_pEpoR_au + observableParameter2_observable_pEpoR_au * (16 * p12EpoRpJAK2 + 16 * p1EpoRpJAK2 + 16 * p2EpoRpJAK2) / init_EpoRJAK2 noiseParameter1_observable_pEpoR_au observableParameter1_observable_pEpoR_au;observableParameter2_observable_pEpoR_au noiseParameter1_observable_pEpoR_au +observable_pJAK2_au observableParameter1_observable_pJAK2_au + observableParameter2_observable_pJAK2_au * (2 * EpoRpJAK2 + 2 * p12EpoRpJAK2 + 2 * p1EpoRpJAK2 + 2 * p2EpoRpJAK2) / init_EpoRJAK2 noiseParameter1_observable_pJAK2_au observableParameter1_observable_pJAK2_au;observableParameter2_observable_pJAK2_au noiseParameter1_observable_pJAK2_au +observable_pSTAT5B_rel observableParameter1_observable_pSTAT5B_rel + 100 * pSTAT5 / (STAT5 + pSTAT5) noiseParameter1_observable_pSTAT5B_rel observableParameter1_observable_pSTAT5B_rel noiseParameter1_observable_pSTAT5B_rel +observable_pSTAT5_au observableParameter1_observable_pSTAT5_au + pSTAT5 * observableParameter2_observable_pSTAT5_au / init_STAT5 noiseParameter1_observable_pSTAT5_au + noiseParameter2_observable_pSTAT5_au observableParameter1_observable_pSTAT5_au;observableParameter2_observable_pSTAT5_au noiseParameter1_observable_pSTAT5_au;noiseParameter2_observable_pSTAT5_au +observable_tSHP1_au observableParameter1_observable_tSHP1_au * (SHP1 + SHP1Act) / init_SHP1 noiseParameter1_observable_tSHP1_au observableParameter1_observable_tSHP1_au noiseParameter1_observable_tSHP1_au +observable_tSTAT5_au observableParameter1_observable_tSTAT5_au * (STAT5 + pSTAT5) / init_STAT5 noiseParameter1_observable_tSTAT5_au observableParameter1_observable_tSTAT5_au noiseParameter1_observable_tSTAT5_au diff --git a/v2/Bachmann_MSB2011/parameters_Bachmann_MSB2011.tsv b/v2/Bachmann_MSB2011/parameters_Bachmann_MSB2011.tsv new file mode 100644 index 0000000..2d09d27 --- /dev/null +++ b/v2/Bachmann_MSB2011/parameters_Bachmann_MSB2011.tsv @@ -0,0 +1,116 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorDistribution priorParameters +CISEqc CISEqc 0.001 10000 432.854027325732 true uniform 0.001;10000 +CISEqcOE CISEqcOE 0.001 1000 0.53027229006794 true uniform 0.001;1000 +CISInh CISInh 0.001 1000000000000 785221045.232906 true uniform 0.001;1000000000000 +CISRNADelay CISRNADelay 0.001 1000 0.144777009620017 true uniform 0.001;1000 +CISRNAEqc CISRNAEqc 0.001 1000 1.0 false uniform 0.001;1000 +CISRNATurn CISRNATurn 0.001 1000 1000.0 true uniform 0.001;1000 +CISTurn CISTurn 0.001 1000 0.008398825029262 true uniform 0.001;1000 +EpoRActJAK2 EpoRActJAK2 0.001 10000 0.267299659481333 true uniform 0.001;10000 +EpoRCISInh EpoRCISInh 0.001 1000000 1000000.0 true uniform 0.001;1000000 +EpoRCISRemove EpoRCISRemove 0.001 1000 5.42989282766407 true uniform 0.001;1000 +JAK2ActEpo JAK2ActEpo 0.001 1000000000 633154.209632843 true uniform 0.001;1000000000 +JAK2EpoRDeaSHP1 JAK2EpoRDeaSHP1 0.001 10000 142.723069412318 true uniform 0.001;10000 +SHP1ActEpoR SHP1ActEpoR 0.001 1000 0.001 true uniform 0.001;1000 +SHP1Dea SHP1Dea 0.001 1000 0.008162255244283 true uniform 0.001;1000 +SHP1ProOE SHP1ProOE 0.001 1000 2.82568032716189 true uniform 0.001;1000 +SOCS3Eqc SOCS3Eqc 0.001 1000 173.64095522801 true uniform 0.001;1000 +SOCS3EqcOE SOCS3EqcOE 0.001 1000 0.679185853534469 true uniform 0.001;1000 +SOCS3Inh SOCS3Inh 0.001 1000 10.4074255973465 true uniform 0.001;1000 +SOCS3RNADelay SOCS3RNADelay 0.001 1000 1.06454014521077 true uniform 0.001;1000 +SOCS3RNAEqc SOCS3RNAEqc 0.001 1000 1.0 false uniform 0.001;1000 +SOCS3RNATurn SOCS3RNATurn 0.001 1000 0.008309263619427 true uniform 0.001;1000 +SOCS3Turn SOCS3Turn 0.001 10000 10000.0 true uniform 0.001;10000 +STAT5ActEpoR STAT5ActEpoR 0.001 1000 38.9972748894298 true uniform 0.001;1000 +STAT5ActJAK2 STAT5ActJAK2 0.001 1000 0.078108833252848 true uniform 0.001;1000 +STAT5Exp STAT5Exp 0.001 1000 0.074514698833232 true uniform 0.001;1000 +STAT5Imp STAT5Imp 0.001 1000 0.026887318057561 true uniform 0.001;1000 +init_EpoRJAK2 init_{EpoRJAK2} 0.001 1000 3.97622379188569 true log10-normal 0.599470870492697;0.193459292722329 +init_SHP1 init_{SHP1} 0.001 1000 26.7251164163486 true uniform 0.001;1000 +init_STAT5 init_{STAT5} 0.001 1000 79.753639977851 true uniform 0.001;1000 +offset_CIS_actd offset_{CIS,actd} 0.001 1000 0.009388328725541 true uniform 0.001;1000 +offset_CIS_cisoe offset_{CIS,cisoe} 0.001 1000 0.030012199170223 true uniform 0.001;1000 +offset_CIS_long offset_{CIS,long} 0.001 1000 0.026460000624405 true uniform 0.001;1000 +offset_CIS_shp1oe offset_{CIS,shp1oe} 0.001 1000 0.058794513917949 true uniform 0.001;1000 +offset_CIS_socs3oe offset_{CIS,socs3oe} 0.001 1000 0.090496783983191 true uniform 0.001;1000 +offset_SOCS3_cisoe offset_{SOCS3,cisoe} 0.001 1000 0.278270301775932 true uniform 0.001;1000 +offset_SOCS3_long offset_{SOCS3,long} 0.001 1000 0.114475234936677 true uniform 0.001;1000 +offset_SOCS3_socs3oe offset_{SOCS3,socs3oe} 0.001 1000 0.025584406819207 true uniform 0.001;1000 +offset_pEpoR_actd offset_{pEpoR,actd} 0.001 1000 0.018840236081137 true uniform 0.001;1000 +offset_pEpoR_cisoe offset_{pEpoR,cisoe} 0.001 1000 0.030210854745913 true uniform 0.001;1000 +offset_pEpoR_cisoe_pepor offset_{pEpoR,cisoe,pepor} 0.001 1000 0.131027220027866 true uniform 0.001;1000 +offset_pEpoR_dr30 offset_{pEpoR,dr30} 0.001 1000 0.001 true uniform 0.001;1000 +offset_pEpoR_dr7 offset_{pEpoR,dr7} 0.001 1000 0.028405110847623 true uniform 0.001;1000 +offset_pEpoR_fine offset_{pEpoR,fine} 0.001 1000 0.064550876993068 true uniform 0.001;1000 +offset_pEpoR_long offset_{pEpoR,long} 0.001 1000 0.004391399791279 true uniform 0.001;1000 +offset_pEpoR_shp1oe offset_{pEpoR,shp1oe} 0.001 1000 0.031327226759826 true uniform 0.001;1000 +offset_pEpoR_socs3oe offset_{pEpoR,socs3oe} 0.001 1000 0.056711915845858 true uniform 0.001;1000 +offset_pJAK2_actd offset_{pJAK2,actd} 0.001 1000 0.017059890602388 true uniform 0.001;1000 +offset_pJAK2_cisoe offset_{pJAK2,cisoe} 0.001 1000 0.021928076840931 true uniform 0.001;1000 +offset_pJAK2_dr30 offset_{pJAK2,dr30} 0.001 1000 0.029944254724382 true uniform 0.001;1000 +offset_pJAK2_dr7 offset_{pJAK2,dr7} 0.001 1000 0.04733977489635 true uniform 0.001;1000 +offset_pJAK2_fine offset_{pJAK2,fine} 0.001 1000 0.021658276199496 true uniform 0.001;1000 +offset_pJAK2_long offset_{pJAK2,long} 0.001 1000 0.009473351822798 true uniform 0.001;1000 +offset_pJAK2_shp1oe offset_{pJAK2,shp1oe} 0.001 1000 0.026667365128327 true uniform 0.001;1000 +offset_pJAK2_socs3oe offset_{pJAK2,socs3oe} 0.001 1000 0.059752453075581 true uniform 0.001;1000 +offset_pSTAT5_actd offset_{pSTAT5,actd} 0.001 1000 0.001868785567417 true uniform 0.001;1000 +offset_pSTAT5_cisoe offset_{pSTAT5,cisoe} 0.001 1000 0.070791697579138 true uniform 0.001;1000 +offset_pSTAT5_conc offset_{pSTAT5,conc} 0.001 1000 0.236827475949589 true uniform 0.001;1000 +offset_pSTAT5_long offset_{pSTAT5,long} 0.001 1000 0.001093070638337 true uniform 0.001;1000 +offset_pSTAT5_shp1oe offset_{pSTAT5,shp1oe} 0.001 1000 0.054941495350482 true uniform 0.001;1000 +offset_pSTAT5_socs3oe offset_{pSTAT5,socs3oe} 0.001 1000 0.005613364786273 true uniform 0.001;1000 +scale1_CIS_dr90 scale1_{CIS,dr90} 0.001 1000 17.5631450183542 true uniform 0.001;1000 +scale2_CIS_dr90 scale2_{CIS,dr90} 0.001 1000 16.1205634424041 true uniform 0.001;1000 +scale_CISRNA_foldA scale_{CISRNA,foldA} 0.001 1000 33.2822368277369 true uniform 0.001;1000 +scale_CISRNA_foldB scale_{CISRNA,foldB} 0.001 1000 31.0176342778512 true uniform 0.001;1000 +scale_CISRNA_foldC scale_{CISRNA,foldC} 0.001 1000 19.6194113406379 true uniform 0.001;1000 +scale_CIS_actd scale_{CIS,actd} 0.001 1000 14.5490143154214 true uniform 0.001;1000 +scale_CIS_cisoe scale_{CIS,cisoe} 0.001 1000 1.37088201048354 true uniform 0.001;1000 +scale_CIS_long scale_{CIS,long} 0.001 1000 16.4036102124066 true uniform 0.001;1000 +scale_CIS_shp1oe scale_{CIS,shp1oe} 0.001 1000 51.7115711834136 true uniform 0.001;1000 +scale_CIS_socs3oe scale_{CIS,socs3oe} 0.001 1000 21.1493834462165 true uniform 0.001;1000 +scale_SHP1_shp1oe scale_{SHP1,shp1oe} 0.001 1000 0.225547534442942 true uniform 0.001;1000 +scale_SOCS3RNA_foldA scale_{SOCS3RNA,foldA} 0.001 1000 56.9631412510002 true uniform 0.001;1000 +scale_SOCS3RNA_foldB scale_{SOCS3RNA,foldB} 0.001 1000 49.074989211721 true uniform 0.001;1000 +scale_SOCS3RNA_foldC scale_{SOCS3RNA,foldC} 0.001 1000 80.7316820439984 true uniform 0.001;1000 +scale_SOCS3_cisoe scale_{SOCS3,cisoe} 0.001 1000 11.5682149955845 true uniform 0.001;1000 +scale_SOCS3_long scale_{SOCS3,long} 0.001 1000 15.485524391452 true uniform 0.001;1000 +scale_SOCS3_socs3oe scale_{SOCS3,socs3oe} 0.001 1000 1.20457246908681 true uniform 0.001;1000 +scale_pEpoR_actd scale_{pEpoR,actd} 0.001 1000 0.215657294488182 true uniform 0.001;1000 +scale_pEpoR_cisoe scale_{pEpoR,cisoe} 0.001 1000 0.273625536372832 true uniform 0.001;1000 +scale_pEpoR_cisoe_pepor scale_{pEpoR,cisoe_pepor} 0.001 1000 0.156616708581292 true uniform 0.001;1000 +scale_pEpoR_dr30 scale_{pEpoR,dr30} 0.001 1000 0.537385100441811 true uniform 0.001;1000 +scale_pEpoR_dr7 scale_{pEpoR,dr7} 0.001 1000 0.101429038197386 true uniform 0.001;1000 +scale_pEpoR_fine scale_{pEpoR,fine} 0.001 1000 0.080269467995686 true uniform 0.001;1000 +scale_pEpoR_long scale_{pEpoR,long} 0.001 1000 0.256529988627087 true uniform 0.001;1000 +scale_pEpoR_shp1oe scale_{pEpoR,shp1oe} 0.001 1000 0.241283495329875 true uniform 0.001;1000 +scale_pEpoR_socs3oe scale_{pEpoR,socs3oe} 0.001 1000 0.637275573973593 true uniform 0.001;1000 +scale_pJAK2_actd scale_{pJAK2,actd} 0.001 1000 0.809491692283694 true uniform 0.001;1000 +scale_pJAK2_cisoe scale_{pJAK2,cisoe} 0.001 1000 1.85429884799069 true uniform 0.001;1000 +scale_pJAK2_dr30 scale_{pJAK2,dr30} 0.001 1000 1.77561150477407 true uniform 0.001;1000 +scale_pJAK2_dr7 scale_{pJAK2,dr7} 0.001 1000 0.506322186585869 true uniform 0.001;1000 +scale_pJAK2_fine scale_{pJAK2,fine} 0.001 1000 0.400770707451671 true uniform 0.001;1000 +scale_pJAK2_long scale_{pJAK2,long} 0.001 1000 0.882775356861714 true uniform 0.001;1000 +scale_pJAK2_shp1oe scale_{pJAK2,shp1oe} 0.001 1000 2.31011130113927 true uniform 0.001;1000 +scale_pJAK2_socs3oe scale_{pJAK2,socs3oe} 0.001 1000 1.266550022901 true uniform 0.001;1000 +scale_pSTAT5_actd scale_{pSTAT5,actd} 0.001 1000 1.09743435047828 true uniform 0.001;1000 +scale_pSTAT5_cisoe scale_{pSTAT5,cisoe} 0.001 1000 2.41904111907135 true uniform 0.001;1000 +scale_pSTAT5_dr10 scale_{pSTAT5,dr10} 0.001 1000 1.00950903665707 true uniform 0.001;1000 +scale_pSTAT5_long scale_{pSTAT5,long} 0.001 1000 1.47372211945355 true uniform 0.001;1000 +scale_pSTAT5_shp1oe scale_{pSTAT5,shp1oe} 0.001 1000 1.15158552971751 true uniform 0.001;1000 +scale_pSTAT5_socs3oe scale_{pSTAT5,socs3oe} 0.001 1000 1.76032560825919 true uniform 0.001;1000 +scale_tSTAT5_actd scale_{tSTAT5,actd} 0.001 1000 0.815207201779241 true uniform 0.001;1000 +scale_tSTAT5_long scale_{tSTAT5,long} 0.001 1000 0.762143611844065 true uniform 0.001;1000 +scale_tSTAT5_shp1oe scale_{tSTAT5,shp1oe} 0.001 1000 0.681101374792296 true uniform 0.001;1000 +sd_CIS_abs sd_{CIS,abs} 0.001 1000 0.071666890399901 true uniform 0.001;1000 +sd_CIS_au sd_{CIS,au} 0.001 1000 0.134037028009804 true uniform 0.001;1000 +sd_JAK2EpoR_au sd_{JAK2EpoR,au} 0.001 1000 0.191838137085675 true uniform 0.001;1000 +sd_RNA_fold sd_{RNA,fold} 0.001 1000 0.103074376969697 true uniform 0.001;1000 +sd_SHP1_abs sd_{SHP1,abs} 0.001 1000 0.064904672549311 true uniform 0.001;1000 +sd_SHP1_au sd_{SHP1,au} 0.001 1000 0.077438644411215 true uniform 0.001;1000 +sd_SOCS3_abs sd_{SOCS3,abs} 0.001 1000 0.10271619027042 true uniform 0.001;1000 +sd_SOCS3_au sd_{SOCS3,au} 0.001 1000 0.076348614779106 true uniform 0.001;1000 +sd_STAT5_abs sd_{STAT5,abs} 0.001 1000 0.119518171917816 true uniform 0.001;1000 +sd_STAT5_au sd_{STAT5,au} 0.001 1000 0.123518909217589 true uniform 0.001;1000 +sd_pSTAT5_rel sd_{pSTAT5,rel} 0.001 1000 2.56704055700378 true uniform 0.001;1000 +sd_pSTAT5_socs3oe sd_{pSTAT5,socs3oe} 0.001 1000 0.573852497761907 true uniform 0.001;1000 diff --git a/v2/Beer_MolBioSystems2014/Beer_MolBioSystems2014.yaml b/v2/Beer_MolBioSystems2014/Beer_MolBioSystems2014.yaml new file mode 100644 index 0000000..f61b831 --- /dev/null +++ b/v2/Beer_MolBioSystems2014/Beer_MolBioSystems2014.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Beer_MolBioSystems2014.tsv +model_files: + model_Beer_MolBioSystems2014: + location: model_Beer_MolBioSystems2014.xml + language: sbml +measurement_files: +- measurementData_Beer_MolBioSystems2014.tsv +condition_files: +- experimentalCondition_Beer_MolBioSystems2014.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Beer_MolBioSystems2014.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Beer_MolBioSystems2014/experimentalCondition_Beer_MolBioSystems2014.tsv b/v2/Beer_MolBioSystems2014/experimentalCondition_Beer_MolBioSystems2014.tsv new file mode 100644 index 0000000..cfa7441 --- /dev/null +++ b/v2/Beer_MolBioSystems2014/experimentalCondition_Beer_MolBioSystems2014.tsv @@ -0,0 +1,115 @@ +conditionId targetId targetValue +typeIDwt_ExpID4 Bacmax Bacmax_typeIDwt_ExpID4 +typeIDT1_ExpID1 Bacmax Bacmax_typeIDT1_ExpID1 +typeIDT1_ExpID2 Bacmax Bacmax_typeIDT1_ExpID2 +typeIDT1_ExpID3 Bacmax Bacmax_typeIDT1_ExpID3 +typeIDT1_ExpID4 Bacmax Bacmax_typeIDT1_ExpID4 +typeIDT1_ExpID5 Bacmax Bacmax_typeIDT1_ExpID5 +typeIDT1_ExpID6 Bacmax Bacmax_typeIDT1_ExpID6 +typeIDT3_ExpID1 Bacmax Bacmax_typeIDT3_ExpID1 +typeIDT3_ExpID2 Bacmax Bacmax_typeIDT3_ExpID2 +typeIDT3_ExpID3 Bacmax Bacmax_typeIDT3_ExpID3 +typeIDT3_ExpID4 Bacmax Bacmax_typeIDT3_ExpID4 +typeIDT3_ExpID5 Bacmax Bacmax_typeIDT3_ExpID5 +typeIDT3_ExpID6 Bacmax Bacmax_typeIDT3_ExpID6 +typeIDT5_ExpID1 Bacmax Bacmax_typeIDT5_ExpID1 +typeIDT5_ExpID2 Bacmax Bacmax_typeIDT5_ExpID2 +typeIDT5_ExpID3 Bacmax Bacmax_typeIDT5_ExpID3 +typeIDT5_ExpID4 Bacmax Bacmax_typeIDT5_ExpID4 +typeIDT5_ExpID5 Bacmax Bacmax_typeIDT5_ExpID5 +typeIDT5_ExpID6 Bacmax Bacmax_typeIDT5_ExpID6 +typeIDwt_ExpID4 beta beta_typeIDwt_ExpID4 +typeIDT1_ExpID1 beta beta_typeIDT1_ExpID1 +typeIDT1_ExpID2 beta beta_typeIDT1_ExpID2 +typeIDT1_ExpID3 beta beta_typeIDT1_ExpID3 +typeIDT1_ExpID4 beta beta_typeIDT1_ExpID4 +typeIDT1_ExpID5 beta beta_typeIDT1_ExpID5 +typeIDT1_ExpID6 beta beta_typeIDT1_ExpID6 +typeIDT3_ExpID1 beta beta_typeIDT3_ExpID1 +typeIDT3_ExpID2 beta beta_typeIDT3_ExpID2 +typeIDT3_ExpID3 beta beta_typeIDT3_ExpID3 +typeIDT3_ExpID4 beta beta_typeIDT3_ExpID4 +typeIDT3_ExpID5 beta beta_typeIDT3_ExpID5 +typeIDT3_ExpID6 beta beta_typeIDT3_ExpID6 +typeIDT5_ExpID1 beta beta_typeIDT5_ExpID1 +typeIDT5_ExpID2 beta beta_typeIDT5_ExpID2 +typeIDT5_ExpID3 beta beta_typeIDT5_ExpID3 +typeIDT5_ExpID4 beta beta_typeIDT5_ExpID4 +typeIDT5_ExpID5 beta beta_typeIDT5_ExpID5 +typeIDT5_ExpID6 beta beta_typeIDT5_ExpID6 +typeIDwt_ExpID4 kdegi kdegi_typeIDwt +typeIDT1_ExpID1 kdegi kdegi_typeIDT1 +typeIDT1_ExpID2 kdegi kdegi_typeIDT1 +typeIDT1_ExpID3 kdegi kdegi_typeIDT1 +typeIDT1_ExpID4 kdegi kdegi_typeIDT1 +typeIDT1_ExpID5 kdegi kdegi_typeIDT1 +typeIDT1_ExpID6 kdegi kdegi_typeIDT1 +typeIDT3_ExpID1 kdegi kdegi_typeIDT3 +typeIDT3_ExpID2 kdegi kdegi_typeIDT3 +typeIDT3_ExpID3 kdegi kdegi_typeIDT3 +typeIDT3_ExpID4 kdegi kdegi_typeIDT3 +typeIDT3_ExpID5 kdegi kdegi_typeIDT3 +typeIDT3_ExpID6 kdegi kdegi_typeIDT3 +typeIDT5_ExpID1 kdegi kdegi_typeIDT5 +typeIDT5_ExpID2 kdegi kdegi_typeIDT5 +typeIDT5_ExpID3 kdegi kdegi_typeIDT5 +typeIDT5_ExpID4 kdegi kdegi_typeIDT5 +typeIDT5_ExpID5 kdegi kdegi_typeIDT5 +typeIDT5_ExpID6 kdegi kdegi_typeIDT5 +typeIDwt_ExpID4 kdim kdim_typeIDwt +typeIDT1_ExpID1 kdim kdim_typeIDT1 +typeIDT1_ExpID2 kdim kdim_typeIDT1 +typeIDT1_ExpID3 kdim kdim_typeIDT1 +typeIDT1_ExpID4 kdim kdim_typeIDT1 +typeIDT1_ExpID5 kdim kdim_typeIDT1 +typeIDT1_ExpID6 kdim kdim_typeIDT1 +typeIDT3_ExpID1 kdim kdim_typeIDT3 +typeIDT3_ExpID2 kdim kdim_typeIDT3 +typeIDT3_ExpID3 kdim kdim_typeIDT3 +typeIDT3_ExpID4 kdim kdim_typeIDT3 +typeIDT3_ExpID5 kdim kdim_typeIDT3 +typeIDT3_ExpID6 kdim kdim_typeIDT3 +typeIDT5_ExpID1 kdim kdim_typeIDT5 +typeIDT5_ExpID2 kdim kdim_typeIDT5 +typeIDT5_ExpID3 kdim kdim_typeIDT5 +typeIDT5_ExpID4 kdim kdim_typeIDT5 +typeIDT5_ExpID5 kdim kdim_typeIDT5 +typeIDT5_ExpID6 kdim kdim_typeIDT5 +typeIDwt_ExpID4 ksyn ksyn_typeIDwt +typeIDT1_ExpID1 ksyn ksyn_typeIDT1 +typeIDT1_ExpID2 ksyn ksyn_typeIDT1 +typeIDT1_ExpID3 ksyn ksyn_typeIDT1 +typeIDT1_ExpID4 ksyn ksyn_typeIDT1 +typeIDT1_ExpID5 ksyn ksyn_typeIDT1 +typeIDT1_ExpID6 ksyn ksyn_typeIDT1 +typeIDT3_ExpID1 ksyn ksyn_typeIDT3 +typeIDT3_ExpID2 ksyn ksyn_typeIDT3 +typeIDT3_ExpID3 ksyn ksyn_typeIDT3 +typeIDT3_ExpID4 ksyn ksyn_typeIDT3 +typeIDT3_ExpID5 ksyn ksyn_typeIDT3 +typeIDT3_ExpID6 ksyn ksyn_typeIDT3 +typeIDT5_ExpID1 ksyn ksyn_typeIDT5 +typeIDT5_ExpID2 ksyn ksyn_typeIDT5 +typeIDT5_ExpID3 ksyn ksyn_typeIDT5 +typeIDT5_ExpID4 ksyn ksyn_typeIDT5 +typeIDT5_ExpID5 ksyn ksyn_typeIDT5 +typeIDT5_ExpID6 ksyn ksyn_typeIDT5 +typeIDwt_ExpID4 tau tau_typeIDwt_ExpID4 +typeIDT1_ExpID1 tau tau_typeIDT1_ExpID1 +typeIDT1_ExpID2 tau tau_typeIDT1_ExpID2 +typeIDT1_ExpID3 tau tau_typeIDT1_ExpID3 +typeIDT1_ExpID4 tau tau_typeIDT1_ExpID4 +typeIDT1_ExpID5 tau tau_typeIDT1_ExpID5 +typeIDT1_ExpID6 tau tau_typeIDT1_ExpID6 +typeIDT3_ExpID1 tau tau_typeIDT3_ExpID1 +typeIDT3_ExpID2 tau tau_typeIDT3_ExpID2 +typeIDT3_ExpID3 tau tau_typeIDT3_ExpID3 +typeIDT3_ExpID4 tau tau_typeIDT3_ExpID4 +typeIDT3_ExpID5 tau tau_typeIDT3_ExpID5 +typeIDT3_ExpID6 tau tau_typeIDT3_ExpID6 +typeIDT5_ExpID1 tau tau_typeIDT5_ExpID1 +typeIDT5_ExpID2 tau tau_typeIDT5_ExpID2 +typeIDT5_ExpID3 tau tau_typeIDT5_ExpID3 +typeIDT5_ExpID4 tau tau_typeIDT5_ExpID4 +typeIDT5_ExpID5 tau tau_typeIDT5_ExpID5 +typeIDT5_ExpID6 tau tau_typeIDT5_ExpID6 diff --git a/v2/Beer_MolBioSystems2014/experiments.tsv b/v2/Beer_MolBioSystems2014/experiments.tsv new file mode 100644 index 0000000..d97dfc7 --- /dev/null +++ b/v2/Beer_MolBioSystems2014/experiments.tsv @@ -0,0 +1,20 @@ +experimentId conditionId time +experiment____typeIDT1_ExpID1 typeIDT1_ExpID1 0 +experiment____typeIDT1_ExpID2 typeIDT1_ExpID2 0 +experiment____typeIDT1_ExpID3 typeIDT1_ExpID3 0 +experiment____typeIDT1_ExpID4 typeIDT1_ExpID4 0 +experiment____typeIDT1_ExpID5 typeIDT1_ExpID5 0 +experiment____typeIDT1_ExpID6 typeIDT1_ExpID6 0 +experiment____typeIDT3_ExpID1 typeIDT3_ExpID1 0 +experiment____typeIDT3_ExpID2 typeIDT3_ExpID2 0 +experiment____typeIDT3_ExpID3 typeIDT3_ExpID3 0 +experiment____typeIDT3_ExpID4 typeIDT3_ExpID4 0 +experiment____typeIDT3_ExpID5 typeIDT3_ExpID5 0 +experiment____typeIDT3_ExpID6 typeIDT3_ExpID6 0 +experiment____typeIDT5_ExpID1 typeIDT5_ExpID1 0 +experiment____typeIDT5_ExpID2 typeIDT5_ExpID2 0 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a/v2/Beer_MolBioSystems2014/model_Beer_MolBioSystems2014.xml b/v2/Beer_MolBioSystems2014/model_Beer_MolBioSystems2014.xml new file mode 100644 index 0000000..a9b8df9 --- /dev/null +++ b/v2/Beer_MolBioSystems2014/model_Beer_MolBioSystems2014.xml @@ -0,0 +1,224 @@ + + + + + + 
PEtab implementation of the model from Beer et al. (2014), Mol Biosyst.;10(7):1709-18
+ + + + + + + + + + Beer + Ralf + + + + + + 2019-11-29T09:41:48Z + + + 2019-11-29T09:41:48Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + init_Bac + + + + + + + + + 0 + + + + + time + tau + + 0 + + + + 1 + + + + + + + + + + + + + + + + + + medium + + + + + + Bac + beta + lag + + + Bacmax + + + Bac + + + + + Bacmax + + + + + + + + + + + + + + + + + + medium + + + Bac + + Glu + ksyn + + + + + + + + + + + + + + + + + + medium + + + + + Bac + Glu + ksyn + + + + + + cGlu + 2 + + kdim + + + + + + + + + + + + + + + + + + + medium + + + + + + + cGlu + 2 + + kdim + + + + Ind + kdegi + + + + + + + + + diff --git a/v2/Beer_MolBioSystems2014/observables_Beer_MolBioSystems2014.tsv b/v2/Beer_MolBioSystems2014/observables_Beer_MolBioSystems2014.tsv new file mode 100644 index 0000000..bda4d05 --- /dev/null +++ b/v2/Beer_MolBioSystems2014/observables_Beer_MolBioSystems2014.tsv @@ -0,0 +1,3 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +Bacnorm Bac noiseParameter1_Bacnorm noiseParameter1_Bacnorm +IndconcNormRange Ind noiseParameter1_IndconcNormRange noiseParameter1_IndconcNormRange diff --git a/v2/Beer_MolBioSystems2014/parameters_Beer_MolBioSystems2014.tsv b/v2/Beer_MolBioSystems2014/parameters_Beer_MolBioSystems2014.tsv new file mode 100644 index 0000000..b0cf7e9 --- /dev/null +++ b/v2/Beer_MolBioSystems2014/parameters_Beer_MolBioSystems2014.tsv @@ -0,0 +1,73 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorParameters +Bacmax_typeIDT1_ExpID1 Bacmax_{typeIDT1,ExpID1} 1e-05 100000 0.690284078913072 true +Bacmax_typeIDT1_ExpID2 Bacmax_{typeIDT1,ExpID2} 1e-05 100000 0.686559360559314 true +Bacmax_typeIDT1_ExpID3 Bacmax_{typeIDT1,ExpID3} 1e-05 100000 0.681379272137127 true +Bacmax_typeIDT1_ExpID4 Bacmax_{typeIDT1,ExpID4} 1e-05 100000 0.689753205882903 true +Bacmax_typeIDT1_ExpID5 Bacmax_{typeIDT1,ExpID5} 1e-05 100000 0.715029075759644 true +Bacmax_typeIDT1_ExpID6 Bacmax_{typeIDT1,ExpID6} 1e-05 100000 0.722510272365865 true +Bacmax_typeIDT3_ExpID1 Bacmax_{typeIDT3,ExpID1} 1e-05 100000 0.858021733557635 true +Bacmax_typeIDT3_ExpID2 Bacmax_{typeIDT3,ExpID2} 1e-05 100000 0.992966373281161 true +Bacmax_typeIDT3_ExpID3 Bacmax_{typeIDT3,ExpID3} 1e-05 100000 0.948424949688061 true +Bacmax_typeIDT3_ExpID4 Bacmax_{typeIDT3,ExpID4} 1e-05 100000 0.850142395850864 true +Bacmax_typeIDT3_ExpID5 Bacmax_{typeIDT3,ExpID5} 1e-05 100000 0.938152168805454 true +Bacmax_typeIDT3_ExpID6 Bacmax_{typeIDT3,ExpID6} 1e-05 100000 0.821652094951978 true +Bacmax_typeIDT5_ExpID1 Bacmax_{typeIDT5,ExpID1} 1e-05 100000 0.815597211556127 true +Bacmax_typeIDT5_ExpID2 Bacmax_{typeIDT5,ExpID2} 1e-05 100000 0.835041084602459 true +Bacmax_typeIDT5_ExpID3 Bacmax_{typeIDT5,ExpID3} 1e-05 100000 0.816959394986618 true +Bacmax_typeIDT5_ExpID4 Bacmax_{typeIDT5,ExpID4} 1e-05 100000 0.821771993968611 true +Bacmax_typeIDT5_ExpID5 Bacmax_{typeIDT5,ExpID5} 1e-05 100000 0.812982240337939 true +Bacmax_typeIDT5_ExpID6 Bacmax_{typeIDT5,ExpID6} 1e-05 100000 0.840059251638254 true +Bacmax_typeIDwt_ExpID4 Bacmax_{typeIDwt,ExpID4} 1e-05 100000 0.627258497884162 true +beta_typeIDT1_ExpID1 beta_{typeIDT1,ExpID1} 1e-05 100000 0.003681582229086 true +beta_typeIDT1_ExpID2 beta_{typeIDT1,ExpID2} 1e-05 100000 0.003719534202825 true +beta_typeIDT1_ExpID3 beta_{typeIDT1,ExpID3} 1e-05 100000 0.003729595354247 true +beta_typeIDT1_ExpID4 beta_{typeIDT1,ExpID4} 1e-05 100000 0.003721065534692 true +beta_typeIDT1_ExpID5 beta_{typeIDT1,ExpID5} 1e-05 100000 0.003672433123878 true +beta_typeIDT1_ExpID6 beta_{typeIDT1,ExpID6} 1e-05 100000 0.003559835717311 true +beta_typeIDT3_ExpID1 beta_{typeIDT3,ExpID1} 1e-05 100000 0.002183139734286 true +beta_typeIDT3_ExpID2 beta_{typeIDT3,ExpID2} 1e-05 100000 0.002164162384219 true +beta_typeIDT3_ExpID3 beta_{typeIDT3,ExpID3} 1e-05 100000 0.002150623215474 true +beta_typeIDT3_ExpID4 beta_{typeIDT3,ExpID4} 1e-05 100000 0.002221651599144 true +beta_typeIDT3_ExpID5 beta_{typeIDT3,ExpID5} 1e-05 100000 0.002094505924306 true +beta_typeIDT3_ExpID6 beta_{typeIDT3,ExpID6} 1e-05 100000 0.002118019861794 true +beta_typeIDT5_ExpID1 beta_{typeIDT5,ExpID1} 1e-05 100000 0.005596426430683 true +beta_typeIDT5_ExpID2 beta_{typeIDT5,ExpID2} 1e-05 100000 0.004185783637797 true +beta_typeIDT5_ExpID3 beta_{typeIDT5,ExpID3} 1e-05 100000 0.004177196195634 true +beta_typeIDT5_ExpID4 beta_{typeIDT5,ExpID4} 1e-05 100000 0.004097660547909 true +beta_typeIDT5_ExpID5 beta_{typeIDT5,ExpID5} 1e-05 100000 0.0047433486867 true +beta_typeIDT5_ExpID6 beta_{typeIDT5,ExpID6} 1e-05 100000 0.003891156360938 true +beta_typeIDwt_ExpID4 beta_{typeIDwt,ExpID4} 1e-05 100000 0.006240568160694 true +init_Bac init_{Bac} 1e-20 100000 0.013816608995338 true +kdegi_typeIDT1 kdegi_{typeIDT1} 1e-05 100000 0.003122537258986 true +kdegi_typeIDT3 kdegi_{typeIDT3} 1e-05 100000 0.003944678241777 true +kdegi_typeIDT5 kdegi_{typeIDT5} 1e-05 100000 3.84500512404274 true +kdegi_typeIDwt kdegi_{typeIDwt} 1e-05 100000 0.010700824999592 true +kdim_typeIDT1 kdim_{typeIDT1} 1e-05 100000 5.83250831890056e-05 true +kdim_typeIDT3 kdim_{typeIDT3} 1e-05 100000 0.001677567484834 true +kdim_typeIDT5 kdim_{typeIDT5} 1e-05 100000 18.1949646811653 true +kdim_typeIDwt kdim_{typeIDwt} 1e-05 100000 7.67023154667708e-05 true +ksyn_typeIDT1 ksyn_{typeIDT1} 1e-05 100000 0.008319481267433 true +ksyn_typeIDT3 ksyn_{typeIDT3} 1e-05 100000 0.000883074159227 true +ksyn_typeIDT5 ksyn_{typeIDT5} 1e-05 100000 0.095782898201617 true +ksyn_typeIDwt ksyn_{typeIDwt} 1e-05 100000 0.005025909238224 true +sd_Bacnorm sd_{Bacnorm} 1e-05 100000 0.037770270062286 true +sd_IndconcNormRange sd_{IndconcNormRange} 1e-05 100000 0.020585215692131 true +tau_typeIDT1_ExpID1 tau_{typeIDT1,ExpID1} 1e-05 100000 0.163686586774761 true +tau_typeIDT1_ExpID2 tau_{typeIDT1,ExpID2} 1e-05 100000 0.055487869019712 true +tau_typeIDT1_ExpID3 tau_{typeIDT1,ExpID3} 1e-05 100000 0.003181239500361 true +tau_typeIDT1_ExpID4 tau_{typeIDT1,ExpID4} 1e-05 100000 2.56941090436867 true +tau_typeIDT1_ExpID5 tau_{typeIDT1,ExpID5} 1e-05 100000 0.064923120511828 true +tau_typeIDT1_ExpID6 tau_{typeIDT1,ExpID6} 1e-05 100000 0.29931942792129 true +tau_typeIDT3_ExpID1 tau_{typeIDT3,ExpID1} 1e-05 100000 0.020024772094431 true +tau_typeIDT3_ExpID2 tau_{typeIDT3,ExpID2} 1e-05 100000 20.2285763267388 true +tau_typeIDT3_ExpID3 tau_{typeIDT3,ExpID3} 1e-05 100000 0.012232114649765 true +tau_typeIDT3_ExpID4 tau_{typeIDT3,ExpID4} 1e-05 100000 36.5402552274508 true +tau_typeIDT3_ExpID5 tau_{typeIDT3,ExpID5} 1e-05 100000 0.000907004547265 true +tau_typeIDT3_ExpID6 tau_{typeIDT3,ExpID6} 1e-05 100000 0.027663606412915 true +tau_typeIDT5_ExpID1 tau_{typeIDT5,ExpID1} 1e-05 100000 223.655024181572 true +tau_typeIDT5_ExpID2 tau_{typeIDT5,ExpID2} 1e-05 100000 0.107117442362155 true +tau_typeIDT5_ExpID3 tau_{typeIDT5,ExpID3} 1e-05 100000 0.001493430452605 true +tau_typeIDT5_ExpID4 tau_{typeIDT5,ExpID4} 1e-05 100000 0.009498406487016 true +tau_typeIDT5_ExpID5 tau_{typeIDT5,ExpID5} 1e-05 100000 152.048602311963 true +tau_typeIDT5_ExpID6 tau_{typeIDT5,ExpID6} 1e-05 100000 0.193284981152434 true +tau_typeIDwt_ExpID4 tau_{typeIDwt,ExpID4} 1e-05 100000 1044.52421452662 true diff --git a/v2/Bertozzi_PNAS2020/conditions.tsv b/v2/Bertozzi_PNAS2020/conditions.tsv new file mode 100644 index 0000000..2af069c --- /dev/null +++ b/v2/Bertozzi_PNAS2020/conditions.tsv @@ -0,0 +1,9 @@ +conditionId targetId targetValue +u_CA N_ 39560000 +u_NY N_ 19540000 +u_CA I0_ I0_CA +u_NY I0_ I0_NY +u_CA R0_ R0_CA +u_NY R0_ R0_NY +u_CA gamma_ gamma_CA +u_NY gamma_ gamma_NY diff --git a/v2/Bertozzi_PNAS2020/experiments.tsv b/v2/Bertozzi_PNAS2020/experiments.tsv new file mode 100644 index 0000000..748488d --- /dev/null +++ b/v2/Bertozzi_PNAS2020/experiments.tsv @@ -0,0 +1,3 @@ +experimentId conditionId time +experiment____u_CA u_CA 0 +experiment____u_NY u_NY 0 diff --git a/v2/Bertozzi_PNAS2020/measurements.tsv b/v2/Bertozzi_PNAS2020/measurements.tsv new file mode 100644 index 0000000..179b218 --- /dev/null +++ b/v2/Bertozzi_PNAS2020/measurements.tsv @@ -0,0 +1,23 @@ +experimentId observableId measurement time datasetId realDate +experiment____u_CA y_I_CA 225 0 data_CA 2020-03-20 +experiment____u_CA y_I_CA 187 1 data_CA 2020-03-21 +experiment____u_CA y_I_CA 282 2 data_CA 2020-03-22 +experiment____u_CA y_I_CA 462 3 data_CA 2020-03-23 +experiment____u_CA y_I_CA 430 4 data_CA 2020-03-24 +experiment____u_CA y_I_CA 460 5 data_CA 2020-03-25 +experiment____u_CA y_I_CA 901 6 data_CA 2020-03-26 +experiment____u_CA y_I_CA 758 7 data_CA 2020-03-27 +experiment____u_CA y_I_CA 437 8 data_CA 2020-03-28 +experiment____u_CA y_I_CA 757 9 data_CA 2020-03-29 +experiment____u_CA y_I_CA 1286 10 data_CA 2020-03-30 +experiment____u_NY y_I_NY 2945 0 data_NY 2020-03-20 +experiment____u_NY y_I_NY 3400 1 data_NY 2020-03-21 +experiment____u_NY y_I_NY 4090 2 data_NY 2020-03-22 +experiment____u_NY y_I_NY 5084 3 data_NY 2020-03-23 +experiment____u_NY y_I_NY 4797 4 data_NY 2020-03-24 +experiment____u_NY y_I_NY 5160 5 data_NY 2020-03-25 +experiment____u_NY y_I_NY 7036 6 data_NY 2020-03-26 +experiment____u_NY y_I_NY 6999 7 data_NY 2020-03-27 +experiment____u_NY y_I_NY 7534 8 data_NY 2020-03-28 +experiment____u_NY y_I_NY 7237 9 data_NY 2020-03-29 +experiment____u_NY y_I_NY 7015 10 data_NY 2020-03-30 diff --git a/v2/Bertozzi_PNAS2020/model.xml b/v2/Bertozzi_PNAS2020/model.xml new file mode 100644 index 0000000..368e299 --- /dev/null +++ b/v2/Bertozzi_PNAS2020/model.xml @@ -0,0 +1,101 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + I0_ + + + + + + + + N_ + I0_ + + + + + + + + + + R0_ + gamma_ + + N_ + + + + + + + + + + + + + + + + + + beta_N + I_ + S_ + + + + + + + + + + + + + + + + gamma_ + I_ + + + + + + + diff --git a/v2/Bertozzi_PNAS2020/observables.tsv b/v2/Bertozzi_PNAS2020/observables.tsv new file mode 100644 index 0000000..66280d8 --- /dev/null +++ b/v2/Bertozzi_PNAS2020/observables.tsv @@ -0,0 +1,3 @@ +observableId observableName observableFormula noiseFormula observablePlaceholders noisePlaceholders +y_I_NY Confirmed infected in NY I_ sd_I_NY +y_I_CA Confirmed infected in CA I_ sd_I_CA diff --git a/v2/Bertozzi_PNAS2020/parameters.tsv b/v2/Bertozzi_PNAS2020/parameters.tsv new file mode 100644 index 0000000..5efee5f --- /dev/null +++ b/v2/Bertozzi_PNAS2020/parameters.tsv @@ -0,0 +1,9 @@ +parameterId lowerBound upperBound nominalValue estimate priorParameters +R0_NY 1.5 5.0 1.5 true +gamma_NY 0.01 0.2 0.15974646749068355 true +I0_NY 1000.0 10000.0 3631.9734930511822 true +sd_I_NY 100.0 1000.0 638.7370177109516 true +R0_CA 1.5 5.0 4.92721680123473 true +gamma_CA 0.01 0.2 0.039032488375217576 true +I0_CA 100.0 1000.0 232.90259817432732 true +sd_I_CA 100.0 1000.0 171.5520042582738 true diff --git a/v2/Bertozzi_PNAS2020/problem.yaml b/v2/Bertozzi_PNAS2020/problem.yaml new file mode 100644 index 0000000..cef1e9b --- /dev/null +++ b/v2/Bertozzi_PNAS2020/problem.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters.tsv +model_files: + model: + location: model.xml + language: sbml +measurement_files: +- measurements.tsv +condition_files: +- conditions.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Blasi_CellSystems2016/Blasi_CellSystems2016.yaml b/v2/Blasi_CellSystems2016/Blasi_CellSystems2016.yaml new file mode 100644 index 0000000..014304b --- /dev/null +++ b/v2/Blasi_CellSystems2016/Blasi_CellSystems2016.yaml @@ -0,0 +1,16 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Blasi_CellSystems2016.tsv +model_files: + model_Blasi_CellSystems2016: + location: model_Blasi_CellSystems2016.xml + language: sbml +measurement_files: +- measurementData_Blasi_CellSystems2016.tsv +condition_files: +- experimentalCondition_Blasi_CellSystems2016.tsv +experiment_files: [] +observable_files: +- observables_Blasi_CellSystems2016.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Blasi_CellSystems2016/experimentalCondition_Blasi_CellSystems2016.tsv b/v2/Blasi_CellSystems2016/experimentalCondition_Blasi_CellSystems2016.tsv new file mode 100644 index 0000000..730c58d --- /dev/null +++ b/v2/Blasi_CellSystems2016/experimentalCondition_Blasi_CellSystems2016.tsv @@ -0,0 +1 @@ +conditionId targetId targetValue diff --git a/v2/Blasi_CellSystems2016/measurementData_Blasi_CellSystems2016.tsv b/v2/Blasi_CellSystems2016/measurementData_Blasi_CellSystems2016.tsv new file mode 100644 index 0000000..a21ab54 --- /dev/null +++ b/v2/Blasi_CellSystems2016/measurementData_Blasi_CellSystems2016.tsv @@ -0,0 +1,253 @@ +experimentId observableId measurement time observableParameters noiseParameters + observable_0ac 0.7477507546 inf sigma + observable_0ac 0.7488324989 inf sigma + observable_0ac 0.7464186187 inf sigma + observable_0ac 0.7460197371 inf sigma + observable_0ac 0.7346777456 inf sigma + observable_0ac 0.7473683449 inf sigma + observable_0ac 0.7115299516 inf sigma + observable_0ac 0.7041180268 inf sigma + observable_0ac 0.687133716 inf sigma + observable_0ac 0.7043109811 inf sigma + observable_0ac 0.6877183143 inf sigma + observable_0ac 0.722193168 inf sigma + observable_0ac 0.7346053206 inf sigma + observable_0ac 0.7317104869 inf sigma + observable_0ac 0.7368055433 inf sigma + observable_0ac 0.7353015316 inf sigma + observable_0ac 0.7860370077 inf sigma + observable_0ac 0.7730402558 inf sigma + observable_k5 0.0357434956 inf sigma + observable_k5 0.0299751007 inf sigma + observable_k5 0.0319485374 inf sigma + observable_k5 0.0356067978 inf sigma + observable_k5 0.0358038875 inf sigma + observable_k5 0.0338619565 inf sigma + observable_k5 0.032286999 inf sigma + observable_k5 0.0386392741 inf sigma + observable_k5 0.0298921207 inf sigma + observable_k5 0.0344702628 inf sigma + observable_k5 0.035647086 inf sigma + observable_k5 0.0416663478 inf sigma + observable_k5 0.0364716656 inf sigma + observable_k5 0.0357468678 inf sigma + observable_k5 0.037757738 inf sigma + observable_k5 0.035665225 inf sigma + observable_k5 0.0328347091 inf sigma + observable_k5 0.0301433562 inf sigma + observable_k8 0.0285863714 inf sigma + observable_k8 0.0360768167 inf sigma + observable_k8 0.032107581 inf sigma + observable_k8 0.0299297615 inf sigma + observable_k8 0.0331305 inf sigma + observable_k8 0.0307525304 inf sigma + observable_k8 0.037988979 inf sigma + observable_k8 0.0333322401 inf sigma + observable_k8 0.0478313941 inf sigma + observable_k8 0.0342602774 inf sigma + observable_k8 0.0339720718 inf sigma + observable_k8 0.0267568853 inf sigma + observable_k8 0.0255184446 inf sigma + observable_k8 0.0302017929 inf sigma + observable_k8 0.0264043215 inf sigma + observable_k8 0.0308265468 inf sigma + observable_k8 0.0245199861 inf sigma + observable_k8 0.0306241172 inf sigma + observable_k12 0.0698911177 inf sigma + observable_k12 0.0657316077 inf sigma + observable_k12 0.0706330493 inf sigma + observable_k12 0.0726269828 inf sigma + observable_k12 0.0719746032 inf sigma + observable_k12 0.0658753768 inf sigma + observable_k12 0.0821448646 inf sigma + observable_k12 0.0800844078 inf sigma + observable_k12 0.0760295558 inf sigma + observable_k12 0.0825408662 inf sigma + observable_k12 0.0893413419 inf sigma + observable_k12 0.0779044736 inf sigma + observable_k12 0.0750340555 inf sigma + observable_k12 0.0847380136 inf sigma + observable_k12 0.0712320521 inf sigma + observable_k12 0.074118084 inf sigma + observable_k12 0.0572650931 inf sigma + observable_k12 0.0623801676 inf sigma + observable_k16 0.0340003746 inf sigma + observable_k16 0.0369876278 inf sigma + observable_k16 0.033021657 inf sigma + observable_k16 0.0316938561 inf sigma + observable_k16 0.0333103419 inf sigma + observable_k16 0.0351303222 inf sigma + observable_k16 0.035258857 inf sigma + observable_k16 0.0374192315 inf sigma + observable_k16 0.0352520559 inf sigma + observable_k16 0.0368370926 inf sigma + observable_k16 0.0403769705 inf sigma + observable_k16 0.0308594544 inf sigma + observable_k16 0.0280646579 inf sigma + observable_k16 0.0301801107 inf sigma + observable_k16 0.0317391594 inf sigma + observable_k16 0.0306364098 inf sigma + observable_k16 0.0331148093 inf sigma + observable_k16 0.0341717472 inf sigma + observable_k5k8 0.0056806576 inf sigma + observable_k5k8 0.0051190482 inf sigma + observable_k5k8 0.0064222373 inf sigma + observable_k5k8 0.006415159 inf sigma + observable_k5k8 0.0071723039 inf sigma + observable_k5k8 0.0053909205 inf sigma + observable_k5k8 0.0070625017 inf sigma + observable_k5k8 0.0055944146 inf sigma + observable_k5k8 0.0062533439 inf sigma + observable_k5k8 0.0060135768 inf sigma + observable_k5k8 0.0073291191 inf sigma + observable_k5k8 0.0063897149 inf sigma + observable_k5k8 0.0065985939 inf sigma + observable_k5k8 0.0066172451 inf sigma + observable_k5k8 0.0063324372 inf sigma + observable_k5k8 0.006899493 inf sigma + observable_k5k8 0.0038748389 inf sigma + observable_k5k8 0.0037448182 inf sigma + observable_k5k12 0.0434158865 inf sigma + observable_k5k12 0.0443789052 inf sigma + observable_k5k12 0.0470881206 inf sigma + observable_k5k12 0.0477700658 inf sigma + observable_k5k12 0.0600586224 inf sigma + observable_k5k12 0.0578341883 inf sigma + observable_k5k12 0.0571466513 inf sigma + observable_k5k12 0.0540117162 inf sigma + observable_k5k12 0.0511675275 inf sigma + observable_k5k12 0.0440053677 inf sigma + observable_k5k12 0.0307945134 inf sigma + observable_k5k12 0.0388013075 inf sigma + observable_k8k12 0.0080967193 inf sigma + observable_k8k12 0.0065363759 inf sigma + observable_k8k12 0.0065426513 inf sigma + observable_k8k12 0.0133786749 inf sigma + observable_k8k12 0.0121658868 inf sigma + observable_k8k12 0.0079245333 inf sigma + observable_k8k12 0.0054277999 inf sigma + observable_k8k12 0.0053220896 inf sigma + observable_k8k12 0.0054696133 inf sigma + observable_k8k12 0.0101090455 inf sigma + observable_k8k12 0.0094183962 inf sigma + observable_k8k12 0.0060419851 inf sigma + observable_k8k16 0.0038262075 inf sigma + observable_k8k16 0.0067116281 inf sigma + observable_k8k16 0.0055278515 inf sigma + observable_k8k16 0.0039600068 inf sigma + observable_k8k16 0.0013848019 inf sigma + observable_k8k16 0.0052229185 inf sigma + observable_k8k16 0.0066441942 inf sigma + observable_k8k16 0.0067009986 inf sigma + observable_k8k16 0.0076181629 inf sigma + observable_k8k16 0.0040375288 inf sigma + observable_k8k16 0.0012796644 inf sigma + observable_k8k16 0.0035808013 inf sigma + observable_k12k16 0.0071480679 inf sigma + observable_k12k16 0.0067384313 inf sigma + observable_k12k16 0.0070938912 inf sigma + observable_k12k16 0.0070100966 inf sigma + observable_k12k16 0.0079196391 inf sigma + observable_k12k16 0.0082749836 inf sigma + observable_k12k16 0.0116770005 inf sigma + observable_k12k16 0.0083859816 inf sigma + observable_k12k16 0.0087131588 inf sigma + observable_k12k16 0.008795474 inf sigma + observable_k12k16 0.0100321792 inf sigma + observable_k12k16 0.0075142106 inf sigma + observable_k12k16 0.0085223315 inf sigma + observable_k12k16 0.0081841044 inf sigma + observable_k12k16 0.0080296142 inf sigma + observable_k12k16 0.00870624 inf sigma + observable_k12k16 0.0069110704 inf sigma + observable_k12k16 0.0061287628 inf sigma + observable_k5k8k12 0.0053520976 inf sigma + observable_k5k8k12 0.0057590151 inf sigma + observable_k5k8k12 0.0060147152 inf sigma + observable_k5k8k12 0.0060189639 inf sigma + observable_k5k8k12 0.006159812 inf sigma + observable_k5k8k12 0.0060299617 inf sigma + observable_k5k8k12 0.0063920421 inf sigma + observable_k5k8k12 0.0063868816 inf sigma + observable_k5k8k12 0.0087433859 inf sigma + observable_k5k8k12 0.0084438032 inf sigma + observable_k5k8k12 0.0086304264 inf sigma + observable_k5k8k12 0.0071407069 inf sigma + observable_k5k8k12 0.0075398194 inf sigma + observable_k5k8k12 0.0057483973 inf sigma + observable_k5k8k12 0.006949499 inf sigma + observable_k5k8k12 0.0066482447 inf sigma + observable_k5k8k12 0.0045629576 inf sigma + observable_k5k8k12 0.0036498681 inf sigma + observable_k5k8k16 0.001472112 inf sigma + observable_k5k8k16 0.00135098 inf sigma + observable_k5k8k16 0.0010207226 inf sigma + observable_k5k8k16 0.0016467234 inf sigma + observable_k5k8k16 0.0012858873 inf sigma + observable_k5k8k16 0.0010164515 inf sigma + observable_k5k8k16 0.0021626724 inf sigma + observable_k5k8k16 0.0014689669 inf sigma + observable_k5k8k16 0.0015825669 inf sigma + observable_k5k8k16 0.001479875 inf sigma + observable_k5k8k16 0.0013319473 inf sigma + observable_k5k8k16 0.0015379107 inf sigma + observable_k5k8k16 0.0011180796 inf sigma + observable_k5k8k16 0.0011762112 inf sigma + observable_k5k8k16 0.0012530127 inf sigma + observable_k5k8k16 0.0009777025 inf sigma + observable_k5k8k16 0.0007228267 inf sigma + observable_k5k8k16 0.0010327739 inf sigma + observable_k5k12k16 0.0014459526 inf sigma + observable_k5k12k16 0.0028546517 inf sigma + observable_k5k12k16 0.0016474004 inf sigma + observable_k5k12k16 0.0015634113 inf sigma + observable_k5k12k16 0.0021988099 inf sigma + observable_k5k12k16 0.0025712943 inf sigma + observable_k5k12k16 0.0030239645 inf sigma + observable_k5k12k16 0.0051696682 inf sigma + observable_k5k12k16 0.0032202149 inf sigma + observable_k5k12k16 0.0039142288 inf sigma + observable_k5k12k16 0.0035694069 inf sigma + observable_k5k12k16 0.0020821695 inf sigma + observable_k5k12k16 0.0034115859 inf sigma + observable_k5k12k16 0.0020275485 inf sigma + observable_k5k12k16 0.0031633495 inf sigma + observable_k5k12k16 0.0017505789 inf sigma + observable_k5k12k16 0.0011259586 inf sigma + observable_k5k12k16 0.002221161 inf sigma + observable_k8k12k16 0.0034915637 inf sigma + observable_k8k12k16 0.0021823912 inf sigma + observable_k8k12k16 0.0034256206 inf sigma + observable_k8k12k16 0.003396277 inf sigma + observable_k8k12k16 0.0032172172 inf sigma + observable_k8k12k16 0.0034887922 inf sigma + observable_k8k12k16 0.0043486252 inf sigma + observable_k8k12k16 0.0043888815 inf sigma + observable_k8k12k16 0.0053253436 inf sigma + observable_k8k12k16 0.0038018268 inf sigma + observable_k8k12k16 0.004321794 inf sigma + observable_k8k12k16 0.0041416352 inf sigma + observable_k8k12k16 0.0037099053 inf sigma + observable_k8k12k16 0.0027575143 inf sigma + observable_k8k12k16 0.0032139497 inf sigma + observable_k8k12k16 0.0039214407 inf sigma + observable_k8k12k16 0.0023350612 inf sigma + observable_k8k12k16 0.0014335656 inf sigma + observable_4ac 0.0025586787 inf sigma + observable_4ac 0.0025276712 inf sigma + observable_4ac 0.0032089475 inf sigma + observable_4ac 0.0026968148 inf sigma + observable_4ac 0.0035432949 inf sigma + observable_4ac 0.0032944225 inf sigma + observable_4ac 0.0032371439 inf sigma + observable_4ac 0.0038015215 inf sigma + observable_4ac 0.0068750527 inf sigma + observable_4ac 0.0056489969 inf sigma + observable_4ac 0.0049831642 inf sigma + observable_4ac 0.0033456395 inf sigma + observable_4ac 0.0035895127 inf sigma + observable_4ac 0.0027663549 inf sigma + observable_4ac 0.0030647938 inf sigma + observable_4ac 0.0031698565 inf sigma + observable_4ac 0.0017445951 inf sigma + observable_4ac 0.0014080101 inf sigma diff --git a/v2/Blasi_CellSystems2016/model_Blasi_CellSystems2016.xml b/v2/Blasi_CellSystems2016/model_Blasi_CellSystems2016.xml new file mode 100644 index 0000000..76ebab6 --- /dev/null +++ b/v2/Blasi_CellSystems2016/model_Blasi_CellSystems2016.xml @@ -0,0 +1,1055 @@ + + + + + + 
PEtab implementation of the model from Blasi et al. (2016), Cell Systems;Volume 2, ISSUE 1, P49-58
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+ + + + + + + + + a_k5k8k12_4ac + x_k5k8k12 + + + + d + x_4ac + + + + + + + + + + + + + + + + + + + a_k5k8k16_4ac + x_k5k8k16 + + + + d + x_4ac + + + + + + + + + + + + + + + + + + + a_k5k12k16_4ac + x_k5k12k16 + + + + d + x_4ac + + + + + + + + + + + + + + + + + + + a_k8k12k16_4ac + x_k8k12k16 + + + + d + x_4ac + + + + + + + + diff --git a/v2/Blasi_CellSystems2016/observables_Blasi_CellSystems2016.tsv b/v2/Blasi_CellSystems2016/observables_Blasi_CellSystems2016.tsv new file mode 100644 index 0000000..c4f1138 --- /dev/null +++ b/v2/Blasi_CellSystems2016/observables_Blasi_CellSystems2016.tsv @@ -0,0 +1,17 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +observable_0ac x_0ac noiseParameter1_observable_0ac noiseParameter1_observable_0ac +observable_4ac x_4ac noiseParameter1_observable_4ac noiseParameter1_observable_4ac +observable_k12 x_k12 noiseParameter1_observable_k12 noiseParameter1_observable_k12 +observable_k12k16 x_k12k16 noiseParameter1_observable_k12k16 noiseParameter1_observable_k12k16 +observable_k16 x_k16 noiseParameter1_observable_k16 noiseParameter1_observable_k16 +observable_k5 x_k5 noiseParameter1_observable_k5 noiseParameter1_observable_k5 +observable_k5k12 x_k5k12 noiseParameter1_observable_k5k12 noiseParameter1_observable_k5k12 +observable_k5k12k16 x_k5k12k16 noiseParameter1_observable_k5k12k16 noiseParameter1_observable_k5k12k16 +observable_k5k16 x_k5k16 noiseParameter1_observable_k5k16 noiseParameter1_observable_k5k16 +observable_k5k8 x_k5k8 noiseParameter1_observable_k5k8 noiseParameter1_observable_k5k8 +observable_k5k8k12 x_k5k8k12 noiseParameter1_observable_k5k8k12 noiseParameter1_observable_k5k8k12 +observable_k5k8k16 x_k5k8k16 noiseParameter1_observable_k5k8k16 noiseParameter1_observable_k5k8k16 +observable_k8 x_k8 noiseParameter1_observable_k8 noiseParameter1_observable_k8 +observable_k8k12 x_k8k12 noiseParameter1_observable_k8k12 noiseParameter1_observable_k8k12 +observable_k8k12k16 x_k8k12k16 noiseParameter1_observable_k8k12k16 noiseParameter1_observable_k8k12k16 +observable_k8k16 x_k8k16 noiseParameter1_observable_k8k16 noiseParameter1_observable_k8k16 diff --git a/v2/Blasi_CellSystems2016/parameters_Blasi_CellSystems2016.tsv b/v2/Blasi_CellSystems2016/parameters_Blasi_CellSystems2016.tsv new file mode 100644 index 0000000..545d9b8 --- /dev/null +++ b/v2/Blasi_CellSystems2016/parameters_Blasi_CellSystems2016.tsv @@ -0,0 +1,11 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorParameters +a_basal a_basal 1e-12 1000 0.066799999926855 true +a_k8 a_k8 1e-12 1000 0.027299999997438 true +a_k5_k5k12 a_k5_k5k12 1e-12 1000 2.06200000024928 true +a_k12_k5k12 a_k12_k5k12 1e-12 1000 0.551899999917063 true +a_k16_k12k16 a_k16_k12k16 1e-12 1000 0.695899999206803 true +a_k5k12_k5k8k12 a_k5k12_k5k8k12 1e-12 1000 0.325299999788883 true +a_k12k16_k8k12k16 a_k12k16_k8k12k16 1e-12 1000 2.2054999994189 true +a_k8k12k16_4ac a_k8k12k16_4ac 1e-12 1000 3.59170000273213 true +d d 1e-12 1000 1.0 false +sigma sigma 1e-12 1000 0.1 true diff --git a/v2/Boehm_JProteomeRes2014/Boehm_JProteomeRes2014.yaml b/v2/Boehm_JProteomeRes2014/Boehm_JProteomeRes2014.yaml new file mode 100644 index 0000000..46fb475 --- /dev/null +++ b/v2/Boehm_JProteomeRes2014/Boehm_JProteomeRes2014.yaml @@ -0,0 +1,16 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Boehm_JProteomeRes2014.tsv +model_files: + model_Boehm_JProteomeRes2014: + location: model_Boehm_JProteomeRes2014.xml + language: sbml +measurement_files: +- measurementData_Boehm_JProteomeRes2014.tsv +condition_files: +- experimentalCondition_Boehm_JProteomeRes2014.tsv +experiment_files: [] +observable_files: +- observables_Boehm_JProteomeRes2014.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Boehm_JProteomeRes2014/experimentalCondition_Boehm_JProteomeRes2014.tsv b/v2/Boehm_JProteomeRes2014/experimentalCondition_Boehm_JProteomeRes2014.tsv new file mode 100644 index 0000000..730c58d --- /dev/null +++ b/v2/Boehm_JProteomeRes2014/experimentalCondition_Boehm_JProteomeRes2014.tsv @@ -0,0 +1 @@ +conditionId targetId targetValue diff --git a/v2/Boehm_JProteomeRes2014/measurementData_Boehm_JProteomeRes2014.tsv b/v2/Boehm_JProteomeRes2014/measurementData_Boehm_JProteomeRes2014.tsv new file mode 100644 index 0000000..bf86118 --- /dev/null +++ b/v2/Boehm_JProteomeRes2014/measurementData_Boehm_JProteomeRes2014.tsv @@ -0,0 +1,49 @@ +experimentId observableId measurement time observableParameters noiseParameters datasetId + pSTAT5A_rel 7.90107299873911 0.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel + pSTAT5A_rel 66.3634939682528 2.5 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel + pSTAT5A_rel 81.1713239165337 5.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel + pSTAT5A_rel 94.7303080627876 10.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel + pSTAT5A_rel 95.1164830493244 15.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel + pSTAT5A_rel 91.44171655392 20.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel + pSTAT5A_rel 91.2570992263545 30.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel + pSTAT5A_rel 93.672297840992 40.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel + pSTAT5A_rel 88.754232823019 50.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel + pSTAT5A_rel 85.2697032178279 60.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel + pSTAT5A_rel 81.1323953369608 80.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel + pSTAT5A_rel 76.135928475796 100.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel + pSTAT5A_rel 65.2480591250229 120.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel + pSTAT5A_rel 42.5996587097166 160.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel + pSTAT5A_rel 25.1577975445976 200.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel + pSTAT5A_rel 15.4301823994994 240.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel + pSTAT5B_rel 4.59653334288927 0.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel + pSTAT5B_rel 29.6345459874189 2.5 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel + pSTAT5B_rel 46.0438064695701 5.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel + pSTAT5B_rel 81.9747336191685 10.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel + pSTAT5B_rel 80.5716092952489 15.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel + pSTAT5B_rel 79.0357196371442 20.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel + pSTAT5B_rel 75.6723803658298 30.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel + pSTAT5B_rel 71.6247198618303 40.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel + pSTAT5B_rel 69.0628632755742 50.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel + pSTAT5B_rel 67.1473843168934 60.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel + pSTAT5B_rel 60.8994762938824 80.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel + pSTAT5B_rel 54.8092577721492 100.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel + pSTAT5B_rel 43.9812899778025 120.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel + pSTAT5B_rel 29.7714581636675 160.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel + pSTAT5B_rel 20.089016562771 200.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel + pSTAT5B_rel 10.961845166698 240.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel + rSTAT5A_rel 14.7231682180584 0.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel + rSTAT5A_rel 33.762342293107 2.5 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel + rSTAT5A_rel 36.7998512942493 5.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel + rSTAT5A_rel 49.7176022859654 10.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel + rSTAT5A_rel 46.9281200952955 15.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel + rSTAT5A_rel 47.8365745550135 20.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel + rSTAT5A_rel 46.9287272497385 30.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel + rSTAT5A_rel 40.5977529351181 40.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel + rSTAT5A_rel 43.783663885071 50.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel + rSTAT5A_rel 44.4573876523855 60.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel + rSTAT5A_rel 41.3271592618297 80.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel + rSTAT5A_rel 41.0627332148332 100.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel + rSTAT5A_rel 39.2358300289377 120.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel + rSTAT5A_rel 36.6194605442418 160.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel + rSTAT5A_rel 34.8937144010561 200.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel + rSTAT5A_rel 32.2110771608676 240.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel diff --git a/v2/Boehm_JProteomeRes2014/model_Boehm_JProteomeRes2014.xml b/v2/Boehm_JProteomeRes2014/model_Boehm_JProteomeRes2014.xml new file mode 100755 index 0000000..b3df1b4 --- /dev/null +++ b/v2/Boehm_JProteomeRes2014/model_Boehm_JProteomeRes2014.xml @@ -0,0 +1,290 @@ + + + + + + 
PEtab implementation of the model from Boehm et al. (2014), J. Proteome Res., 13, 12, 5685-5694
+ + + + + + + + + + Boehm + Martin + + + + + + 2019-11-29T09:41:48Z + + + 2019-11-29T09:41:48Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 207.6 + ratio + + + + + + + + 207.6 + + + 207.6 + ratio + + + + + + + + + + + 1.25 -7 + + + + + -1 + Epo_degradation_BaF3 + t + + + + + + + + + + + + + + + + + + + cyt + BaF3_Epo + + + STAT5A + 2 + + k_phos + + + + + + + + + + + + + + + + + cyt + BaF3_Epo + STAT5A + STAT5B + k_phos + + + + + + + + + + + + + + + + cyt + BaF3_Epo + + + STAT5B + 2 + + k_phos + + + + + + + + + + + + + + + + cyt + k_imp_homo + pApA + + + + + + + + + + + + + + + + cyt + k_imp_hetero + pApB + + + + + + + + + + + + + + + + cyt + k_imp_homo + pBpB + + + + + + + + + + + + + + + + nuc + k_exp_homo + nucpApA + + + + + + + + + + + + + + + + + nuc + k_exp_hetero + nucpApB + + + + + + + + + + + + + + + + nuc + k_exp_homo + nucpBpB + + + + + + + diff --git a/v2/Boehm_JProteomeRes2014/observables_Boehm_JProteomeRes2014.tsv b/v2/Boehm_JProteomeRes2014/observables_Boehm_JProteomeRes2014.tsv new file mode 100644 index 0000000..226bc81 --- /dev/null +++ b/v2/Boehm_JProteomeRes2014/observables_Boehm_JProteomeRes2014.tsv @@ -0,0 +1,4 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +pSTAT5A_rel (100 * pApB + 200 * pApA * specC17) / (pApB + STAT5A * specC17 + 2 * pApA * specC17) noiseParameter1_pSTAT5A_rel noiseParameter1_pSTAT5A_rel +pSTAT5B_rel -(100 * pApB - 200 * pBpB * (specC17 - 1)) / ((STAT5B * (specC17 - 1) - pApB) + 2 * pBpB * (specC17 - 1)) noiseParameter1_pSTAT5B_rel noiseParameter1_pSTAT5B_rel +rSTAT5A_rel (100 * pApB + 100 * STAT5A * specC17 + 200 * pApA * specC17) / (2 * pApB + STAT5A * specC17 + 2 * pApA * specC17 - STAT5B * (specC17 - 1) - 2 * pBpB * (specC17 - 1)) noiseParameter1_rSTAT5A_rel noiseParameter1_rSTAT5A_rel diff --git a/v2/Boehm_JProteomeRes2014/parameters_Boehm_JProteomeRes2014.tsv b/v2/Boehm_JProteomeRes2014/parameters_Boehm_JProteomeRes2014.tsv new file mode 100644 index 0000000..12fff19 --- /dev/null +++ b/v2/Boehm_JProteomeRes2014/parameters_Boehm_JProteomeRes2014.tsv @@ -0,0 +1,12 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorParameters +Epo_degradation_BaF3 EPO_{degradation,BaF3} 1e-05 100000 0.026982514033029 true +k_exp_hetero k_{exp,hetero} 1e-05 100000 1.00067973851508e-05 true +k_exp_homo k_{exp,homo} 1e-05 100000 0.006170228086381 true +k_imp_hetero k_{imp,hetero} 1e-05 100000 0.0163679184468 true +k_imp_homo k_{imp,homo} 1e-05 100000 97749.3794024716 true +k_phos k_{phos} 1e-05 100000 15766.5070195731 true +ratio ratio 0.0 5 0.693 false +sd_pSTAT5A_rel \sigma_{pSTAT5A,rel} 1e-05 100000 3.85261197844677 true +sd_pSTAT5B_rel \sigma_{pSTAT5B,rel} 1e-05 100000 6.59147818673419 true +sd_rSTAT5A_rel \sigma_{rSTAT5A,rel} 1e-05 100000 3.15271275648527 true +specC17 specC17 -5.0 5 0.107 false diff --git a/v2/Borghans_BiophysChem1997/Borghans_BiophysChem1997.yaml b/v2/Borghans_BiophysChem1997/Borghans_BiophysChem1997.yaml new file mode 100644 index 0000000..8bf5e2b --- /dev/null +++ b/v2/Borghans_BiophysChem1997/Borghans_BiophysChem1997.yaml @@ -0,0 +1,16 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Borghans_BiophysChem1997.tsv +model_files: + model_Borghans_BiophysChem1997: + location: model_Borghans_BiophysChem1997.xml + language: sbml +measurement_files: +- measurementData_Borghans_BiophysChem1997.tsv +condition_files: +- experimentalCondition_Borghans_BiophysChem1997.tsv +experiment_files: [] +observable_files: +- observables_Borghans_BiophysChem1997.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Borghans_BiophysChem1997/experimentalCondition_Borghans_BiophysChem1997.tsv b/v2/Borghans_BiophysChem1997/experimentalCondition_Borghans_BiophysChem1997.tsv new file mode 100644 index 0000000..730c58d --- /dev/null +++ b/v2/Borghans_BiophysChem1997/experimentalCondition_Borghans_BiophysChem1997.tsv @@ -0,0 +1 @@ +conditionId targetId targetValue diff --git a/v2/Borghans_BiophysChem1997/measurementData_Borghans_BiophysChem1997.tsv b/v2/Borghans_BiophysChem1997/measurementData_Borghans_BiophysChem1997.tsv new file mode 100644 index 0000000..85a986b --- /dev/null +++ b/v2/Borghans_BiophysChem1997/measurementData_Borghans_BiophysChem1997.tsv @@ -0,0 +1,112 @@ +experimentId observableId measurement time observableParameters noiseParameters + Ca 0.349094093638448 0.029484867 offset;scale sigma + Ca 0.373435333160542 0.147620899 offset;scale sigma + Ca 0.344146723385644 0.312814778 offset;scale sigma + Ca 0.373879840720067 0.445614618 offset;scale sigma + Ca 0.341839728595424 0.566227379 offset;scale sigma + Ca 0.366203193266489 0.699263097 offset;scale sigma + Ca 0.806581379884596 0.724620082 offset;scale sigma + Ca 1.0 0.79062687 offset;scale sigma + Ca 0.88193431945531 0.840515264 offset;scale sigma + Ca 0.715586217044644 0.922325941 offset;scale sigma + Ca 0.57342377569059 1.017974848 offset;scale sigma + Ca 0.608437644020494 1.090940065 offset;scale sigma + Ca 0.557537072025878 1.167679344 offset;scale sigma + Ca 0.635485935145917 1.223857844 offset;scale sigma + Ca 0.538943315809607 1.302602094 offset;scale sigma + Ca 0.643784893959343 1.38740057 offset;scale sigma + Ca 0.804941146565706 1.42502326 offset;scale sigma + Ca 0.611744781101873 1.508013332 offset;scale sigma + Ca 0.437408876409874 1.634876884 offset;scale sigma + Ca 0.338225881241447 1.743538446 offset;scale sigma + Ca 0.394762810266858 1.845359519 offset;scale sigma + Ca 0.633912377935369 1.96896008 offset;scale sigma + Ca 0.5588483692833 2.046760814 offset;scale sigma + Ca 0.505285195613442 2.138517719 offset;scale sigma + Ca 0.368536858933986 2.26373012 offset;scale sigma + Ca 0.46798655800823 2.333864789 offset;scale sigma + Ca 0.280137619586846 2.401719295 offset;scale sigma + Ca 0.339426051447788 2.548121486 offset;scale sigma + Ca 0.326090821603334 2.608309927 offset;scale sigma + Ca 0.35573503801813 2.681511023 offset;scale sigma + Ca 0.323783827035306 2.861722528 offset;scale sigma + Ca 0.353450268572356 2.949823309 offset;scale sigma + Ca 0.310826428312556 3.17520563 offset;scale sigma + Ca 0.343333274053228 3.367486273 offset;scale sigma + Ca 0.394678354621965 3.588740712 offset;scale sigma + Ca 0.880743038194813 3.641892098 offset;scale sigma + Ca 0.730592795087591 3.782593882 offset;scale sigma + Ca 0.636690551539262 3.831420821 offset;scale sigma + Ca 0.679714448974595 3.874232847 offset;scale sigma + Ca 0.572432523769101 3.953448856 offset;scale sigma + Ca 0.586034458442371 4.072056646 offset;scale sigma + Ca 0.492176664823728 4.150682957 offset;scale sigma + Ca 0.588941537789398 4.220935566 offset;scale sigma + Ca 0.457496177738232 4.301213029 offset;scale sigma + Ca 0.583794139570807 4.370168304 offset;scale sigma + Ca 0.44156502300655 4.421118154 offset;scale sigma + Ca 0.524950215087214 4.521759832 offset;scale sigma + Ca 0.374688844357398 4.587963185 offset;scale sigma + Ca 0.554705558748284 4.669459357 offset;scale sigma + Ca 0.597751680842474 4.727171069 offset;scale sigma + Ca 0.681070196412287 4.783113689 offset;scale sigma + Ca 0.584505351843597 4.846958254 offset;scale sigma + Ca 0.622226271721573 4.934705217 offset;scale sigma + Ca 0.528279577700738 4.953732784 offset;scale sigma + Ca 0.611620319093598 5.02457509 offset;scale sigma + Ca 0.493487963041773 5.029764427 offset;scale sigma + Ca 0.544633014733628 5.116921693 offset;scale sigma + Ca 0.429274385295461 5.181591833 offset;scale sigma + Ca 0.257601080899329 5.293437761 offset;scale sigma + Ca 0.33286511843398 5.349734199 offset;scale sigma + Ca 0.319552114019656 5.424822326 offset;scale sigma + Ca 0.354588208134813 5.512687229 offset;scale sigma + Ca 0.317133992462572 5.603736497 offset;scale sigma + Ca 0.357539739182399 5.691365521 offset;scale sigma + Ca 0.311986593371782 5.752969235 offset;scale sigma + Ca 0.341608584643843 5.811270645 offset;scale sigma + Ca 0.288023185287976 5.888127864 offset;scale sigma + Ca 0.379396181027403 5.943716666 offset;scale sigma + Ca 0.317822978969054 6.065626761 offset;scale sigma + Ca 0.744777035298493 6.091573444 offset;scale sigma + Ca 0.90870701559717 6.188676938 offset;scale sigma + Ca 0.849707514479775 6.235970664 offset;scale sigma + Ca 0.688773514844277 6.347344833 offset;scale sigma + Ca 0.62717808684206 6.454355242 offset;scale sigma + Ca 0.522514313746179 6.488754253 offset;scale sigma + Ca 0.603170228052092 6.559714499 offset;scale sigma + Ca 0.439484726955729 6.62650755 offset;scale sigma + Ca 0.565760463769103 6.680563139 offset;scale sigma + Ca 0.493359055506962 6.743346248 offset;scale sigma + Ca 0.576655346534321 6.784389183 offset;scale sigma + Ca 0.659996088984154 6.855231489 offset;scale sigma + Ca 0.504342840391355 6.906771036 offset;scale sigma + Ca 0.670935421945509 6.988856904 offset;scale sigma + Ca 0.569045375130751 7.08273672 offset;scale sigma + Ca 0.660396145843614 7.123425836 offset;scale sigma + Ca 0.612180398865166 7.200047176 offset;scale sigma + Ca 0.660596173934895 7.257523009 offset;scale sigma + Ca 0.475365385841722 7.280560518 offset;scale sigma + Ca 0.633836812643268 7.318301148 offset;scale sigma + Ca 0.515726680866965 7.33839017 offset;scale sigma + Ca 0.585665516659488 7.424721859 offset;scale sigma + Ca 0.523936738148843 7.442334153 offset;scale sigma + Ca 0.548211301026941 7.515771128 offset;scale sigma + Ca 0.44625457856736 7.564951885 offset;scale sigma + Ca 0.628933892539604 7.631430431 offset;scale sigma + Ca 0.524381245802199 7.740327872 offset;scale sigma + Ca 0.629133921488965 7.765527604 offset;scale sigma + Ca 0.532591301395887 7.844271855 offset;scale sigma + Ca 0.570334447197311 7.946918504 offset;scale sigma + Ca 0.444169837167304 7.967361345 offset;scale sigma + Ca 0.659089292208728 8.047324303 offset;scale sigma + Ca 0.514175349571299 8.098392092 offset;scale sigma + Ca 0.565320400550841 8.185549358 offset;scale sigma + Ca 0.369372533316219 8.223958311 offset;scale sigma + Ca 0.294308523547599 8.301759045 offset;scale sigma + Ca 0.267593613396788 8.392336556 offset;scale sigma + Ca 0.318738664768809 8.479493821 offset;scale sigma + Ca 0.297393406799128 8.569835453 offset;scale sigma + Ca 0.329722449084925 8.642918609 offset;scale sigma + Ca 0.327326552952011 8.836732465 offset;scale sigma + Ca 0.370506027839561 8.983842293 offset;scale sigma diff --git a/v2/Borghans_BiophysChem1997/model_Borghans_BiophysChem1997.xml b/v2/Borghans_BiophysChem1997/model_Borghans_BiophysChem1997.xml new file mode 100644 index 0000000..86105ac --- /dev/null +++ b/v2/Borghans_BiophysChem1997/model_Borghans_BiophysChem1997.xml @@ -0,0 +1,367 @@ + + + + + + 
PEtab implementation of the model from Borghans et al. (1997), Biophysical Chemistry 66(1) 25-41
+ + + + + + + + + + Borghans + José + + + + + + 2019-11-29T09:41:48Z + + + 2019-11-29T09:41:48Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + init_Z_state + + + + + init_Y_state + + + + + init_A_state + + + + + + + + + + + + + cytosol + + + v0 + + + beta_par + v1 + + + + + + + + + + + + + + + + + + cytosol + + + + + Vm2 + + + Z_state + 2 + + + + + + + K2 + 2 + + + + Z_state + 2 + + + + + + + + + + + + + + + + + + + + + + + intravesicular + + + + + + + A_state + 4 + + Vm3 + + + Y_state + 2 + + + + Z_state + 4 + + + + + + + + + A_state + 4 + + + + Ka + 4 + + + + + + + Ky + 2 + + + + Y_state + 2 + + + + + + + Kz + 4 + + + + Z_state + 4 + + + + + + + + + + + + + + + + + + + + intravesicular + Kf + Y_state + + + + + + + + + + + + + cytosol + K_par + Z_state + + + + + + + + + + + + + cytosol + Vp + beta_par + + + + + + + + + + + + + + + + cytosol + + + + + + + A_state + 2 + + Vd + + + Z_state + n_par + + + + + + + + + Kd + n_par + + + + Z_state + n_par + + + + + + + A_state + 2 + + + + Kp + 2 + + + + + + + + + + + + + + + + + cytosol + A_state + epsilon_par + + + + + + + diff --git a/v2/Borghans_BiophysChem1997/observables_Borghans_BiophysChem1997.tsv b/v2/Borghans_BiophysChem1997/observables_Borghans_BiophysChem1997.tsv new file mode 100644 index 0000000..b61a184 --- /dev/null +++ b/v2/Borghans_BiophysChem1997/observables_Borghans_BiophysChem1997.tsv @@ -0,0 +1,2 @@ +observableId observableFormula observableName noiseDistribution noiseFormula observablePlaceholders noisePlaceholders +Ca observableParameter1_Ca + Z_state * observableParameter2_Ca noiseParameter1_Ca observableParameter1_Ca;observableParameter2_Ca noiseParameter1_Ca diff --git a/v2/Borghans_BiophysChem1997/parameters_Borghans_BiophysChem1997.tsv b/v2/Borghans_BiophysChem1997/parameters_Borghans_BiophysChem1997.tsv new file mode 100644 index 0000000..a978c79 --- /dev/null +++ b/v2/Borghans_BiophysChem1997/parameters_Borghans_BiophysChem1997.tsv @@ -0,0 +1,24 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorParameters +K2 K2 0.001 100000 0.09994855801565 true +K_par K_{par} 0.001 100000 11.4120804594265 true +Ka Ka 0.001 100000 0.197593940310187 true +Kd Kd 0.001 100000 0.392497512107474 true +Kf Kf 0.001 100000 1.13794968361236 true +Kp Kp 0.001 100000 0.996567464196472 true +Ky Ky 0.001 100000 0.200364133028272 true +Kz Kz 0.001 100000 0.303353547057472 true +Vd Vd 0.001 100000 92.8739300577976 true +Vm2 Vm2 0.001 100000 7.45712445492225 true +Vm3 Vm3 0.001 100000 22.7025248825352 true +Vp Vp 0.001 100000 2.75685784345759 true +beta_par beta_{par} 0.001 100000 1.12395230256787 true +epsilon_par epsilon_{par} 0.001 100000 0.163232195306188 true +init_A_state init_{A,state} 0.0 1 0.99999999999996 true +init_Y_state init_{Y,state} 0.0 1 0.999348084438687 true +init_Z_state init_{Z,state} 0.0 1 0.087920524425504 true +n_par n_{par} 0.001 100000 4.1025144127497 true +offset offset 0.001 100000 0.300763662073358 true +scale scale 0.001 100000 0.658073142979721 true +sigma sigma 0.001 100000 0.104922918935031 true +v0 v0 0.001 100000 2.31778715779187 true +v1 v1 0.001 100000 1.00488755696677 true diff --git a/v2/Brannmark_JBC2010/Brannmark_JBC2010.yaml b/v2/Brannmark_JBC2010/Brannmark_JBC2010.yaml new file mode 100644 index 0000000..9ddffd0 --- /dev/null +++ b/v2/Brannmark_JBC2010/Brannmark_JBC2010.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Brannmark_JBC2010.tsv +model_files: + model_Brannmark_JBC2010: + location: model_Brannmark_JBC2010.xml + language: sbml +measurement_files: +- measurementData_Brannmark_JBC2010.tsv +condition_files: +- experimentalCondition_Brannmark_JBC2010.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Brannmark_JBC2010.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Brannmark_JBC2010/experimentalCondition_Brannmark_JBC2010.tsv b/v2/Brannmark_JBC2010/experimentalCondition_Brannmark_JBC2010.tsv new file mode 100644 index 0000000..cbb6a2e --- /dev/null +++ b/v2/Brannmark_JBC2010/experimentalCondition_Brannmark_JBC2010.tsv @@ -0,0 +1,33 @@ +conditionId targetId targetValue +Dose_0 insulin_time_1 0.0 +Dose_001 insulin_time_1 0.0 +Dose_01 insulin_time_1 0.0 +Dose_1 insulin_time_1 0.0 +Dose_3 insulin_time_1 0.0 +Dose_10 insulin_time_1 0.0 +Dose_100 insulin_time_1 0.0 +TwoSteps insulin_time_1 0.0 +Dose_0 insulin_dose_1 0.0 +Dose_001 insulin_dose_1 0.01 +Dose_01 insulin_dose_1 0.1 +Dose_1 insulin_dose_1 0.3 +Dose_3 insulin_dose_1 1.0 +Dose_10 insulin_dose_1 10.0 +Dose_100 insulin_dose_1 100.0 +TwoSteps insulin_dose_1 1.2 +Dose_0 insulin_time_2 0.0 +Dose_001 insulin_time_2 0.0 +Dose_01 insulin_time_2 0.0 +Dose_1 insulin_time_2 0.0 +Dose_3 insulin_time_2 0.0 +Dose_10 insulin_time_2 0.0 +Dose_100 insulin_time_2 0.0 +TwoSteps insulin_time_2 4.0 +Dose_0 insulin_dose_2 0.0 +Dose_001 insulin_dose_2 0.0 +Dose_01 insulin_dose_2 0.0 +Dose_1 insulin_dose_2 0.0 +Dose_3 insulin_dose_2 0.0 +Dose_10 insulin_dose_2 0.0 +Dose_100 insulin_dose_2 0.0 +TwoSteps insulin_dose_2 8.8 diff --git a/v2/Brannmark_JBC2010/experiments.tsv b/v2/Brannmark_JBC2010/experiments.tsv new file mode 100644 index 0000000..d588b7f --- /dev/null +++ b/v2/Brannmark_JBC2010/experiments.tsv @@ -0,0 +1,17 @@ +experimentId conditionId time +experiment__Dose_0___Dose_0 Dose_0 -inf +experiment__Dose_0___Dose_0 Dose_0 0.0 +experiment__Dose_0___Dose_001 Dose_0 -inf +experiment__Dose_0___Dose_001 Dose_001 0.0 +experiment__Dose_0___Dose_01 Dose_0 -inf +experiment__Dose_0___Dose_01 Dose_01 0.0 +experiment__Dose_0___Dose_1 Dose_0 -inf +experiment__Dose_0___Dose_1 Dose_1 0.0 +experiment__Dose_0___Dose_10 Dose_0 -inf +experiment__Dose_0___Dose_10 Dose_10 0.0 +experiment__Dose_0___Dose_100 Dose_0 -inf +experiment__Dose_0___Dose_100 Dose_100 0.0 +experiment__Dose_0___Dose_3 Dose_0 -inf +experiment__Dose_0___Dose_3 Dose_3 0.0 +experiment__Dose_0___TwoSteps Dose_0 -inf +experiment__Dose_0___TwoSteps TwoSteps 0.0 diff --git a/v2/Brannmark_JBC2010/measurementData_Brannmark_JBC2010.tsv b/v2/Brannmark_JBC2010/measurementData_Brannmark_JBC2010.tsv new file mode 100644 index 0000000..366dbe9 --- /dev/null +++ b/v2/Brannmark_JBC2010/measurementData_Brannmark_JBC2010.tsv @@ -0,0 +1,44 @@ +experimentId observableId measurement time observableParameters noiseParameters experiment_id_49153f7b-5405-4cd6-ac86-bac6addcccf0 independentVariableId +experiment__Dose_0___Dose_0 IRS1_P_DosR 18.385 10.0 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 +experiment__Dose_0___Dose_001 IRS1_P_DosR 29.115 10.0 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 +experiment__Dose_0___Dose_01 IRS1_P_DosR 26.365 10.0 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 +experiment__Dose_0___Dose_1 IRS1_P_DosR 28.292 10.0 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 +experiment__Dose_0___Dose_3 IRS1_P_DosR 42.308 10.0 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 +experiment__Dose_0___Dose_10 IRS1_P_DosR 105.029 10.0 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 +experiment__Dose_0___Dose_100 IRS1_P_DosR 94.971 10.0 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 +experiment__Dose_0___Dose_100 IR1_P 0.0 0.0 k_IRP_1Step sigmaY1TimR one_step_time_response time +experiment__Dose_0___Dose_100 IR1_P 100.0 0.9 k_IRP_1Step sigmaY1TimR one_step_time_response time +experiment__Dose_0___Dose_100 IR1_P 82.667 1.15 k_IRP_1Step sigmaY1TimR one_step_time_response time +experiment__Dose_0___Dose_100 IR1_P 77.333 1.3 k_IRP_1Step sigmaY1TimR one_step_time_response time +experiment__Dose_0___Dose_100 IR1_P 60.0 2.3 k_IRP_1Step sigmaY1TimR one_step_time_response time +experiment__Dose_0___Dose_100 IR1_P 50.667 3.3 k_IRP_1Step sigmaY1TimR one_step_time_response time +experiment__Dose_0___Dose_100 IR1_P 56.667 5.3 k_IRP_1Step sigmaY1TimR one_step_time_response time +experiment__Dose_0___Dose_100 IR1_P 45.667 7.0 k_IRP_1Step sigmaY1TimR one_step_time_response time +experiment__Dose_0___Dose_100 IR1_P 52.333 10.0 k_IRP_1Step sigmaY1TimR one_step_time_response time +experiment__Dose_0___Dose_100 IR1_P 41.333 15.0 k_IRP_1Step sigmaY1TimR one_step_time_response time +experiment__Dose_0___Dose_100 IR1_P 42.667 20.0 k_IRP_1Step sigmaY1TimR one_step_time_response time +experiment__Dose_0___Dose_100 IR1_P 35.333 30.0 k_IRP_1Step sigmaY1TimR one_step_time_response time +experiment__Dose_0___Dose_100 IRS1_P 0.0 0.0 k_IRSiP_1Step sigmaY2TimR one_step_time_response time +experiment__Dose_0___Dose_100 IRS1_P 227.667 0.9 k_IRSiP_1Step sigmaY2TimR one_step_time_response time +experiment__Dose_0___Dose_100 IRS1_P 205.0 1.15 k_IRSiP_1Step sigmaY2TimR one_step_time_response time +experiment__Dose_0___Dose_100 IRS1_P 169.667 1.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time +experiment__Dose_0___Dose_100 IRS1_P 145.5 2.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time +experiment__Dose_0___Dose_100 IRS1_P 121.667 3.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time +experiment__Dose_0___Dose_100 IRS1_P 110.333 5.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time +experiment__Dose_0___Dose_100 IRS1_P 95.0 7.0 k_IRSiP_1Step sigmaY2TimR one_step_time_response time +experiment__Dose_0___Dose_100 IRS1_P 110.0 10.0 k_IRSiP_1Step sigmaY2TimR one_step_time_response time +experiment__Dose_0___Dose_100 IRS1_P 86.667 15.0 k_IRSiP_1Step sigmaY2TimR one_step_time_response time +experiment__Dose_0___Dose_100 IRS1_P 73.0 20.0 k_IRSiP_1Step sigmaY2TimR one_step_time_response time +experiment__Dose_0___Dose_100 IRS1_P 100.0 30.0 k_IRSiP_1Step sigmaY2TimR one_step_time_response time +experiment__Dose_0___TwoSteps IRS1_P 14.417 0.0 k_IRSiP_2Step sigmaY2Step two_step_time_response time +experiment__Dose_0___TwoSteps IRS1_P 26.724 0.34 k_IRSiP_2Step sigmaY2Step two_step_time_response time +experiment__Dose_0___TwoSteps IRS1_P 42.035 0.6 k_IRSiP_2Step sigmaY2Step two_step_time_response time +experiment__Dose_0___TwoSteps IRS1_P 58.258 0.9 k_IRSiP_2Step sigmaY2Step two_step_time_response time +experiment__Dose_0___TwoSteps IRS1_P 58.752 1.2 k_IRSiP_2Step sigmaY2Step two_step_time_response time +experiment__Dose_0___TwoSteps IRS1_P 52.465 1.5 k_IRSiP_2Step sigmaY2Step two_step_time_response time +experiment__Dose_0___TwoSteps IRS1_P 56.405 4.0 k_IRSiP_2Step sigmaY2Step two_step_time_response time +experiment__Dose_0___TwoSteps IRS1_P 67.901 4.34 k_IRSiP_2Step sigmaY2Step two_step_time_response time +experiment__Dose_0___TwoSteps IRS1_P 66.297 4.6 k_IRSiP_2Step sigmaY2Step two_step_time_response time +experiment__Dose_0___TwoSteps IRS1_P 69.522 4.9 k_IRSiP_2Step sigmaY2Step two_step_time_response time +experiment__Dose_0___TwoSteps IRS1_P 74.644 5.2 k_IRSiP_2Step sigmaY2Step two_step_time_response time +experiment__Dose_0___TwoSteps IRS1_P 70.367 5.5 k_IRSiP_2Step sigmaY2Step two_step_time_response time diff --git a/v2/Brannmark_JBC2010/model_Brannmark_JBC2010.xml b/v2/Brannmark_JBC2010/model_Brannmark_JBC2010.xml new file mode 100644 index 0000000..aa76abf --- /dev/null +++ b/v2/Brannmark_JBC2010/model_Brannmark_JBC2010.xml @@ -0,0 +1,400 @@ + + + + + + 
PEtab implementation of the model from Brannmark et al. (2010), THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 285, NO. 26, pp. 20171–20179,
+ + + + + + + + + + Brannmark + Cecilia + + + + + + 2019-11-29T09:41:48Z + + + 2019-11-29T09:41:48Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + insulin_dose_1 + + + 0 + + + + + time + insulin_time_1 + + 0 + + + + 1 + + + + + + insulin_dose_2 + + + 0 + + + + + time + insulin_time_2 + + 0 + + + + 1 + + + + + + + + + + + + + + + + + + + + cyt + + + + + IR + k1aBasic + + + + IR + insulin + k1a + + + + + + + + + + + + + + + + + + cyt + IRins + k1b + + + + + + + + + + + + + + + + cyt + IRins + k1c + + + + + + + + + + + + + + + + cyt + IRp + k1d + + + + + + + + + + + + + + + + + + + cyt + IRiP + + + k1e + + + + + Xp + k1f + + + + Xp + 1 + + + + + + + + + + + + + + + + + + + cyt + IRp + k1g + + + + + + + + + + + + + + + + cyt + IRi + k1r + + + + + + + + + + + + + + + + + + + + cyt + IRS + k21 + + + IRp + + + IRiP + k22 + + + + + + + + + + + + + + + + + + cyt + IRSiP + km2 + + + + + + + + + + + + + + + + + + + cyt + IRSiP + X + k3 + + + + + + + + + + + + + + + + cyt + Xp + km3 + + + + + + + diff --git a/v2/Brannmark_JBC2010/observables_Brannmark_JBC2010.tsv b/v2/Brannmark_JBC2010/observables_Brannmark_JBC2010.tsv new file mode 100644 index 0000000..d34d309 --- /dev/null +++ b/v2/Brannmark_JBC2010/observables_Brannmark_JBC2010.tsv @@ -0,0 +1,4 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +IR1_P IR1_P observableParameter1_IR1_P * (IRp + IRiP) noiseParameter1_IR1_P observableParameter1_IR1_P noiseParameter1_IR1_P +IRS1_P IRS1_P observableParameter1_IRS1_P * IRSiP noiseParameter1_IRS1_P observableParameter1_IRS1_P noiseParameter1_IRS1_P +IRS1_P_DosR IRS1_P_DosR observableParameter1_IRS1_P_DosR * IRSiP noiseParameter1_IRS1_P_DosR observableParameter1_IRS1_P_DosR noiseParameter1_IRS1_P_DosR diff --git a/v2/Brannmark_JBC2010/parameters_Brannmark_JBC2010.tsv b/v2/Brannmark_JBC2010/parameters_Brannmark_JBC2010.tsv new file mode 100644 index 0000000..4ca500c --- /dev/null +++ b/v2/Brannmark_JBC2010/parameters_Brannmark_JBC2010.tsv @@ -0,0 +1,23 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorParameters +k1a k1a 1e-06 500000.000000001 0.177219477727669 true +k1aBasic k1aBasic 1e-06 500000.000000001 0.000392767904337 true +k1b k1b 1e-06 500000.000000001 0.174695978547559 true +k1c k1c 1e-06 500000.000000001 0.050857471885817 true +k1d k1d 1e-06 500000.000000001 499999.999999977 true +k1e k1e 1e-06 500000.000000001 1.00000000000009e-06 true +k1f k1f 1e-06 500000.000000001 499999.99200416 true +k1g k1g 1e-06 500000.000000001 1729.3765495871 true +k1r k1r 1e-06 500000.000000001 0.026696391080189 true +k21 k21 1e-06 500000.000000001 2.10238165504418 true +k22 k22 1e-06 500000.000000001 666.8355739795 true +k3 k3 1e-06 500000.000000001 4.94410392362901e-05 true +k_IRP_1Step k_{IRP,1Step} 10.0 200000.0 199999.840171263 true +k_IRSiP_1Step k_{IRSiP,1Step} 10.0 200000.0 45.1583098084992 true +k_IRSiP_2Step k_{IRSiP,2Step} 10.0 200000.0 27.0146739112635 true +k_IRSiP_DosR k_{IRSiP,DosR} 10.0 200000.0 37.943517943785 true +km2 km2 1e-06 500000.000000001 1.15970741690448 true +km3 km3 1e-06 500000.000000001 0.416382500906785 true +sigmaY1TimR \sigma_{Y1TimR} 1e-05 1000.0 2.96681079960572 true +sigmaY2Step \sigma_{Y2Step} 1e-05 1000.0 5.15364156671777 true +sigmaY2TimR \sigma_{Y2TimR} 1e-05 1000.0 10.3675897036965 true +sigmaYDosR \sigma_{YDosR} 1e-05 1000.0 17.5783273408723 true diff --git a/v2/Bruno_JExpBot2016/Bruno_JExpBot2016.yaml b/v2/Bruno_JExpBot2016/Bruno_JExpBot2016.yaml new file mode 100644 index 0000000..e9af863 --- /dev/null +++ b/v2/Bruno_JExpBot2016/Bruno_JExpBot2016.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Bruno_JExpBot2016.tsv +model_files: + model_Bruno_JExpBot2016: + location: model_Bruno_JExpBot2016.xml + language: sbml +measurement_files: +- measurementData_Bruno_JExpBot2016.tsv +condition_files: +- experimentalCondition_Bruno_JExpBot2016.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Bruno_JExpBot2016.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Bruno_JExpBot2016/experimentalCondition_Bruno_JExpBot2016.tsv b/v2/Bruno_JExpBot2016/experimentalCondition_Bruno_JExpBot2016.tsv new file mode 100644 index 0000000..b6a2dca --- /dev/null +++ b/v2/Bruno_JExpBot2016/experimentalCondition_Bruno_JExpBot2016.tsv @@ -0,0 +1,67 @@ +conditionId targetId targetValue +model1_data1 init_b10 init_b10_1 +model1_data2 init_b10 0 +model1_data3 init_b10 0 +model1_data4 init_b10 0 +model1_data5 init_b10 0 +model1_data6 init_b10 0 +model1_data1 init_bcar 0 +model1_data2 init_bcar init_bcar1 +model1_data3 init_bcar init_bcar2 +model1_data4 init_bcar 0 +model1_data5 init_bcar 0 +model1_data6 init_bcar 0 +model1_data1 init_bcry 0 +model1_data2 init_bcry 0 +model1_data3 init_bcry 0 +model1_data4 init_bcry init_bcry_1 +model1_data5 init_bcry 0 +model1_data6 init_bcry 0 +model1_data1 init_ohb10 0 +model1_data2 init_ohb10 0 +model1_data3 init_ohb10 0 +model1_data4 init_ohb10 0 +model1_data5 init_ohb10 init_ohb10_1 +model1_data6 init_ohb10 0 +model1_data1 init_zea 0 +model1_data2 init_zea 0 +model1_data3 init_zea 0 +model1_data4 init_zea 0 +model1_data5 init_zea 0 +model1_data6 init_zea init_zea_1 +model1_data1 k5_multiplier 0 +model1_data2 k5_multiplier 1 +model1_data3 k5_multiplier szea +model1_data4 k5_multiplier 1 +model1_data5 k5_multiplier 0 +model1_data6 k5_multiplier szea +model1_data1 kb1_multiplier 0 +model1_data2 kb1_multiplier 1 +model1_data3 kb1_multiplier szea +model1_data4 kb1_multiplier 0 +model1_data5 kb1_multiplier 0 +model1_data6 kb1_multiplier 0 +model1_data1 kb2_multiplier 1 +model1_data2 kb2_multiplier 1 +model1_data3 kb2_multiplier szea +model1_data4 kb2_multiplier 1 +model1_data5 kb2_multiplier 1 +model1_data6 kb2_multiplier 0 +model1_data1 kc1_multiplier 1 +model1_data2 kc1_multiplier 0 +model1_data3 kc1_multiplier szea +model1_data4 kc1_multiplier 1 +model1_data5 kc1_multiplier 0 +model1_data6 kc1_multiplier 0 +model1_data1 kc2_multiplier 0 +model1_data2 kc2_multiplier 0 +model1_data3 kc2_multiplier szea +model1_data4 kc2_multiplier 1 +model1_data5 kc2_multiplier 0 +model1_data6 kc2_multiplier 0 +model1_data1 kc4_multiplier 1 +model1_data2 kc4_multiplier 0 +model1_data3 kc4_multiplier szea +model1_data4 kc4_multiplier 1 +model1_data5 kc4_multiplier 1 +model1_data6 kc4_multiplier szea diff --git a/v2/Bruno_JExpBot2016/experiments.tsv b/v2/Bruno_JExpBot2016/experiments.tsv new file mode 100644 index 0000000..2b9fbb2 --- /dev/null +++ b/v2/Bruno_JExpBot2016/experiments.tsv @@ -0,0 +1,7 @@ +experimentId conditionId time +experiment____model1_data1 model1_data1 0 +experiment____model1_data2 model1_data2 0 +experiment____model1_data3 model1_data3 0 +experiment____model1_data4 model1_data4 0 +experiment____model1_data5 model1_data5 0 +experiment____model1_data6 model1_data6 0 diff --git a/v2/Bruno_JExpBot2016/measurementData_Bruno_JExpBot2016.tsv b/v2/Bruno_JExpBot2016/measurementData_Bruno_JExpBot2016.tsv new file mode 100644 index 0000000..2e20ef2 --- /dev/null +++ b/v2/Bruno_JExpBot2016/measurementData_Bruno_JExpBot2016.tsv @@ -0,0 +1,78 @@ +experimentId observableId measurement time observableParameters noiseParameters datasetId +experiment____model1_data1 ob10 3.973385 5 0.406451 model1_data1_ob10 +experiment____model1_data1 ob10 3.976118 15 0.406728 model1_data1_ob10 +experiment____model1_data1 ob10 3.12959 30 0.320749 model1_data1_ob10 +experiment____model1_data1 ob10 3.131418 60 0.320935 model1_data1_ob10 +experiment____model1_data1 ob10 3.105543 90 0.31831 model1_data1_ob10 +experiment____model1_data1 ob10 2.279702 120 0.234682 model1_data1_ob10 +experiment____model1_data1 ob10 1.321613 180 0.138555 model1_data1_ob10 +experiment____model1_data2 obcar 3.83496 15 0.251006 model1_data2_obcar +experiment____model1_data2 obcar 2.68932 30 0.179664 model1_data2_obcar +experiment____model1_data2 obcar 2.12541 45 0.145321 model1_data2_obcar +experiment____model1_data2 obcar 1.55414 60 0.111703 model1_data2_obcar +experiment____model1_data2 obcar 0.90185 90 0.076761 model1_data2_obcar +experiment____model1_data2 obcar 0.62496 120 0.064455 model1_data2_obcar +experiment____model1_data2 obcar 0.30276 180 0.054089 model1_data2_obcar +experiment____model1_data2 ob10 0.87947 15 0.110017 model1_data2_ob10 +experiment____model1_data2 ob10 1.61775 30 0.194075 model1_data2_ob10 +experiment____model1_data2 ob10 2.0221 45 0.240978 model1_data2_ob10 +experiment____model1_data2 ob10 2.51711 60 0.298703 model1_data2_ob10 +experiment____model1_data2 ob10 2.24951 90 0.267467 model1_data2_ob10 +experiment____model1_data2 ob10 2.46923 120 0.29311 model1_data2_ob10 +experiment____model1_data2 ob10 2.09599 180 0.249578 model1_data2_ob10 +experiment____model1_data3 obcar 2.792 15 0.161073 model1_data3_obcar +experiment____model1_data3 obcar 2.51 30 0.146065 model1_data3_obcar +experiment____model1_data3 obcar 2.101 45 0.124582 model1_data3_obcar +experiment____model1_data3 obcar 1.917 60 0.115071 model1_data3_obcar +experiment____model1_data3 obcar 1.598 90 0.098916 model1_data3_obcar +experiment____model1_data3 obcar 1.135 120 0.076702 model1_data3_obcar +experiment____model1_data3 obcar 0.824 180 0.063285 model1_data3_obcar +experiment____model1_data3 ob10 0.573 15 0.066702 model1_data3_ob10 +experiment____model1_data3 ob10 0.849 30 0.092359 model1_data3_ob10 +experiment____model1_data3 ob10 0.968 45 0.10382 model1_data3_ob10 +experiment____model1_data3 ob10 1.212 60 0.127709 model1_data3_ob10 +experiment____model1_data3 ob10 1.411 90 0.147436 model1_data3_ob10 +experiment____model1_data3 ob10 1.612 120 0.167498 model1_data3_ob10 +experiment____model1_data3 ob10 2.168 180 0.223405 model1_data3_ob10 +experiment____model1_data4 obcry 4.804181 15 0.43054 model1_data4_obcry +experiment____model1_data4 obcry 3.874252 30 0.353484 model1_data4_obcry +experiment____model1_data4 obcry 3.687507 45 0.338201 model1_data4_obcry +experiment____model1_data4 obcry 2.905136 60 0.275261 model1_data4_obcry +experiment____model1_data4 obcry 2.471236 90 0.241465 model1_data4_obcry +experiment____model1_data4 obcry 2.243992 120 0.224241 model1_data4_obcry +experiment____model1_data4 obcry 0.922679 180 0.137702 model1_data4_obcry +experiment____model1_data4 ob10 0.186897 15 0.043179 model1_data4_ob10 +experiment____model1_data4 ob10 0.238582 30 0.046576 model1_data4_ob10 +experiment____model1_data4 ob10 0.268357 45 0.048771 model1_data4_ob10 +experiment____model1_data4 ob10 0.377915 60 0.057968 model1_data4_ob10 +experiment____model1_data4 ob10 0.332696 90 0.053988 model1_data4_ob10 +experiment____model1_data4 ob10 0.410503 120 0.060963 model1_data4_ob10 +experiment____model1_data4 ob10 0.487949 180 0.068419 model1_data4_ob10 +experiment____model1_data4 oohb10 0.750567 15 0.146042 model1_data4_oohb10 +experiment____model1_data4 oohb10 0.957066 30 0.185626 model1_data4_oohb10 +experiment____model1_data4 oohb10 1.058638 45 0.205133 model1_data4_oohb10 +experiment____model1_data4 oohb10 1.40061 60 0.270906 model1_data4_oohb10 +experiment____model1_data4 oohb10 1.342636 90 0.259748 model1_data4_oohb10 +experiment____model1_data4 oohb10 1.652208 120 0.319353 model1_data4_oohb10 +experiment____model1_data4 oohb10 2.005941 180 0.387509 model1_data4_oohb10 +experiment____model1_data5 oohb10 2.187219 5 0.365852 model1_data5_oohb10 +experiment____model1_data5 oohb10 1.490176 15 0.249545 model1_data5_oohb10 +experiment____model1_data5 oohb10 1.243819 30 0.208483 model1_data5_oohb10 +experiment____model1_data5 oohb10 1.100679 60 0.184647 model1_data5_oohb10 +experiment____model1_data5 oohb10 1.142316 90 0.191578 model1_data5_oohb10 +experiment____model1_data5 oohb10 0.794621 120 0.13378 model1_data5_oohb10 +experiment____model1_data5 oohb10 0.696621 180 0.117543 model1_data5_oohb10 +experiment____model1_data6 oohb10 0.098 15 0.023108 model1_data6_oohb10 +experiment____model1_data6 oohb10 0.1573 30 0.030931 model1_data6_oohb10 +experiment____model1_data6 oohb10 0.165 45 0.032031 model1_data6_oohb10 +experiment____model1_data6 oohb10 0.23 60 0.041749 model1_data6_oohb10 +experiment____model1_data6 oohb10 0.374 90 0.064588 model1_data6_oohb10 +experiment____model1_data6 oohb10 0.445 120 0.076127 model1_data6_oohb10 +experiment____model1_data6 oohb10 0.46 180 0.090733 model1_data6_oohb10 +experiment____model1_data6 ozea 2.761 15 0.172674 model1_data6_ozea +experiment____model1_data6 ozea 2.93 30 0.183243 model1_data6_ozea +experiment____model1_data6 ozea 2.842 45 0.17774 model1_data6_ozea +experiment____model1_data6 ozea 2.763 60 0.172799 model1_data6_ozea +experiment____model1_data6 ozea 2.581 90 0.161417 model1_data6_ozea +experiment____model1_data6 ozea 2.449 120 0.153161 model1_data6_ozea +experiment____model1_data6 ozea 2.128 180 0.133086 model1_data6_ozea diff --git a/v2/Bruno_JExpBot2016/model_Bruno_JExpBot2016.xml b/v2/Bruno_JExpBot2016/model_Bruno_JExpBot2016.xml new file mode 100644 index 0000000..ace4c22 --- /dev/null +++ b/v2/Bruno_JExpBot2016/model_Bruno_JExpBot2016.xml @@ -0,0 +1,222 @@ + + + + + + 
PEtab implementation of the model from Bruno et al. (2016), J Exp Bot.; 67(21): 5993–6005
+ + + + + + + + + + Bruno + Mark + + + + + + 2019-11-29T09:41:48Z + + + 2019-11-29T09:41:48Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + init_bcar + + + + + init_b10 + + + + + init_bcry + + + + + init_ohb10 + + + + + init_zea + + + + + + + + + + + + + + + + + cyt + bcar + kb1 + kb1_multiplier + + + + + + + + + + + + + + + + cyt + b10 + kb2 + kb2_multiplier + + + + + + + + + + + + + + + + + cyt + bcry + kc1 + kc1_multiplier + + + + + + + + + + + + + + + + + cyt + bcry + kc2 + kc2_multiplier + + + + + + + + + + + + + + + + cyt + kc4 + kc4_multiplier + ohb10 + + + + + + + + + + + + + + + + + cyt + k5 + k5_multiplier + zea + + + + + + + diff --git a/v2/Bruno_JExpBot2016/observables_Bruno_JExpBot2016.tsv b/v2/Bruno_JExpBot2016/observables_Bruno_JExpBot2016.tsv new file mode 100644 index 0000000..f45be11 --- /dev/null +++ b/v2/Bruno_JExpBot2016/observables_Bruno_JExpBot2016.tsv @@ -0,0 +1,7 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +ob10 b10 noiseParameter1_ob10 noiseParameter1_ob10 +obcar bcar noiseParameter1_obcar noiseParameter1_obcar +obcry bcry noiseParameter1_obcry noiseParameter1_obcry +obio bio noiseParameter1_obio noiseParameter1_obio +oohb10 ohb10 noiseParameter1_oohb10 noiseParameter1_oohb10 +ozea zea noiseParameter1_ozea noiseParameter1_ozea diff --git a/v2/Bruno_JExpBot2016/parameters_Bruno_JExpBot2016.tsv b/v2/Bruno_JExpBot2016/parameters_Bruno_JExpBot2016.tsv new file mode 100644 index 0000000..290f7ec --- /dev/null +++ b/v2/Bruno_JExpBot2016/parameters_Bruno_JExpBot2016.tsv @@ -0,0 +1,14 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorParameters +init_b10_1 init_{b10} 1e-05 1000 4.22228991356159 true +init_bcar1 init_{bcar1} 1e-05 1000 4.44029572277168 true +init_bcar2 init_{bcar2} 1e-05 1000 3.30171980495163 true +init_bcry_1 init_{bcry} 1e-05 1000 5.21693865661801 true +init_ohb10_1 init_{ohb10} 1e-05 1000 1.73724675926262 true +init_zea_1 init_{zea} 1e-05 1000 2.95812301577671 true +k5 k5 1e-05 1000 0.003086673219173 true +kb1 kb1 1e-05 1000 0.016628409992721 true +kb2 kb2 1e-05 1000 0.005843831819271 true +kc1 kc1 1e-05 1000 0.001678825242274 true +kc2 kc2 1e-05 1000 0.006975989070463 true +kc4 kc4 1e-05 1000 0.006082700899195 true +szea szea 1e-05 1000 0.516831766210391 true diff --git a/v2/Chen_MSB2009/Chen_MSB2009.yaml b/v2/Chen_MSB2009/Chen_MSB2009.yaml new file mode 100644 index 0000000..510f713 --- /dev/null +++ b/v2/Chen_MSB2009/Chen_MSB2009.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Chen_MSB2009.tsv +model_files: + model_Chen_MSB2009: + location: model_Chen_MSB2009.xml + language: sbml +measurement_files: +- measurementData_Chen_MSB2009.tsv +condition_files: +- experimentalCondition_Chen_MSB2009.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Chen_MSB2009.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Chen_MSB2009/experimentalCondition_Chen_MSB2009.tsv b/v2/Chen_MSB2009/experimentalCondition_Chen_MSB2009.tsv new file mode 100644 index 0000000..4843b06 --- /dev/null +++ b/v2/Chen_MSB2009/experimentalCondition_Chen_MSB2009.tsv @@ -0,0 +1,9 @@ +conditionId targetId targetValue +model1_data1 c1 5e-09 +model1_data2 c1 0.0 +model1_data3 c1 1e-11 +model1_data4 c1 0.0 +model1_data1 c514 0.0 +model1_data2 c514 5e-09 +model1_data3 c514 0.0 +model1_data4 c514 1e-10 diff --git a/v2/Chen_MSB2009/experiments.tsv b/v2/Chen_MSB2009/experiments.tsv new file mode 100644 index 0000000..c8b3857 --- /dev/null +++ b/v2/Chen_MSB2009/experiments.tsv @@ -0,0 +1,5 @@ +experimentId conditionId time +experiment____model1_data1 model1_data1 0 +experiment____model1_data2 model1_data2 0 +experiment____model1_data3 model1_data3 0 +experiment____model1_data4 model1_data4 0 diff --git a/v2/Chen_MSB2009/measurementData_Chen_MSB2009.tsv b/v2/Chen_MSB2009/measurementData_Chen_MSB2009.tsv new file mode 100644 index 0000000..744c69d --- /dev/null +++ b/v2/Chen_MSB2009/measurementData_Chen_MSB2009.tsv @@ -0,0 +1,121 @@ +experimentId observableId measurement time observableParameters noiseParameters datasetId +experiment____model1_data1 ERB_B1_P_tot 0.0 1800 EGFR_t 0.1 model1_data1_ERB_B1_P_tot +experiment____model1_data1 ERB_B1_P_tot 65.0 1950 EGFR_t 7.4 model1_data1_ERB_B1_P_tot +experiment____model1_data1 ERB_B1_P_tot 72.0 2100 EGFR_t 6.8 model1_data1_ERB_B1_P_tot +experiment____model1_data1 ERB_B1_P_tot 75.0 2250 EGFR_t 8.9 model1_data1_ERB_B1_P_tot +experiment____model1_data1 ERB_B1_P_tot 77.0 2400 EGFR_t 4.7 model1_data1_ERB_B1_P_tot +experiment____model1_data1 ERB_B1_P_tot 83.0 2700 EGFR_t 4.7 model1_data1_ERB_B1_P_tot +experiment____model1_data1 ERB_B1_P_tot 87.0 3600 EGFR_t 2.5 model1_data1_ERB_B1_P_tot +experiment____model1_data1 ERB_B1_P_tot 98.0 4500 EGFR_t 2.4 model1_data1_ERB_B1_P_tot +experiment____model1_data1 ERB_B1_P_tot 87.0 5400 EGFR_t 13.1 model1_data1_ERB_B1_P_tot +experiment____model1_data1 ERB_B1_P_tot 86.0 9000 EGFR_t 13.1 model1_data1_ERB_B1_P_tot +experiment____model1_data1 ERK_PP 0.0 1800 ERK_t 0.1 model1_data1_ERK_PP +experiment____model1_data1 ERK_PP 60.0 1950 ERK_t 0.46 model1_data1_ERK_PP +experiment____model1_data1 ERK_PP 88.0 2100 ERK_t 1.9 model1_data1_ERK_PP +experiment____model1_data1 ERK_PP 97.0 2250 ERK_t 1.5 model1_data1_ERK_PP +experiment____model1_data1 ERK_PP 98.0 2400 ERK_t 1.2 model1_data1_ERK_PP +experiment____model1_data1 ERK_PP 86.0 2700 ERK_t 3.1 model1_data1_ERK_PP +experiment____model1_data1 ERK_PP 65.0 3600 ERK_t 2.8 model1_data1_ERK_PP +experiment____model1_data1 ERK_PP 56.0 4500 ERK_t 2.9 model1_data1_ERK_PP +experiment____model1_data1 ERK_PP 50.0 5400 ERK_t 3.7 model1_data1_ERK_PP +experiment____model1_data1 ERK_PP 46.0 9000 ERK_t 1.5 model1_data1_ERK_PP +experiment____model1_data1 AKT_PP 0.0 1800 AKT_t 0.1 model1_data1_AKT_PP +experiment____model1_data1 AKT_PP 0.0 1950 AKT_t 0.1 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PEtab implementation of the model from Chen et al. (2009), Mol Syst Biol. ;5:239
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c484 + c497 + c498) / observableParameter1_AKT_PP noiseParameter1_AKT_PP observableParameter1_AKT_PP noiseParameter1_AKT_PP +ERB_B1_P_tot (2 * c5 + 2 * c7 + 2 * c8 + 2 * c15 + 2 * c17 + 2 * c18 + 2 * c19 + 2 * c20 + 2 * c21 + 2 * c23 + 2 * c25 + 2 * c27 + 2 * c29 + 2 * c32 + 2 * c33 + 2 * c34 + 2 * c35 + 2 * c36 + 2 * c37 + 2 * c63 + 2 * c64 + 2 * c65 + 2 * c66 + 2 * c67 + 2 * c68 + 2 * c88 + 2 * c89 + 2 * c90 + 2 * c91 + 2 * c92 + 2 * c93 + 2 * c94 + 2 * c95 + 2 * c96 + 2 * c97 + 2 * c98 + 2 * c99 + 2 * c100 + 2 * c104 + c130 + c131 + c132 + 2 * c136 + c148 + c149 + c150 + c151 + c152 + c153 + c162 + c163 + c164 + c165 + c166 + c167 + c171 + c172 + c173 + c174 + c175 + c176 + c180 + c181 + c182 + c183 + c184 + c185 + c189 + c190 + c191 + c192 + c193 + c194 + c195 + c196 + c197 + c198 + c199 + c200 + c201 + c202 + c203 + c204 + c205 + c206 + c207 + c208 + c209 + c210 + c211 + c212 + c213 + c214 + c215 + c216 + c217 + c218 + c219 + c220 + c221 + c222 + c223 + c224 + c225 + c226 + c227 + 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1e-05 1000.0 5.0 true +kd109 kd109 1e-05 1000.0 0.1 true +kd110 kd110 1e-05 1000.0 0.1 true +kd111 kd111 1e-05 1000.0 6.57 true +kd112 kd112 1e-05 1000.0 0.1 true +kd113 kd113 1e-05 1000.0 177.827999999999 true +kd114 kd114 1e-05 1000.0 0.1 true +kd115 kd115 1e-05 1000.0 1.0 true +kd116 kd116 -5.0 3.0 0.0 false +kd117 kd117 1e-05 1000.0 0.1 true +kd118 kd118 1e-05 1000.0 0.03 true +kd119 kd119 1e-05 1000.0 0.0103115 true +kd120 kd120 1e-05 1000.0 0.1 true +kd123 kd123 1e-05 1000.0 0.177828 true +kd123h kd123h 1e-05 1000.0 0.1 true +kd15 kd15 -5.0 3.0 0.0 false +kd17 kd17 1e-05 1000.0 0.06 true +kd18 kd18 1e-05 1000.0 1.3 true +kd19 kd19 1e-05 1000.0 0.5 true +kd2 kd2 1e-05 1000.0 0.16 true +kd20 kd20 1e-05 1000.0 0.4 true +kd21 kd21 1e-05 1000.0 0.23 true +kd22 kd22 1e-05 1000.0 0.1 true +kd22b kd22b 1e-05 1000.0 0.1 true +kd23 kd23 1e-05 1000.0 0.06 true +kd24 kd24 1e-05 1000.0 0.55 true +kd25 kd25 1e-05 1000.0 0.0214 true +kd28 kd28 1e-05 1000.0 0.0053 true +kd29 kd29 1e-05 1000.0 3.1 true +kd2b kd2b 1e-05 1000.0 0.016 true +kd32 kd32 1e-05 1000.0 0.1 true +kd33 kd33 1e-05 1000.0 0.2 true +kd34 kd34 1e-05 1000.0 0.03 true +kd35 kd35 1e-05 1000.0 0.0015 true +kd36 kd36 -5.0 3.0 0.0 false +kd37 kd37 1e-05 1000.0 0.3 true +kd4 kd4 1e-05 1000.0 0.000166 true +kd40 kd40 1e-05 1000.0 0.064 true +kd41 kd41 1e-05 1000.0 0.0429 true +kd42 kd42 1e-05 1000.0 0.0141589 true +kd43 kd43 1e-05 1000.0 31.6228000000003 true +kd44 kd44 1e-05 1000.0 0.01833 true +kd45 kd45 1e-05 1000.0 1.9 true +kd47 kd47 1e-05 1000.0 0.800000000000001 true +kd48 kd48 1e-05 1000.0 0.789999999999999 true +kd49 kd49 1e-05 1000.0 0.112387 true +kd5 kd5 1e-05 1000.0 0.808329999999999 true +kd50 kd50 1e-05 1000.0 0.252982 true +kd52 kd52 1e-05 1000.0 0.033 true +kd53 kd53 1e-05 1000.0 0.28 true +kd55 kd55 1e-05 1000.0 70.1661999999996 true +kd56 kd56 1e-05 1000.0 5.0 true +kd57 kd57 1e-05 1000.0 0.0076 true +kd58 kd58 1e-05 1000.0 56.7861999999997 true +kd5b kd5b 1e-05 1000.0 0.0080833 true +kd60 kd60 -5.0 3.0 0.0 false +kd60b kd60b -5.0 3.0 0.0 false +kd61 kd61 -5.0 3.0 0.0 false +kd63 kd63 1e-05 1000.0 0.275 true +kd64 kd64 1e-05 1000.0 0.3 true +kd65 kd65 1e-05 1000.0 0.2 true +kd66 kd66 1e-05 1000.0 0.2 true +kd67 kd67 1e-05 1000.0 0.02 true +kd68 kd68 1e-05 1000.0 0.2 true +kd68b kd68b 1e-05 1000.0 20.4999999999998 true +kd69 kd69 1e-05 1000.0 0.1 true +kd6b kd6b -5.0 3.0 0.0 false +kd7 kd7 1e-05 1000.0 0.000138 true +kd70 kd70 1e-05 1000.0 0.1 true +kd71 kd71 1e-05 1000.0 25.1999999999998 true +kd72 kd72 1e-05 1000.0 5.01187 true +kd73 kd73 1e-05 1000.0 0.5 true +kd74 kd74 1e-05 1000.0 0.355656 true +kd75 kd75 1e-05 1000.0 0.00633957 true +kd76 kd76 1e-05 1000.0 142.261999999999 true +kd8 kd8 1e-05 1000.0 0.2 true +kd8b kd8b 1e-05 1000.0 0.02 true +kd94 kd94 1e-05 1000.0 0.01 true +kd95 kd95 1e-05 1000.0 33.0000000000002 true +kd96 kd96 1e-05 1000.0 0.1 true +kd97 kd97 1e-05 1000.0 0.015 true +kd97c kd97c 1e-05 1000.0 0.001 true +kd98 kd98 1e-05 1000.0 0.001 true +kd99 kd99 1e-05 1000.0 0.5 true diff --git a/v2/Crauste_CellSystems2017/Crauste_CellSystems2017.yaml b/v2/Crauste_CellSystems2017/Crauste_CellSystems2017.yaml new file mode 100644 index 0000000..341e653 --- /dev/null +++ b/v2/Crauste_CellSystems2017/Crauste_CellSystems2017.yaml @@ -0,0 +1,16 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Crauste_CellSystems2017.tsv +model_files: + model_Crauste_CellSystems2017: + location: model_Crauste_CellSystems2017.xml + language: sbml +measurement_files: +- measurementData_Crauste_CellSystems2017.tsv +condition_files: +- experimentalCondition_Crauste_CellSystems2017.tsv +experiment_files: [] +observable_files: +- observables_Crauste_CellSystems2017.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Crauste_CellSystems2017/experimentalCondition_Crauste_CellSystems2017.tsv b/v2/Crauste_CellSystems2017/experimentalCondition_Crauste_CellSystems2017.tsv new file mode 100644 index 0000000..730c58d --- /dev/null +++ b/v2/Crauste_CellSystems2017/experimentalCondition_Crauste_CellSystems2017.tsv @@ -0,0 +1 @@ +conditionId targetId targetValue diff --git a/v2/Crauste_CellSystems2017/measurementData_Crauste_CellSystems2017.tsv b/v2/Crauste_CellSystems2017/measurementData_Crauste_CellSystems2017.tsv new file mode 100644 index 0000000..e208b0f --- /dev/null +++ b/v2/Crauste_CellSystems2017/measurementData_Crauste_CellSystems2017.tsv @@ -0,0 +1,22 @@ +experimentId observableId measurement time observableParameters noiseParameters + observable_Naive 459 4 290 + observable_Naive 74 6 64 + observable_EarlyEffector 386 4 266 + observable_EarlyEffector 1172 6 526 + observable_EarlyEffector 47470 7 23855 + observable_EarlyEffector 175825 8 19722 + observable_EarlyEffector 4911 13 3048 + observable_EarlyEffector 7417 15 2924 + observable_EarlyEffector 3359 22 1540 + observable_LateEffector 888 6 182 + observable_LateEffector 4577 7 1976 + observable_LateEffector 32860 8 4105 + observable_LateEffector 46727 13 23601 + observable_LateEffector 27586 15 6841 + observable_LateEffector 13650 22 7266 + observable_LateEffector 3936 28 2705 + observable_Memory 289 8 80 + observable_Memory 9564 13 4206 + observable_Memory 15631 15 5745 + observable_Memory 41744 22 15987 + observable_Memory 32705 28 7909 diff --git a/v2/Crauste_CellSystems2017/model_Crauste_CellSystems2017.xml b/v2/Crauste_CellSystems2017/model_Crauste_CellSystems2017.xml new file mode 100644 index 0000000..a5ebb9a --- /dev/null +++ b/v2/Crauste_CellSystems2017/model_Crauste_CellSystems2017.xml @@ -0,0 +1,283 @@ + + + + + + 
PEtab implementation of the model from Crauste et al. (2017), Cell Syst. 2017 Mar 22;4(3):306-317.e4
+ + + + + + + + + + Crauste + Fabien + + + + + + 2019-11-29T09:41:48Z + + + 2019-11-29T09:41:48Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Naive + mu_N + + + + + + + + + + + + + + + + + + + Naive + Pathogen + delta_NE + + + + + + + + + + + + + + + + + EarlyEffector + Pathogen + rho_E + + + + + + + + + + + + + + + EarlyEffector + 2 + + mu_EE + + + + + + + + + + + + + + + + EarlyEffector + delta_EL + + + + + + + + + + + + + + + LateEffector + 2 + + mu_LL + + + + + + + + + + + + + + + + EarlyEffector + LateEffector + mu_LE + + + + + + + + + + + + + + + + LateEffector + delta_LM + + + + + + + + + + + + + + + + + + Pathogen + 2 + + rho_P + + + + + + + + + + + + + + + + EarlyEffector + Pathogen + mu_PE + + + + + + + + + + + + + + + + LateEffector + Pathogen + mu_PL + + + + + + + + + + + + + Pathogen + mu_P + + + + + + + diff --git a/v2/Crauste_CellSystems2017/observables_Crauste_CellSystems2017.tsv b/v2/Crauste_CellSystems2017/observables_Crauste_CellSystems2017.tsv new file mode 100644 index 0000000..889ff9a --- /dev/null +++ b/v2/Crauste_CellSystems2017/observables_Crauste_CellSystems2017.tsv @@ -0,0 +1,5 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +observable_EarlyEffector EarlyEffector noiseParameter1_observable_EarlyEffector noiseParameter1_observable_EarlyEffector +observable_LateEffector LateEffector noiseParameter1_observable_LateEffector noiseParameter1_observable_LateEffector +observable_Memory Memory noiseParameter1_observable_Memory noiseParameter1_observable_Memory +observable_Naive Naive noiseParameter1_observable_Naive noiseParameter1_observable_Naive diff --git a/v2/Crauste_CellSystems2017/parameters_Crauste_CellSystems2017.tsv b/v2/Crauste_CellSystems2017/parameters_Crauste_CellSystems2017.tsv new file mode 100644 index 0000000..07d57b2 --- /dev/null +++ b/v2/Crauste_CellSystems2017/parameters_Crauste_CellSystems2017.tsv @@ -0,0 +1,13 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorParameters +delta_EL delta_{EL} 1e-05 1000 0.517945937424841 true +delta_LM delta_{LM} 1e-05 1000 0.022580636941607 true +delta_NE delta_{NE} 1e-05 1000 0.011930787933602 true +mu_EE mu_{EE} 1e-05 1000 3.91359465940441e-05 true +mu_LE mu_{LE} 1e-10 1000 1.00000000000007e-10 true +mu_LL mu_{LL} 1e-10 1000 8.11520130499257e-06 true +mu_N mu_{N} 1e-05 1000 0.739907304399124 true +mu_P mu_{P} 1e-05 1000 1.00000003522094e-05 true +mu_PE mu_{PE} 1e-10 1000 1.41248724084794e-10 true +mu_PL mu_{PL} 1e-05 1000 3.63403086241783e-05 true +rho_E rho_{E} 1e-05 1000 0.507415649004014 true +rho_P rho_{P} 1e-05 1000 0.126382292625502 true diff --git a/v2/Elowitz_Nature2000/Elowitz_Nature2000.yaml b/v2/Elowitz_Nature2000/Elowitz_Nature2000.yaml new file mode 100644 index 0000000..0cd374d --- /dev/null +++ b/v2/Elowitz_Nature2000/Elowitz_Nature2000.yaml @@ -0,0 +1,16 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Elowitz_Nature2000.tsv +model_files: + model_Elowitz_Nature2000: + location: model_Elowitz_Nature2000.xml + language: sbml +measurement_files: +- measurementData_Elowitz_Nature2000.tsv +condition_files: +- experimentalCondition_Elowitz_Nature2000.tsv +experiment_files: [] +observable_files: +- observables_Elowitz_Nature2000.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Elowitz_Nature2000/experimentalCondition_Elowitz_Nature2000.tsv b/v2/Elowitz_Nature2000/experimentalCondition_Elowitz_Nature2000.tsv new file mode 100644 index 0000000..730c58d --- /dev/null +++ b/v2/Elowitz_Nature2000/experimentalCondition_Elowitz_Nature2000.tsv @@ -0,0 +1 @@ +conditionId targetId targetValue diff --git a/v2/Elowitz_Nature2000/measurementData_Elowitz_Nature2000.tsv b/v2/Elowitz_Nature2000/measurementData_Elowitz_Nature2000.tsv new file mode 100644 index 0000000..bdcbdd3 --- /dev/null +++ b/v2/Elowitz_Nature2000/measurementData_Elowitz_Nature2000.tsv @@ -0,0 +1,59 @@ +experimentId observableId measurement time observableParameters noiseParameters + fluorescence 0.251497006 10 background;scale sigma + fluorescence 0.089820359 30 background;scale sigma + fluorescence 0.167664671 50 background;scale sigma + fluorescence 0.113772455 60 background;scale sigma + fluorescence 0.131736527 70 background;scale sigma + fluorescence 0.143712575 80 background;scale sigma + fluorescence 0.215568862 90 background;scale sigma + fluorescence 0.443113772 100 background;scale sigma + fluorescence 0.640718563 110 background;scale sigma + fluorescence 0.634730539 120 background;scale sigma + fluorescence 0.634730539 130 background;scale sigma + fluorescence 0.71257485 140 background;scale sigma + fluorescence 0.604790419 150 background;scale sigma + fluorescence 0.574850299 160 background;scale sigma + fluorescence 0.449101796 170 background;scale sigma + fluorescence 0.347305389 180 background;scale sigma + fluorescence 0.359281437 190 background;scale sigma + fluorescence 0.407185629 200 background;scale sigma + fluorescence 0.377245509 210 background;scale sigma + fluorescence 0.353293413 220 background;scale sigma + fluorescence 0.317365269 230 background;scale sigma + fluorescence 0.383233533 240 background;scale sigma + fluorescence 0.323353293 250 background;scale sigma + fluorescence 0.323353293 260 background;scale sigma + fluorescence 0.383233533 270 background;scale sigma + fluorescence 0.706586826 280 background;scale sigma + fluorescence 0.892215569 290 background;scale sigma + fluorescence 0.982035928 300 background;scale sigma + fluorescence 0.946107784 310 background;scale sigma + fluorescence 0.892215569 320 background;scale sigma + fluorescence 0.886227545 330 background;scale sigma + fluorescence 0.874251497 340 background;scale sigma + fluorescence 0.640718563 350 background;scale sigma + fluorescence 0.688622754 360 background;scale sigma + fluorescence 0.616766467 370 background;scale sigma + fluorescence 0.640718563 380 background;scale sigma + fluorescence 0.526946108 390 background;scale sigma + fluorescence 0.479041916 400 background;scale sigma + fluorescence 0.604790419 410 background;scale sigma + fluorescence 0.730538922 420 background;scale sigma + fluorescence 0.862275449 430 background;scale sigma + fluorescence 0.886227545 440 background;scale sigma + fluorescence 1.0 450 background;scale sigma + fluorescence 0.928143713 460 background;scale sigma + fluorescence 0.874251497 470 background;scale sigma + fluorescence 0.808383234 480 background;scale sigma + fluorescence 0.706586826 490 background;scale sigma + fluorescence 0.706586826 500 background;scale sigma + fluorescence 0.658682635 510 background;scale sigma + fluorescence 0.634730539 520 background;scale sigma + fluorescence 0.562874251 530 background;scale sigma + fluorescence 0.443113772 540 background;scale sigma + fluorescence 0.347305389 550 background;scale sigma + fluorescence 0.431137725 560 background;scale sigma + fluorescence 0.449101796 570 background;scale sigma + fluorescence 0.520958084 580 background;scale sigma + fluorescence 0.54491018 590 background;scale sigma + fluorescence 0.467065868 600 background;scale sigma diff --git a/v2/Elowitz_Nature2000/model_Elowitz_Nature2000.xml b/v2/Elowitz_Nature2000/model_Elowitz_Nature2000.xml new file mode 100644 index 0000000..3046b4e --- /dev/null +++ b/v2/Elowitz_Nature2000/model_Elowitz_Nature2000.xml @@ -0,0 +1,665 @@ + + + + + + 
PEtab implementation of the model from Elowitz et al. (2000), Nature. 2000 Jan 20;403(6767):335-8
+ + + + + + + + + + Elowitz + Micheal + + + + + + 2019-11-29T09:41:48Z + + + 2019-11-29T09:41:48Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + init_X_protein + + + + + init_Y_protein + + + + + init_Z_protein + + + + + init_GFP + + + + + init_X_mRNA + + + + + init_Y_mRNA + + + + + init_Z_mRNA + + + + + init_GFP_mRNA + + + + + + + + + + + + + cell + + + + + X_mRNA + + + 2 + + + tau_mRNA + + + + + + + + + + + + + + cell + + + + + Y_mRNA + + + 2 + + + tau_mRNA + + + + + + + + + + + + + + cell + + + + + Z_mRNA + + + 2 + + + tau_mRNA + + + + + + + + + + + + + + cell + + + + + GFP_mRNA + + + 2 + + + tau_mRNA_GFP + + + + + + + + + + + + + + + + + cell + + + + + X_mRNA + eff + + tau_mRNA + + + + + + + + + + + + + + + + + cell + + + + + Y_mRNA + eff + + tau_mRNA + + + + + + + + + + + + + + + + + cell + + + + + Z_mRNA + eff + + tau_mRNA + + + + + + + + + + + + + + + + + cell + + + + + GFP_mRNA + eff_GFP + + tau_mRNA_GFP + + + + + + + + + + + + + + cell + + + + + X_protein + + + 2 + + + tau_prot + + + + + + + + + + + + + + cell + + + + + Y_protein + + + 2 + + + tau_prot + + + + + + + + + + + + + + cell + + + + + Z_protein + + + 2 + + + tau_prot + + + + + + + + + + + + + + cell + + + + + GFP + + + 2 + + + tau_prot_GFP + + + + + + + + + + + + + + + + + cell + + + + + 60 + tps_repr + + + + + + + + KM + n_Hill + + + + + + 60 + tps_repr + + + + 60 + tps_active + + + + + + + + KM + n_Hill + + + + Z_protein + n_Hill + + + + + + + + + + + + + + + + + + + + cell + + + + + 60 + tps_repr + + + + + + + + KM + n_Hill + + + + + + 60 + tps_repr + + + + 60 + tps_active + + + + + + + + KM + n_Hill + + + + X_protein + n_Hill + + + + + + + + + + + + + + + + + + + + cell + + + + + 60 + tps_repr + + + + + + + + KM + n_Hill + + + + + + 60 + tps_repr + + + + 60 + tps_active + + + + + + + + KM + n_Hill + + + + Y_protein + n_Hill + + + + + + + + + + + + + + + + + + + + cell + + + + + 60 + tps_repr + + + + + + + + KM + n_Hill + + + + + + 60 + tps_repr + + + + 60 + tps_active + + + + + + + + KM + n_Hill + + + + X_protein + n_Hill + + + + + + + + + + + diff --git a/v2/Elowitz_Nature2000/observables_Elowitz_Nature2000.tsv b/v2/Elowitz_Nature2000/observables_Elowitz_Nature2000.tsv new file mode 100644 index 0000000..55cfc7a --- /dev/null +++ b/v2/Elowitz_Nature2000/observables_Elowitz_Nature2000.tsv @@ -0,0 +1,2 @@ +observableId observableFormula observableName noiseDistribution noiseFormula observablePlaceholders noisePlaceholders +fluorescence observableParameter1_fluorescence + GFP * observableParameter2_fluorescence noiseParameter1_fluorescence observableParameter1_fluorescence;observableParameter2_fluorescence noiseParameter1_fluorescence diff --git a/v2/Elowitz_Nature2000/parameters_Elowitz_Nature2000.tsv b/v2/Elowitz_Nature2000/parameters_Elowitz_Nature2000.tsv new file mode 100644 index 0000000..4aafbb0 --- /dev/null +++ b/v2/Elowitz_Nature2000/parameters_Elowitz_Nature2000.tsv @@ -0,0 +1,22 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorParameters +KM KM 1e-05 1000 1.00013184764193e-05 true +background background 1e-05 1000 1.04454130394407e-05 true +eff eff 1e-05 1000 0.030159280362287 true +eff_GFP eff_{GFP} 1e-05 1000 0.001952121970966 true +init_GFP init_{GFP} 1e-05 1000 3.38716998236184e-05 true +init_GFP_mRNA init_{GFP,mRNA} 1e-05 1000 131.43573778956 true +init_X_mRNA init_{X,mRNA} 1e-05 1000 2.55665758135759 true +init_X_protein init_{X,protein} 1e-05 1000 30.8087735629583 true +init_Y_mRNA init_{Y,mRNA} 1e-05 1000 999.999945990865 true +init_Y_protein init_{Y,protein} 1e-05 1000 0.000818268062901 true +init_Z_mRNA init_{Z,mRNA} 1e-05 1000 19.3670294497273 true +init_Z_protein init_{Z,protein} 1e-05 1000 994.381959318229 true +n_Hill n_{Hill} 1e-05 1000 1.52254567553984 true +scale scale 1e-05 1000 0.52599663700947 true +sigma \sigma 1e-05 1000 0.071841413831614 true +tau_mRNA tau_{mRNA} 1e-05 1000 12.6248245707722 true +tau_mRNA_GFP tau_{mRNA,GFP} 1e-05 1000 0.000404064377463 true +tau_prot tau_{prot} 1e-05 1000 5.35926527470062 true +tau_prot_GFP tau_{prot,GFP} 1e-05 1000 71.9312640934976 true +tps_active tps_{active} 1e-05 1000 0.612278991244992 true +tps_repr tps_{repr} 1e-05 1000 1.00000000000882e-05 true diff --git a/v2/Fiedler_BMCSystBiol2016/Fiedler_BMCSystBiol2016.yaml b/v2/Fiedler_BMCSystBiol2016/Fiedler_BMCSystBiol2016.yaml new file mode 100644 index 0000000..c7e8fe9 --- /dev/null +++ b/v2/Fiedler_BMCSystBiol2016/Fiedler_BMCSystBiol2016.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Fiedler_BMCSystBiol2016.tsv +model_files: + model_Fiedler_BMCSystBiol2016: + location: model_Fiedler_BMCSystBiol2016.xml + language: sbml +measurement_files: +- measurementData_Fiedler_BMCSystBiol2016.tsv +condition_files: +- experimentalCondition_Fiedler_BMCSystBiol2016.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Fiedler_BMCSystBiol2016.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Fiedler_BMCSystBiol2016/experimentalCondition_Fiedler_BMCSystBiol2016.tsv b/v2/Fiedler_BMCSystBiol2016/experimentalCondition_Fiedler_BMCSystBiol2016.tsv new file mode 100644 index 0000000..261e978 --- /dev/null +++ b/v2/Fiedler_BMCSystBiol2016/experimentalCondition_Fiedler_BMCSystBiol2016.tsv @@ -0,0 +1,7 @@ +conditionId targetId targetValue +model1_data1 Sorafenib 0 +model1_data2 Sorafenib 5 +model1_data3 Sorafenib 0 +model1_data1 UO126 0 +model1_data2 UO126 0 +model1_data3 UO126 30 diff --git a/v2/Fiedler_BMCSystBiol2016/experiments.tsv b/v2/Fiedler_BMCSystBiol2016/experiments.tsv new file mode 100644 index 0000000..49ce0ba --- /dev/null +++ b/v2/Fiedler_BMCSystBiol2016/experiments.tsv @@ -0,0 +1,4 @@ +experimentId conditionId time +experiment____model1_data1 model1_data1 0 +experiment____model1_data2 model1_data2 0 +experiment____model1_data3 model1_data3 0 diff --git a/v2/Fiedler_BMCSystBiol2016/measurementData_Fiedler_BMCSystBiol2016.tsv b/v2/Fiedler_BMCSystBiol2016/measurementData_Fiedler_BMCSystBiol2016.tsv new file mode 100644 index 0000000..79328dc --- /dev/null +++ b/v2/Fiedler_BMCSystBiol2016/measurementData_Fiedler_BMCSystBiol2016.tsv @@ -0,0 +1,73 @@ +experimentId observableId measurement time observableParameters noiseParameters datasetId +experiment____model1_data1 pErk 0.037959 0.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +experiment____model1_data1 pErk 0.042262 0.25 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +experiment____model1_data1 pErk 0.162628 1.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +experiment____model1_data1 pErk 0.052124 5.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +experiment____model1_data1 pErk 0.023196 7.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +experiment____model1_data1 pErk 0.037687 8.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +experiment____model1_data1 pErk 0.028724 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+experiment____model1_data2 pMek 0.07 10.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib +experiment____model1_data3 pMek 1.724493879 1.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +experiment____model1_data3 pMek 1.683168571 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +experiment____model1_data3 pMek 1.470175735 7.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +experiment____model1_data3 pMek 1.557371739 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +experiment____model1_data3 pMek 1.559108205 10.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +experiment____model1_data3 pMek 5.857600733 1.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 +experiment____model1_data3 pMek 2.857976654 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 +experiment____model1_data3 pMek 4.607660706 7.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 +experiment____model1_data3 pMek 2.789397964 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 +experiment____model1_data3 pMek 1.623004546 10.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 diff --git a/v2/Fiedler_BMCSystBiol2016/model_Fiedler_BMCSystBiol2016.xml b/v2/Fiedler_BMCSystBiol2016/model_Fiedler_BMCSystBiol2016.xml new file mode 100644 index 0000000..e1abbe2 --- /dev/null +++ b/v2/Fiedler_BMCSystBiol2016/model_Fiedler_BMCSystBiol2016.xml @@ -0,0 +1,3540 @@ + + + + + + 
PEtab implementation of the model from Fiedler et al. (2016), BMC Systems Biology volume 10, Article number: 80
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+ + + + + + + + + + + + + + + + + cyt + k6 + pERK + + + + + + + diff --git a/v2/Fiedler_BMCSystBiol2016/observables_Fiedler_BMCSystBiol2016.tsv b/v2/Fiedler_BMCSystBiol2016/observables_Fiedler_BMCSystBiol2016.tsv new file mode 100644 index 0000000..7cd120d --- /dev/null +++ b/v2/Fiedler_BMCSystBiol2016/observables_Fiedler_BMCSystBiol2016.tsv @@ -0,0 +1,3 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +pErk pERK * observableParameter1_pErk noiseParameter1_pErk*noiseParameter2_pErk observableParameter1_pErk noiseParameter1_pErk;noiseParameter2_pErk +pMek pMEK * observableParameter1_pMek noiseParameter1_pMek*noiseParameter2_pMek observableParameter1_pMek noiseParameter1_pMek;noiseParameter2_pMek diff --git a/v2/Fiedler_BMCSystBiol2016/parameters_Fiedler_BMCSystBiol2016.tsv b/v2/Fiedler_BMCSystBiol2016/parameters_Fiedler_BMCSystBiol2016.tsv new file mode 100644 index 0000000..e8bcf30 --- /dev/null +++ b/v2/Fiedler_BMCSystBiol2016/parameters_Fiedler_BMCSystBiol2016.tsv @@ -0,0 +1,26 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorParameters +ERK_total ERK_{total} 1e-05 1000 1.0 false +K_1 {K_1} 1e-05 1000 1.0000122099653e-05 true +K_2 {K_2} 1e-05 1000 1.51121996768986 true +K_3 {K_3} 1e-05 1000 0.960465656770682 true +MEK_total MEK_{total} 1e-05 1000 1.0 false +RAF_total RAF_{total} 1e-05 1000 1.0 false +k10 {k10} 1e-05 100000 0.026413685021474 true +k11 {k11} 1e-05 100000 163.162367794459 true +k2 {k2} 1e-05 100000 1.22622424049592 true +k3 {k3} 1e-05 100000 769.159517169525 true +k4 {k4} 1e-05 100000 2.90693427220412 true +k5 {k5} 1e-05 100000 577.552181196191 true +k6 {k6} 1e-05 100000 3.60757835904195 true +s_pErk_20140430_gel1 s_{pErk,20140430,gel1} 1e-05 1000 0.369256805232789 true +s_pErk_20140430_gel2 s_{pErk,20140430,gel2} 1e-05 1000 0.250134156378628 true +s_pErk_20140505_gel1 s_{pErk,20140505,gel1} 1e-05 1000 8.92600078593847 true +s_pErk_20140505_gel2 s_{pErk,20140505,gel2} 1e-05 1000 2.85637035018243 true +s_pMek_20140430_gel1 s_{pMek,20140430,gel1} 1e-05 1000 77.7404398920619 true +s_pMek_20140430_gel2 s_{pMek,20140430,gel2} 1e-05 1000 404.217160578548 true +s_pMek_20140505_gel1 s_{pMek,20140505,gel1} 1e-05 1000 392.45653075379 true +s_pMek_20140505_gel2 s_{pMek,20140505,gel2} 1e-05 1000 999.992845715073 true +sigma_pErk \sigma_{pErk} 1e-05 1000 0.045270131337451 true +sigma_pMek \sigma_{pMek} 1e-05 1000 0.000580451138215 true +tau1 \tau_{1} 1e-08 100000000 0.242822010781068 true +tau2 \tau_{2} 1e-08 100000000 0.021140927521636 true diff --git a/v2/Fujita_SciSignal2010/Fujita_SciSignal2010.yaml b/v2/Fujita_SciSignal2010/Fujita_SciSignal2010.yaml new file mode 100644 index 0000000..5b0ed1a --- /dev/null +++ b/v2/Fujita_SciSignal2010/Fujita_SciSignal2010.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Fujita_SciSignal2010.tsv +model_files: + model_Fujita_SciSignal2010: + location: model_Fujita_SciSignal2010.xml + language: sbml +measurement_files: +- measurementData_step_Fujita_SciSignal2010.tsv +condition_files: +- experimentalCondition_Fujita_SciSignal2010.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Fujita_SciSignal2010.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Fujita_SciSignal2010/experimentalCondition_Fujita_SciSignal2010.tsv b/v2/Fujita_SciSignal2010/experimentalCondition_Fujita_SciSignal2010.tsv new file mode 100644 index 0000000..37dd26b --- /dev/null +++ b/v2/Fujita_SciSignal2010/experimentalCondition_Fujita_SciSignal2010.tsv @@ -0,0 +1,49 @@ +conditionId targetId targetValue +condition_step_00_1 EGF_0 0.1 +condition_step_00_3 EGF_0 0.3 +condition_step_01_0 EGF_0 1.0 +condition_step_03_0 EGF_0 3.0 +condition_step_10_0 EGF_0 10.0 +condition_step_30_0 EGF_0 30.0 +condition_pulse_00_1 EGF_0 0.1 +condition_pulse_00_3 EGF_0 0.3 +condition_pulse_01_0 EGF_0 1.0 +condition_pulse_03_0 EGF_0 3.0 +condition_pulse_10_0 EGF_0 10.0 +condition_pulse_30_0 EGF_0 30.0 +condition_ramp_8_3Enegative06 EGF_0 0.0 +condition_ramp_8_3Enegative05 EGF_0 0.0 +condition_ramp_8_3Enegative04 EGF_0 0.0 +condition_ramp_8_3Enegative03 EGF_0 0.0 +condition_step_00_1 EGF_rate 0.0 +condition_step_00_3 EGF_rate 0.0 +condition_step_01_0 EGF_rate 0.0 +condition_step_03_0 EGF_rate 0.0 +condition_step_10_0 EGF_rate 0.0 +condition_step_30_0 EGF_rate 0.0 +condition_pulse_00_1 EGF_rate 0.0 +condition_pulse_00_3 EGF_rate 0.0 +condition_pulse_01_0 EGF_rate 0.0 +condition_pulse_03_0 EGF_rate 0.0 +condition_pulse_10_0 EGF_rate 0.0 +condition_pulse_30_0 EGF_rate 0.0 +condition_ramp_8_3Enegative06 EGF_rate 8.333333333333334e-06 +condition_ramp_8_3Enegative05 EGF_rate 8.333333333333333e-05 +condition_ramp_8_3Enegative04 EGF_rate 0.0008333333333333333 +condition_ramp_8_3Enegative03 EGF_rate 0.008333333333333333 +condition_step_00_1 EGF_end 3600.0 +condition_step_00_3 EGF_end 3600.0 +condition_step_01_0 EGF_end 3600.0 +condition_step_03_0 EGF_end 3600.0 +condition_step_10_0 EGF_end 3600.0 +condition_step_30_0 EGF_end 3600.0 +condition_pulse_00_1 EGF_end 60.0 +condition_pulse_00_3 EGF_end 60.0 +condition_pulse_01_0 EGF_end 60.0 +condition_pulse_03_0 EGF_end 60.0 +condition_pulse_10_0 EGF_end 60.0 +condition_pulse_30_0 EGF_end 60.0 +condition_ramp_8_3Enegative06 EGF_end 3600.0 +condition_ramp_8_3Enegative05 EGF_end 3600.0 +condition_ramp_8_3Enegative04 EGF_end 3600.0 +condition_ramp_8_3Enegative03 EGF_end 3600.0 diff --git a/v2/Fujita_SciSignal2010/experiments.tsv b/v2/Fujita_SciSignal2010/experiments.tsv new file mode 100644 index 0000000..376b3c2 --- /dev/null +++ b/v2/Fujita_SciSignal2010/experiments.tsv @@ -0,0 +1,7 @@ +experimentId conditionId time +experiment____condition_step_00_1 condition_step_00_1 0 +experiment____condition_step_00_3 condition_step_00_3 0 +experiment____condition_step_01_0 condition_step_01_0 0 +experiment____condition_step_03_0 condition_step_03_0 0 +experiment____condition_step_10_0 condition_step_10_0 0 +experiment____condition_step_30_0 condition_step_30_0 0 diff --git a/v2/Fujita_SciSignal2010/measurementData_step_Fujita_SciSignal2010.tsv b/v2/Fujita_SciSignal2010/measurementData_step_Fujita_SciSignal2010.tsv new file mode 100644 index 0000000..5113080 --- /dev/null +++ b/v2/Fujita_SciSignal2010/measurementData_step_Fujita_SciSignal2010.tsv @@ -0,0 +1,145 @@ +experimentId observableId measurement time observableParameters noiseParameters datasetId +experiment____condition_step_00_1 pEGFR_tot 0.0 0 scaling_pEGFR_tot 0.01 condition_step_00_1_pEGFR_tot +experiment____condition_step_00_1 pEGFR_tot 0.00495502124323188 60 scaling_pEGFR_tot 0.01 condition_step_00_1_pEGFR_tot +experiment____condition_step_00_1 pEGFR_tot 0.00403395805839657 120 scaling_pEGFR_tot 0.01 condition_step_00_1_pEGFR_tot +experiment____condition_step_00_1 pEGFR_tot 0.00636740948965264 300 scaling_pEGFR_tot 0.01 condition_step_00_1_pEGFR_tot +experiment____condition_step_00_1 pEGFR_tot 0.0108590905848178 600 scaling_pEGFR_tot 0.01 condition_step_00_1_pEGFR_tot +experiment____condition_step_00_1 pEGFR_tot 0.00713529112795963 900 scaling_pEGFR_tot 0.01 condition_step_00_1_pEGFR_tot +experiment____condition_step_00_1 pEGFR_tot 0.00371026458752022 1800 scaling_pEGFR_tot 0.01 condition_step_00_1_pEGFR_tot +experiment____condition_step_00_1 pEGFR_tot 0.0067693198844283 3600 scaling_pEGFR_tot 0.01 condition_step_00_1_pEGFR_tot +experiment____condition_step_00_1 pAkt_tot 0.0 0 scaling_pAkt_tot 0.01 condition_step_00_1_pAkt_tot +experiment____condition_step_00_1 pAkt_tot 0.0312319063363424 60 scaling_pAkt_tot 0.01 condition_step_00_1_pAkt_tot +experiment____condition_step_00_1 pAkt_tot 0.0934440605778122 120 scaling_pAkt_tot 0.01 condition_step_00_1_pAkt_tot +experiment____condition_step_00_1 pAkt_tot 0.23689070684454 300 scaling_pAkt_tot 0.01 condition_step_00_1_pAkt_tot +experiment____condition_step_00_1 pAkt_tot 0.149728787111733 600 scaling_pAkt_tot 0.01 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condition_step_30_0_pS6_tot +experiment____condition_step_30_0 pS6_tot 0.620879461942708 1800 scaling_pS6_tot 0.035 condition_step_30_0_pS6_tot +experiment____condition_step_30_0 pS6_tot 0.320844147774031 3600 scaling_pS6_tot 0.07 condition_step_30_0_pS6_tot diff --git a/v2/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml b/v2/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml new file mode 100644 index 0000000..2f26142 --- /dev/null +++ b/v2/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml @@ -0,0 +1,334 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + init_EGFR + + + + + init_AKT + + + + + init_S6 + + + + + + + + + + + + + EGF_rate + time + + EGF_0 + + + + time + EGF_end + + + + 0 + + + + + + + + + + + + + + + + + + Cell + + + + + EGF + EGFR + reaction_1_k1 + + + + EGF_EGFR + reaction_1_k2 + + + + + + + + + + + + + + + + + + + Cell + + + + + Akt + pEGFR + reaction_2_k1 + + + + pEGFR_Akt + reaction_2_k2 + + + + + + + + + + + + + + + + + + + Cell + pEGFR_Akt + reaction_3_k1 + + + + + + + + + + + + + Cell + pEGFR + reaction_4_k1 + + + + + + + + + + + + + + + + + Cell + + + + + S6 + pAkt + reaction_5_k1 + + + + pAkt_S6 + reaction_5_k2 + + + + + + + + + + + + + + + + + + + Cell + pAkt_S6 + reaction_6_k1 + + + + + + + + + + + + + + + + Cell + pAkt + reaction_7_k1 + + + + + + + + + + + + + + + + Cell + pS6 + reaction_8_k1 + + + + + + + + + + + + + + + + Cell + EGF_EGFR + reaction_9_k1 + + + + + + + + + + + + + Cell + EGFR + EGFR_turnover + + + + + + + + + + + + + Cell + 68190 + EGFR_turnover + + + + + + + diff --git a/v2/Fujita_SciSignal2010/observables_Fujita_SciSignal2010.tsv b/v2/Fujita_SciSignal2010/observables_Fujita_SciSignal2010.tsv new file mode 100644 index 0000000..e64ebc1 --- /dev/null +++ b/v2/Fujita_SciSignal2010/observables_Fujita_SciSignal2010.tsv @@ -0,0 +1,4 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +pAkt_tot observableParameter1_pAkt_tot * (pAkt + pAkt_S6) noiseParameter1_pAkt_tot observableParameter1_pAkt_tot noiseParameter1_pAkt_tot +pEGFR_tot observableParameter1_pEGFR_tot * (pEGFR + pEGFR_Akt) noiseParameter1_pEGFR_tot observableParameter1_pEGFR_tot noiseParameter1_pEGFR_tot +pS6_tot pS6 * observableParameter1_pS6_tot noiseParameter1_pS6_tot observableParameter1_pS6_tot noiseParameter1_pS6_tot diff --git a/v2/Fujita_SciSignal2010/parameters_Fujita_SciSignal2010.tsv b/v2/Fujita_SciSignal2010/parameters_Fujita_SciSignal2010.tsv new file mode 100644 index 0000000..fd5b438 --- /dev/null +++ b/v2/Fujita_SciSignal2010/parameters_Fujita_SciSignal2010.tsv @@ -0,0 +1,20 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorType priorParameters hierarchicalOptimization (optional) +EGFR_turnover EGFR_{turnover} 1e-08 100000000 0.001479614562719 true +init_AKT init_{AKT} 1e-08 100000000 0.026930923029049 true +init_EGFR init_{EGFR} 1e-08 100000000 37536153.8059105 true +init_S6 init_{S6} 1e-08 100000000 188.063148677911 true +reaction_1_k1 reaction_{1,k1} 1e-08 100000000 0.003690766129111 true +reaction_1_k2 reaction_{1,k2} 1e-08 100000000 0.002301175486005 true +reaction_2_k1 reaction_{2,k1} 1e-08 100000000 0.000936500808211 true +reaction_2_k2 reaction_{2,k2} 1e-08 100000000 60965.2066642586 true +reaction_3_k1 reaction_{3,k1} 1e-08 100000000 0.433225051651771 true +reaction_4_k1 reaction_{4,k1} 1e-08 100000000 0.030155177423024 true +reaction_5_k1 reaction_{5,k1} 1e-08 100000000 3.27310803801897e-06 true +reaction_5_k2 reaction_{5,k2} 1e-08 100000000 0.000398546299782 true +reaction_6_k1 reaction_{6,k1} 1e-08 100000000 5.46319692934546e-06 true +reaction_7_k1 reaction_{7,k1} 1e-08 100000000 0.011803208311735 true +reaction_8_k1 reaction_{8,k1} 1e-08 100000000 0.000944761775113 true +reaction_9_k1 reaction_{9,k1} 1e-08 100000000 0.028510798479438 true +scaling_pAkt_tot scaling_{pAkt}_tot 1e-08 100000000 41.3771031603841 true +scaling_pEGFR_tot scaling_{pEGFR}_tot 1e-08 100000000 5.64785460492811e-08 true +scaling_pS6_tot scaling_{pS6}_tot 1e-08 100000000 78521.9513232784 true diff --git a/v2/Giordano_Nature2020/Giordano_Nature2020.yaml b/v2/Giordano_Nature2020/Giordano_Nature2020.yaml new file mode 100644 index 0000000..61e328c --- /dev/null +++ b/v2/Giordano_Nature2020/Giordano_Nature2020.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Giordano_Nature2020.tsv +model_files: + model_Giordano_Nature2020: + location: model_Giordano_Nature2020.xml + language: sbml +measurement_files: +- measurementData_Giordano_Nature2020.tsv +condition_files: +- experimentalCondition_Giordano_Nature2020.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Giordano_Nature2020.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Giordano_Nature2020/experimentalCondition_Giordano_Nature2020.tsv 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observable_DiagHome 0.00092100345375 44.0 sd_DiagHome test +experiment____pred1 observable_DiagHome 0.0009720036612 45.0 sd_DiagHome test +experiment____pred1 observable_Hospit 9e-07 3.0 sd_Hospit test +experiment____pred1 observable_Hospit 1.65e-06 3.99 sd_Hospit test +experiment____pred1 observable_Hospit 1.9e-06 5.0 sd_Hospit test +experiment____pred1 observable_Hospit 2.13e-06 6.0 sd_Hospit test +experiment____pred1 observable_Hospit 4.13e-06 7.0 sd_Hospit test +experiment____pred1 observable_Hospit 5.75e-06 8.0 sd_Hospit test +experiment____pred1 observable_Hospit 6.68e-06 9.0 sd_Hospit test +experiment____pred1 observable_Hospit 1.07e-05 10.0 sd_Hospit test +experiment____pred1 observable_Hospit 1.24e-05 11.0 sd_Hospit test +experiment____pred1 observable_Hospit 1.72e-05 11.99 sd_Hospit test +experiment____pred1 observable_Hospit 2.24e-05 13.0 sd_Hospit test +experiment____pred1 observable_Hospit 2.98e-05 14.0 sd_Hospit test +experiment____pred1 observable_Hospit 3.99e-05 15.0 sd_Hospit test +experiment____pred1 observable_Hospit 4.42e-05 16.0 sd_Hospit test +experiment____pred1 observable_Hospit 5.93e-05 17.0 sd_Hospit test +experiment____pred1 observable_Hospit 7.19e-05 18.0 sd_Hospit test +experiment____pred1 observable_Hospit 8.4e-05 19.0 sd_Hospit test +experiment____pred1 observable_Hospit 9.73e-05 20.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.00011100045325 21.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.0001240005084 22.01 sd_Hospit test +experiment____pred1 observable_Hospit 0.000140000576333 23.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.000161000665467 24.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.0001840007636 25.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.000215000895833 26.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.000239000999817 27.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.0002630011046 27.99 sd_Hospit test +experiment____pred1 observable_Hospit 0.00026700112585 29.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.000295001248833 30.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.00033100140675 31.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.000345001472 32.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.0003660015677 33.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.0003850016555 34.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.000413001782783 35.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.000434001880667 36.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.00044500193575 37.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.0004560019912 37.99 sd_Hospit test +experiment____pred1 observable_Hospit 0.000463002029483 39.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.000470002068 40.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.000473002089083 41.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.000476002110267 42.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.00047900213155 43.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.000484002161867 44.0 sd_Hospit test +experiment____pred1 observable_Hospit 0.000482002160967 45.0 sd_Hospit test +experiment____pred1 observable_ICU 4.33e-07 3.0 sd_ICU test +experiment____pred1 observable_ICU 3.83e-07 3.99 sd_ICU test +experiment____pred1 observable_ICU 5.83e-07 5.0 sd_ICU test +experiment____pred1 observable_ICU 6e-07 6.0 sd_ICU test +experiment____pred1 observable_ICU 9.33e-07 7.0 sd_ICU test +experiment____pred1 observable_ICU 1.07e-06 8.0 sd_ICU test +experiment____pred1 observable_ICU 1.75e-06 9.0 sd_ICU test +experiment____pred1 observable_ICU 2.33e-06 10.0 sd_ICU test +experiment____pred1 observable_ICU 2.77e-06 11.0 sd_ICU test +experiment____pred1 observable_ICU 3.82e-06 11.99 sd_ICU test +experiment____pred1 observable_ICU 4.92e-06 13.0 sd_ICU test +experiment____pred1 observable_ICU 5.85e-06 14.0 sd_ICU test +experiment____pred1 observable_ICU 7.7e-06 15.0 sd_ICU test +experiment____pred1 observable_ICU 9.45e-06 16.0 sd_ICU test +experiment____pred1 observable_ICU 1.08e-05 17.0 sd_ICU test +experiment____pred1 observable_ICU 1.22e-05 18.0 sd_ICU test +experiment____pred1 observable_ICU 1.46e-05 19.0 sd_ICU test +experiment____pred1 observable_ICU 1.71e-05 20.0 sd_ICU test +experiment____pred1 observable_ICU 1.92e-05 21.0 sd_ICU test +experiment____pred1 observable_ICU 2.21e-05 22.01 sd_ICU test +experiment____pred1 observable_ICU 2.53e-05 23.0 sd_ICU test +experiment____pred1 observable_ICU 2.79e-05 24.0 sd_ICU test +experiment____pred1 observable_ICU 3.09e-05 25.0 sd_ICU test +experiment____pred1 observable_ICU 3.43e-05 26.0 sd_ICU test +experiment____pred1 observable_ICU 3.76e-05 27.0 sd_ICU test +experiment____pred1 observable_ICU 4.16e-05 27.99 sd_ICU test +experiment____pred1 observable_ICU 4.43e-05 29.0 sd_ICU test +experiment____pred1 observable_ICU 4.76e-05 30.0 sd_ICU test +experiment____pred1 observable_ICU 5.02e-05 31.0 sd_ICU test +experiment____pred1 observable_ICU 5.34e-05 32.0 sd_ICU test +experiment____pred1 observable_ICU 5.66e-05 33.0 sd_ICU test +experiment____pred1 observable_ICU 5.82e-05 34.0 sd_ICU test +experiment____pred1 observable_ICU 6.02e-05 35.0 sd_ICU test +experiment____pred1 observable_ICU 6.22e-05 36.0 sd_ICU test +experiment____pred1 observable_ICU 6.43e-05 37.0 sd_ICU test +experiment____pred1 observable_ICU 6.51e-05 37.99 sd_ICU test +experiment____pred1 observable_ICU 6.64e-05 39.0 sd_ICU test +experiment____pred1 observable_ICU 6.71e-05 40.0 sd_ICU test +experiment____pred1 observable_ICU 6.73e-05 41.0 sd_ICU test +experiment____pred1 observable_ICU 6.76e-05 42.0 sd_ICU test +experiment____pred1 observable_ICU 6.78e-05 43.0 sd_ICU test +experiment____pred1 observable_ICU 6.66e-05 44.0 sd_ICU test +experiment____pred1 observable_ICU 6.63e-05 45.0 sd_ICU test diff --git a/v2/Giordano_Nature2020/model_Giordano_Nature2020.xml b/v2/Giordano_Nature2020/model_Giordano_Nature2020.xml new file mode 100644 index 0000000..0324dbd --- /dev/null +++ b/v2/Giordano_Nature2020/model_Giordano_Nature2020.xml @@ -0,0 +1,3801 @@ + + + + + + + 
This is a model created on COPASI 4.27 (Build 217) which reproduces the Figures 2b, 2d, 3b, 3d, 4b, 4d in the article - https://www.nature.com/articles/s41591-020-0883-7
+
+To reproduce Fig 2b and 2d, set Event_trigger_Fig3b = 0, Event_trigger_Fig3d = 0, Event_trigger_Fig4b = 0, Event_trigger_Fig4d = 0, epsilon_modifer = 1, alpha_modifer = 1 and run for t = 45 d (for Fig 2b) and t = 350 days (for Fig 2d).
+Set alpha_modifier = 0 for the remaining 4 cases
+To reproduce Fig 3b, set Event_trigger_Fig3b = 1, Event_trigger_Fig3d = 0, Event_trigger_Fig4b = 0, Event_trigger_Fig4d = 0, epsilon_modifer = 1 and run for t = 350 days.
+To reproduce Fig 3d, set Event_trigger_Fig3b = 0, Event_trigger_Fig3d = 1, Event_trigger_Fig4b = 0, Event_trigger_Fig4d = 0, epsilon_modifer = 1 and run for t = 350 days.
+To reproduce Fig 4b, set Event_trigger_Fig3b = 0, Event_trigger_Fig3d = 0, Event_trigger_Fig4b = 1, Event_trigger_Fig4d = 0, epsilon_modifer = 0 and run for t = 350 days.
+To reproduce Fig 4d, set Event_trigger_Fig3b = 0, Event_trigger_Fig3d = 0, Event_trigger_Fig4b = 0, Event_trigger_Fig4d = 1, epsilon_modifer = 0 and run for t = 350 days.
+
+
+
+Modelling the COVID-19 epidemic and implementation of population-wide interventions in Italy
+Giulia Giordano, Franco Blanchini, Raffaele Bruno, Patrizio Colaneri, Alessandro Di Filippo, Angela Di Matteo and Marta Colaneri
+Journal - Nature Medicine
+DOI - 10.1038/s41591-020-0883-7
+
+In Italy, 128,948 confirmed cases and 15,887 deaths of people who tested positive for SARS-CoV-2 were registered as of 5 April 2020. Ending the global SARS-CoV-2 pandemic requires implementation of multiple population-wide strategies, including social distancing, testing and contact tracing. We propose a new model that predicts the course of the epidemic to help plan an effective control strategy. The model considers eight stages of infection: susceptible (S), infected (I), diagnosed (D), ailing (A), recognized (R), threatened (T), healed (H) and extinct (E), collectively termed SIDARTHE. Our SIDARTHE model discriminates between infected individuals depending on whether they have been diagnosed and on the severity of their symptoms. The distinction between diagnosed and non-diagnosed individuals is important because the former are typically isolated and hence less likely to spread the infection. This delineation also helps to explain misperceptions of the case fatality rate and of the epidemic spread. We compare simulation results with real data on the COVID-19 epidemic in Italy, and we model possible scenarios of implementation of countermeasures. Our results demonstrate that restrictive social-distancing measures will need to be combined with widespread testing and contact tracing to end the ongoing COVID-19 pandemic.
+ + + + + + + + + + Sheriff + Rahuman + + sheriff@ebi.ac.uk + + European Bioinformatics Institute, European Molecular Biology Laboratory + + + + + Ramachandran + Kausthubh + + kramachandran@ebi.ac.uk + + European Bioinformatics Institute, European Molecular Biology Laboratory + + + + + Tiwari + Krishna + + ktiwari@ebi.ac.uk + + European Bioinformatics Institute, European Molecular Biology Laboratory + + + + + + 2020-07-13T21:17:26Z + + + 2020-07-17T02:10:46Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2020-07-13T21:17:26Z + + + + + ktiwari@ebi.ac.uk + + + Tiwari + Krishna + + + + + European Bioinformatics Institute, European Molecular Biology Laboratory + + + + + + + kramachandran@ebi.ac.uk + + + Ramachandran + Kausthubh + + + + + European Bioinformatics Institute, European Molecular Biology Laboratory + + + + + + + sheriff@ebi.ac.uk + + + Sheriff + Rahuman + + + + + European Bioinformatics Institute, European Molecular Biology Laboratory + + + + + + + 2020-07-17T02:10:46 + + + + + + + + + + + + + + + 2020-07-13T21:42:52Z + + + + + + + + + + S + + + alpha + + + I + + + beta + + + D + + + gamma + + + A + + + delta + + + R + + + + S + + + + + alpha + I + + + + beta + D + + + + gamma + A + + + + delta + R + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2020-07-13T21:20:49Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2020-07-13T21:20:55Z + + + + + + + + + + + + 
Infected ND AS - non-diagnosed, asymptomatic (I)
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Infected D AS - diagnosed, asymptomatic (D)
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Infected ND S - non-diagnosed, symptomatic (A)
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Infected D S - diagnosed, symptomatic (R)
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Infected D IC - diagnosed, life-threatening symptoms (T)
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noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +observable_TotalCases TotalCases CumulativeDiagnosed noiseParameter1_observable_TotalCases normal noiseParameter1_observable_TotalCases +observable_Deaths Deaths Extinct noiseParameter1_observable_Deaths normal noiseParameter1_observable_Deaths +observable_Recovered Recovered DiagnosedHealed noiseParameter1_observable_Recovered normal noiseParameter1_observable_Recovered +observable_CurrentCases CurrentCases CurrentDiagnosedInfected noiseParameter1_observable_CurrentCases normal noiseParameter1_observable_CurrentCases +observable_DiagHome DiagnosedIsolatedHome Diagnosed noiseParameter1_observable_DiagHome normal noiseParameter1_observable_DiagHome +observable_Hospit Hospitalised Recognized noiseParameter1_observable_Hospit normal noiseParameter1_observable_Hospit +observable_ICU CriticalCondition Threatened noiseParameter1_observable_ICU normal noiseParameter1_observable_ICU diff --git a/v2/Giordano_Nature2020/parameters_Giordano_Nature2020.tsv b/v2/Giordano_Nature2020/parameters_Giordano_Nature2020.tsv new file mode 100644 index 0000000..0fb1d88 --- /dev/null +++ b/v2/Giordano_Nature2020/parameters_Giordano_Nature2020.tsv @@ -0,0 +1,51 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorParameters +alpha_0 alpha_0 0.001 10 0.57 true +beta_0 beta_0 0.001 10 0.011 true +delta_0 delta_0 0.001 10 0.011 true +epsilon_0 epsilon_0 0.001 10 0.171 true +eta_0 eta_0 0.001 10 0.125 true +gamma_0 gamma_0 0.001 10 0.456 true +kappa_0 kappa_0 0.001 10 0.017 true +lam_0 lam_0 0.001 10 0.034 true +mu_0 mu_0 0.001 10 0.017 true +nu_0 nu_0 0.001 10 0.027 true +rho_0 rho_0 0.001 10 0.034 true +sigma_0 sigma_0 0.001 10 0.017 true +tau tau 0.001 10 0.01 true +theta theta 0.001 10 0.371 true +xi_0 xi_0 0.001 10 0.017 true +zeta_0 zeta_0 0.001 10 0.125 true +alpha_4 alpha_4 0.001 10 0.422 true +alpha_22 alpha_22 0.001 10 0.36 true +alpha_28 alpha_28 0.001 10 0.21 true +beta_4 beta_4 0.001 10 0.0057 true +beta_22 beta_22 0.001 10 0.005 true +delta_4 delta_4 0.001 10 0.0057 true +delta_22 delta_22 0.001 10 0.005 true +epsilon_12 epsilon_12 0.001 10 0.143 true +epsilon_38 epsilon_38 0.001 10 0.2 true +eta_22 eta_22 0.001 10 0.034 true +eta_38 eta_38 0.001 10 0.025 true +gamma_4 gamma_4 0.001 10 0.285 true +gamma_22 gamma_22 0.001 10 0.2 true +gamma_28 gamma_28 0.001 10 0.11 true +kappa_22 kappa_22 0.001 10 0.017 true +kappa_38 kappa_38 0.001 10 0.02 true +lam_22 lam_22 0.001 10 0.08 true +mu_22 mu_22 0.001 10 0.008 true +nu_22 nu_22 0.001 10 0.015 true +rho_22 rho_22 0.001 10 0.017 true +rho_38 rho_38 0.001 10 0.02 true +sigma_22 sigma_22 0.001 10 0.017 true +sigma_38 sigma_38 0.001 10 0.01 true +xi_22 xi_22 0.001 10 0.017 true +xi_38 xi_38 0.001 10 0.02 true +zeta_22 zeta_22 0.001 10 0.034 true +zeta_38 zeta_38 0.001 10 0.025 true +sd_TotalCases sd_TotalCases 1e-08 10 1.0 true +sd_Deaths sd_Deaths 1e-08 10 1.0 true +sd_Recovered sd_Recovered 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s_pRII_JI09_150330_Drg353_351_CycNuc JI09_150330_Drg353_351_CycNuc JI09_150330_Drg353_351_CycNuc__Rp_cAMPS_pAB_and_ctrl Drg353 +experiment__model1_data49___model1_data78 pRII_Microscopy 909.43624182519 35 s_pRII_JI09_150330_Drg353_351_CycNuc s_pRII_JI09_150330_Drg353_351_CycNuc JI09_150330_Drg353_351_CycNuc JI09_150330_Drg353_351_CycNuc__Rp_cAMPS_pAB_and_ctrl Drg353 +experiment__model1_data49___model1_data78 pRII_Microscopy 927.64717255043 35 s_pRII_JI09_150330_Drg353_351_CycNuc s_pRII_JI09_150330_Drg353_351_CycNuc JI09_150330_Drg353_351_CycNuc JI09_150330_Drg353_351_CycNuc__Rp_cAMPS_pAB_and_ctrl Drg353 +experiment__model1_data49___model1_data79 pRII_Microscopy 906.459532906084 35 s_pRII_JI09_150330_Drg353_351_CycNuc s_pRII_JI09_150330_Drg353_351_CycNuc JI09_150330_Drg353_351_CycNuc JI09_150330_Drg353_351_CycNuc__Rp_cAMPS_pAB_and_ctrl Drg353 +experiment__model1_data49___model1_data79 pRII_Microscopy 1021.19441703927 35 s_pRII_JI09_150330_Drg353_351_CycNuc 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s_pRII_JI09_150330_Drg353_351_CycNuc JI09_150330_Drg353_351_CycNuc JI09_150330_Drg353_351_CycNuc__Rp_cAMPS_pAB_and_ctrl Drg353 +experiment__model1_data49___model1_data81 pRII_Microscopy 937.257245038578 35 s_pRII_JI09_150330_Drg353_351_CycNuc s_pRII_JI09_150330_Drg353_351_CycNuc JI09_150330_Drg353_351_CycNuc JI09_150330_Drg353_351_CycNuc__Rp_cAMPS_pAB_and_ctrl Drg353 +experiment__model1_data49___model1_data81 pRII_Microscopy 960.07894975606 35 s_pRII_JI09_150330_Drg353_351_CycNuc s_pRII_JI09_150330_Drg353_351_CycNuc JI09_150330_Drg353_351_CycNuc JI09_150330_Drg353_351_CycNuc__Rp_cAMPS_pAB_and_ctrl Drg353 +experiment__model1_data49___model1_data81 pRII_Microscopy 1024.72737362604 35 s_pRII_JI09_150330_Drg353_351_CycNuc s_pRII_JI09_150330_Drg353_351_CycNuc JI09_150330_Drg353_351_CycNuc JI09_150330_Drg353_351_CycNuc__Rp_cAMPS_pAB_and_ctrl Drg353 +experiment__model1_data49___model1_data82 pRII_Microscopy 1626.67382727075 35 s_pRII_JI09_150330_Drg353_351_CycNuc 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JI09_151102_Drg421_418_Age__ctrl_and_ctrl Drg421 +experiment__model1_data49___model1_data110 pRII_Microscopy 965.974629342757 61 s_pRII_JI09_151102_Drg421_418_Age s_pRII_JI09_151102_Drg421_418_Age JI09_151102_Drg421_418_Age JI09_151102_Drg421_418_Age__ctrl_and_ctrl Drg421 +experiment__model1_data49___model1_data110 pRII_Microscopy 941.189262243799 65 s_pRII_JI09_151102_Drg421_418_Age s_pRII_JI09_151102_Drg421_418_Age JI09_151102_Drg421_418_Age JI09_151102_Drg421_418_Age__ctrl_and_ctrl Drg421 +experiment__model1_data49___model1_data110 pRII_Microscopy 1023.46700642819 75 s_pRII_JI09_151102_Drg421_418_Age s_pRII_JI09_151102_Drg421_418_Age JI09_151102_Drg421_418_Age JI09_151102_Drg421_418_Age__ctrl_and_ctrl Drg421 +experiment__model1_data49___model1_data110 pRII_Microscopy 1033.31727712093 90 s_pRII_JI09_151102_Drg421_418_Age s_pRII_JI09_151102_Drg421_418_Age JI09_151102_Drg421_418_Age JI09_151102_Drg421_418_Age__ctrl_and_ctrl Drg421 +experiment__model1_data49___model1_data110 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b/v2/Isensee_JCB2018/model_Isensee_JCB2018.xml @@ -0,0 +1,1364 @@ + + + + + + 
PEtab implementation of the model from Isensee et al. (2018), The Journal of Cell Biology Jun 2018, 217 (6) 2167-2184
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cyt + KD_Fsk + kf_Fsk + pAC_Fsk + + + + + + + + + + + + + + + + + + + cyt + AC + Csub + kp_AC + + + + + + + + + + + + + + + + + + + cyt + AC_Fsk + Csub + kp_AC + + + + + + + + + + + + + + + + cyt + kdp_AC + pAC + + + + + + + + + + + + + + + + cyt + kdp_AC + pAC_Fsk + + + + + + + + + + + + + + + + + cyt + ks_AC_cAMP + + + AC + + + pAC + xi_pAC + + + + + + + + + + + + + + + + + + + cyt + ks_AC_cAMP + xi_AC_cAMP_Fsk + + + AC_Fsk + + + pAC_Fsk + xi_pAC + + + + + + + + + + + + + + + + + + + + cyt + + + + + KD_IBMX + cAMP + kdeg_cAMP_free + + + PDE + + + pPDE + xi_pPDE + + + + + + IBMX + KD_IBMX + + + + + + + + + + + + + + + + + + + cyt + RII_C_2 + kf_RII_C_2__RII_2 + + + + + + + + + + + + + + + + + cyt + Csub + RII_2 + kf_RII_2__RII_C_2 + + + + + + + + + + + + + + + + + cyt + RIIp_C_2 + kf_RII_C_2__RII_2 + xi_kf_RII_C_2__RII_2 + + + + + + + + + + + + + + + + + cyt + Csub + RIIp_2 + kf_RII_2__RII_C_2 + xi_kf_RII_2__RII_C_2 + + + + + + + + + + + + + + + + cyt + RIIp_2 + kf_RIIp_2__RII_2 + + + + + + + + + + + + + + + + cyt + RII_C_2 + kf_RII_C_2__RIIp_C_2 + + + + + + + + + + + + + + + + cyt + RIIp_C_2 + kf_RIIp_C_2__RII_C_2 + + + + + + + + + + + + + + + + + + + cyt + RIIp_C_2 + cAMP + kf_cAMP + + + + + + + + + + + + + + + + cyt + KD_cAMP + RIIp_cAMP_C_2 + kf_cAMP + + + + + + + + + + + + + + + + + + + + + cyt + + + + + KD_IBMX + RIIp_cAMP_C_2 + kdeg_cAMP + + + PDE + + + pPDE + xi_pPDE + + + + + + IBMX + KD_IBMX + + + + + + + + + + + + + + + + + + + cyt + RIIp_cAMP_C_2 + kf_RIIp_cAMP_C_2__RIIp_2 + + + + + + + + + + + + + + + + cyt + KD_cAMP + RIIp_cAMP_2 + kf_cAMP + + + + + + + + + + + + + + + + + + + + + cyt + + + + + KD_IBMX + RIIp_cAMP_2 + kdeg_cAMP + + + PDE + + + pPDE + xi_pPDE + + + + + + IBMX + KD_IBMX + + + + + + + + + + + + + + + + + + + + + cyt + RIIp_C_2 + Rp8_Br_cAMPS + kf_cAMP + xi_b_Rp8_Br_cAMPS + + + + + + + + + + + + + + + + cyt + KD_cAMP + RIIp_Rp8_Br_cAMPS_C_2 + kf_cAMP + xi_b_Rp8_Br_cAMPS + xi_KD_Rp8_Br_cAMPS + + + + + + + + + + + + + + + + + + + cyt + RIIp_C_2 + Rp8_pCPT_cAMPS + kf_cAMP + xi_b_Rp8_pCPT_cAMPS + + + + + + + + + + + + + + + + cyt + KD_cAMP + RIIp_Rp8_pCPT_cAMPS_C_2 + kf_cAMP + xi_b_Rp8_pCPT_cAMPS + xi_KD_Rp8_pCPT_cAMPS + + + + + + + + + + + + + + + + + + + cyt + RIIp_C_2 + Rp_cAMPS + kf_cAMP + xi_b_Rp_cAMPS + + + + + + + + + + + + + + + + cyt + KD_cAMP + RIIp_Rp_cAMPS_C_2 + kf_cAMP + xi_b_Rp_cAMPS + xi_KD_Rp_cAMPS + + + + + + + + + + + + + + + + + + + cyt + RIIp_C_2 + Sp8_Br_cAMPS + kf_cAMP + xi_b_Sp8_Br_cAMPS + + + + + + + + + + + + + + + + cyt + KD_cAMP + RIIp_Sp8_Br_cAMPS_C_2 + kf_cAMP + xi_b_Sp8_Br_cAMPS + xi_KD_Sp8_Br_cAMPS + + + + + + + + + + + + + + + + + cyt + RIIp_Sp8_Br_cAMPS_C_2 + kf_RIIp_cAMP_C_2__RIIp_2 + + + + + + + + + + + + + + + + cyt + KD_cAMP + RIIp_Sp8_Br_cAMPS_2 + kf_cAMP + xi_b_Sp8_Br_cAMPS + xi_KD_Sp8_Br_cAMPS + + + + + + + + + + + + + + + + cyt + Csub + H89 + kf_H89 + + + + + + + + + + + + + + + + cyt + Csub_H89 + KD_H89 + kf_H89 + + + + + + + + + + + + + + + + + + + cyt + Csub + PDE + kf_PDE_Csub + + + + + + + + + + + + + + + + cyt + KD_PDE_Csub + kf_PDE_Csub + pPDE + + + + + + + diff --git a/v2/Isensee_JCB2018/observables_Isensee_JCB2018.tsv b/v2/Isensee_JCB2018/observables_Isensee_JCB2018.tsv new file mode 100644 index 0000000..24c13ef --- /dev/null +++ b/v2/Isensee_JCB2018/observables_Isensee_JCB2018.tsv @@ -0,0 +1,4 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +pRII_Microscopy observableParameter1_pRII_Microscopy * (b_pRII_global + s_pRII_global * (2 * RIIp_2 + 2 * RIIp_cAMP_2 + 2 * RIIp_Sp8_Br_cAMPS_2 + 2 * rel_open * (RIIp_C_2 + RIIp_Rp_cAMPS_C_2 + RIIp_Rp8_Br_cAMPS_C_2 + RIIp_Rp8_pCPT_cAMPS_C_2) + 2 * (RIIp_cAMP_C_2 + RIIp_Sp8_Br_cAMPS_C_2) * (rel_open - xi_rel_open * (rel_open - 1)))) noiseParameter1_pRII_Microscopy * s_pRII_global * rho_pRII_Microscopy observableParameter1_pRII_Microscopy noiseParameter1_pRII_Microscopy +pRII_Western s_pRII_Western * (2 * RIIp_2 + 2 * RIIp_C_2 + 2 * RIIp_cAMP_2 + 2 * RIIp_cAMP_C_2 + 2 * RIIp_Rp_cAMPS_C_2 + 2 * RIIp_Sp8_Br_cAMPS_2 + 2 * RIIp_Rp8_Br_cAMPS_C_2 + 2 * RIIp_Sp8_Br_cAMPS_C_2 + 2 * RIIp_Rp8_pCPT_cAMPS_C_2) s_pRII_Western * rho_pRII_Western +Calpha_Microscopy observableParameter1_Calpha_Microscopy * (b_Calpha_global + s_Calpha_global * (2 * Csub + 2 * Csub_H89 + 2 * rel_open * (RIIp_C_2 + RIIp_Rp_cAMPS_C_2 + RIIp_Rp8_Br_cAMPS_C_2 + RIIp_Rp8_pCPT_cAMPS_C_2) + 2 * (RIIp_cAMP_C_2 + RIIp_Sp8_Br_cAMPS_C_2) * (rel_open - xi_rel_open * (rel_open - 1)))) s_Calpha_global * rho_Calpha_Microscopy observableParameter1_Calpha_Microscopy diff --git a/v2/Isensee_JCB2018/parameters_Isensee_JCB2018.tsv b/v2/Isensee_JCB2018/parameters_Isensee_JCB2018.tsv new file mode 100644 index 0000000..83a5591 --- /dev/null +++ b/v2/Isensee_JCB2018/parameters_Isensee_JCB2018.tsv @@ -0,0 +1,51 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorDistribution priorParameters model_selection_group +AC_total AC_{total} 1e-05 1000.0 1.0 false uniform 1e-05;1000.0 +KD_Fsk KD_{Fsk} 1e-05 1000.0 14.2805171742694 true log10-normal 0.845098040014257;0.2 +KD_H89 KD_{H89} 1e-05 1000.0 0.048074027232332 true log10-normal -1.318758762624413;0.2 +KD_IBMX KD_{IBMX} 1e-05 1000.0 11.960772655864 true log10-normal 1.0;0.2 +KD_cAMP KD_{cAMP} 1e-05 1000.0 2.85002019924967 true log10-normal 0.462397997898956;0.2 +PDE_total PDE_{total} 1e-05 1000.0 1.0 false uniform 1e-05;1000.0 +RII2_total RII2_{total} 1e-05 1000.0 1.0 false uniform 1e-05;1000.0 +b_Calpha_global b_{Calpha,global} 0.001 1000.0 101.662732662228 true log10-normal 2;0.1 +b_pRII_global b_{pRII,global} 0.001 1000.0 99.7184671220999 true log10-normal 2;0.1 +kdeg_cAMP kdeg_{cAMP} 1e-05 1000.0 1.00000660182181e-05 true uniform 1e-05;1000.0 +kdeg_cAMP_free kdeg_{cAMP,free} 1e-05 1000.0 7.38363782272545 true uniform 1e-05;1000.0 +kf_Fsk kf_{Fsk} 1e-05 1000.0 999.999958296064 true uniform 1e-05;1000.0 +kf_H89 kf_{H89} 1e-05 1000.0 0.000742716621349 true uniform 1e-05;1000.0 +kf_RII_2__RII_C_2 kf_{RII_2,RII_C_2} 1e-05 100000.0 1.26446106685121 true uniform 1e-05;100000.0 +kf_RII_C_2__RII_2 kf_{RII_C_2,RII_2} 1e-05 1000.0 0.018746739843535 true uniform 1e-05;1000.0 +kf_RII_C_2__RIIp_C_2 kf_{RII_C_2,RIIp_C_2} 1e-05 1000.0 0.022767932816744 true uniform 1e-05;1000.0 +kf_RIIp_2__RII_2 kf_{RIIp_2,RII_2} 1e-05 1000.0 0.03230162532087 true uniform 1e-05;1000.0 +kf_RIIp_C_2__RII_C_2 kf_{RIIp_C_2,RII_C_2} 1e-05 1000.0 0.025703919542656 true uniform 1e-05;1000.0 +kf_RIIp_cAMP_C_2__RIIp_2 kf_{RIIp_cAMP_C_2,RIIp_2} 1e-05 1000.0 0.105283748414996 true uniform 1e-05;1000.0 +kf_cAMP kf_{cAMP} 1e-05 1000.0 0.501542412469253 true uniform 1e-05;1000.0 +ki_IBMX ki_{IBMX} 1e-05 1000.0 999.99999999947 true uniform 1e-05;1000.0 +ki_Rp8_Br_cAMPS_pAB ki_{Rp8,Br,cAMPS,pAB} 1e-05 1000.0 6.44560005260773 true uniform 1e-05;1000.0 +ki_Rp8_pCPT_cAMPS_pAB ki_{Rp8,pCPT,cAMPS,pAB} 1e-05 1000.0 9.3898794585472 true uniform 1e-05;1000.0 +ki_Rp_cAMPS_pAB ki_{Rp,cAMPS,pAB} 1e-05 1000.0 0.016320587381729 true uniform 1e-05;1000.0 +ki_Sp8_Br_cAMPS_AM ki_{Sp8,Br,cAMPS,AM} 1e-05 1000.0 0.131657936881857 true uniform 1e-05;1000.0 +ks_AC_cAMP ks_{AC,cAMP} 1e-05 1000.0 0.423150583624568 true uniform 1e-05;1000.0 +rel_open rel_{open} 1e-05 1.0 0.232684484588385 true uniform 1e-05;1.0 +s_Calpha_JI09_160201_Drg453_452_CycNuc s_{Calpha,JI09,160201,Drg453,452,CycNuc} 1e-05 1000.0 1.0 false uniform 1e-05;1000.0 +s_Calpha_global s_{Calpha,global} 1000.0 3162.27766016838 1758.15501421399 true uniform 1000.0;3162.27766016838 +s_pRII_JI09_150302_Drg345_343_CycNuc s_{pRII,JI09,150302,Drg345,343,CycNuc} 0.001 1000.0 1.1029976101468 true log10-normal 0;0.1 +s_pRII_JI09_150330_Drg350_348_CycNuc s_{pRII,JI09,150330,Drg350,348,CycNuc} 0.001 1000.0 0.9067516915655 true log10-normal 0;0.1 +s_pRII_JI09_150330_Drg353_351_CycNuc s_{pRII,JI09,150330,Drg353,351,CycNuc} 0.001 1000.0 0.934506349283962 true log10-normal 0;0.1 +s_pRII_JI09_151102_Drg421_418_Age s_{pRII,JI09,151102,Drg421,418,Age} 0.001 1000.0 1.06693094665605 true log10-normal 0;0.1 +s_pRII_Western s_{pRII,Western} 0.1 100000.0 1.14849828435972 true uniform 0.1;100000.0 +s_pRII_global s_{pRII,global} 1000.0 3162.27766016838 2206.77137565008 true uniform 1000.0;3162.27766016838 +rho_Calpha_Microscopy \rho_{Calpha,Microscopy} 1e-05 1000.0 0.049753182233122 true uniform 1e-05;1000.0 +rho_pRII_Microscopy \rho_{pRII,Microscopy} 1e-05 1000.0 0.040685236621013 true uniform 1e-05;1000.0 +rho_pRII_Western \rho_{pRII,Western} 1e-05 1000.0 0.099334983213923 true uniform 1e-05;1000.0 +xi_AC_cAMP_Fsk \xi_{AC_{cAMP,Fsk} 1e-05 1000.0 642.370332155571 true uniform 1e-05;1000.0 +xi_b_Rp8_Br_cAMPS \xi_{b,Rp8,Br,cAMPS} 1e-05 100000.0 0.040559301141753 true log10-normal 0;3 +xi_b_Rp8_pCPT_cAMPS \xi_{b,Rp8,pCPT,cAMPS} 1e-05 100000.0 0.026684466293791 true log10-normal 0;3 +xi_b_Rp_cAMPS \xi_{b,Rp,cAMPS} 1e-05 100000.0 0.603928050380137 true log10-normal 0;3 +xi_b_Sp8_Br_cAMPS \xi_{b,Sp8,Br,cAMPS} 1e-05 100000.0 21.6150210996832 true log10-normal 0;3 +xi_kf_RII_2__RII_C_2 \xi_{kf_RII_2,RII_C_2} 1e-05 1.0 0.01893099823943 true log10-normal -1.742435698117109;0.1 +xi_kf_RII_C_2__RII_2 \xi_{kf_RII_C_2,RII_2} 1e-05 100000.0 0.810991675177056 true log10-normal -0.062147906748844;0.1 +xi_rel_open \xi_{rel,open} 1e-05 1.0 0.749424660751357 true uniform 1e-05;1.0 +xi_KD_Rp8_Br_cAMPS \xi_{KD,Rp8,Br,cAMPS} 1e-05 100000.0 0.039962383560766 true log10-normal 0;3 H1: different KD +xi_KD_Rp8_pCPT_cAMPS \xi_{KD,Rp8,pCPT,cAMPS} 1e-05 100000.0 0.194212924719718 true log10-normal 0;3 H1: different KD +xi_KD_Rp_cAMPS \xi_{KD,Rp,cAMPS} 1e-05 100000.0 0.163047074866588 true log10-normal 0;3 H1: different KD +xi_KD_Sp8_Br_cAMPS \xi_{KD,Sp8,Br,cAMPS} 1e-05 100000.0 0.22324026500667 true log10-normal 0;3 H1: different KD diff --git a/v2/Lang_PLOSComputBiol2024/Lang_PLOSComputBiol2024.yaml b/v2/Lang_PLOSComputBiol2024/Lang_PLOSComputBiol2024.yaml new file mode 100644 index 0000000..c64d8df --- /dev/null +++ b/v2/Lang_PLOSComputBiol2024/Lang_PLOSComputBiol2024.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Lang_PLOSComputBiol2024.tsv +model_files: + model_Lang_PLOSComputBiol2024: + location: model_Lang_PLOSComputBiol2024.xml + language: sbml +measurement_files: +- measurementData_Lang_PLOSComputBiol2024.tsv +condition_files: +- experimentalCondition_Lang_PLOSComputBiol2024.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Lang_PLOSComputBiol2024.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Lang_PLOSComputBiol2024/experimentalCondition_Lang_PLOSComputBiol2024.tsv b/v2/Lang_PLOSComputBiol2024/experimentalCondition_Lang_PLOSComputBiol2024.tsv new file mode 100644 index 0000000..d43cfc8 --- /dev/null +++ b/v2/Lang_PLOSComputBiol2024/experimentalCondition_Lang_PLOSComputBiol2024.tsv @@ -0,0 +1,125 @@ +conditionId targetId targetValue +wt _Cyt__CCND ic_wt_Cyt__CCND +wt _Cyt__CCNE_CDKN1A_B_ ic_wt_Cyt__CCNE_CDKN1A_B_ +wt _Cyt__E2F_DBD_RB1_Ser332u_ ic_wt_Cyt__E2F_DBD_RB1_Ser332u_ +wt _Cyt__E2F_DBD_RB1_Ser332p_ ic_wt_Cyt__E2F_DBD_RB1_Ser332p_ +wt _Cyt__CCNA_CDKN1A_B_ ic_wt_Cyt__CCNA_CDKN1A_B_ +wt _Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_ ic_wt_Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_ +wt _Cyt__E2F_DBD_RB1_1_Ser332u__RB1_E2F_1_Ser807_Ser811u_ ic_wt_Cyt__E2F_DBD_RB1_1_Ser332u__RB1_E2F_1_Ser807_Ser811u_ +wt _Cyt__E2F_DBD_RB1_1_Ser332p__RB1_E2F_1_Ser807_Ser811u_ ic_wt_Cyt__E2F_DBD_RB1_1_Ser332p__RB1_E2F_1_Ser807_Ser811u_ +wt _Cyt__RB1_E2F_Ser807_Ser811u_ ic_wt_Cyt__RB1_E2F_Ser807_Ser811u_ +wt _Cyt__RB1_E2F_Ser807_Ser811p_ ic_wt_Cyt__RB1_E2F_Ser807_Ser811p_ +wt _Cyt__PPP2R2B_ENSA_ARPP19_ ic_wt_Cyt__PPP2R2B_ENSA_ARPP19_ +wt _Cyt__APC_FBXO5_FZR1_CDC20_Ser355u_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_Ser355u_ +wt _Cyt__CDC20_APC_ ic_wt_Cyt__CDC20_APC_ +wt _Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355p__CDC20_APC_1_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355p__CDC20_APC_1_ +wt _Cyt__APC_FBXO5_FZR1_CDC20_Ser355p_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_Ser355p_ +wt _Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355u__FZR1_APC_1_FBXO5_nTermu_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355u__FZR1_APC_1_FBXO5_nTermu_ +wt _Cyt__FZR1_APC_FBXO5_nTermu_ ic_wt_Cyt__FZR1_APC_FBXO5_nTermu_ +wt _Cyt__FZR1_APC_FBXO5_nTermp_ ic_wt_Cyt__FZR1_APC_FBXO5_nTermp_ +wt _Cyt__APC_FBXO5_1_FZR1_CDC20_2_Ser355u__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ ic_wt_Cyt__APC_FBXO5_1_FZR1_CDC20_2_Ser355u__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ +wt _Cyt__FBXO5_APC_FZR1_Ser182u_ ic_wt_Cyt__FBXO5_APC_FZR1_Ser182u_ +wt _Cyt__APC_FBXO5_1_FZR1_CDC20_2_Ser355p__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ ic_wt_Cyt__APC_FBXO5_1_FZR1_CDC20_2_Ser355p__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ +wt _Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355p__FZR1_APC_1_FBXO5_nTermu_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355p__FZR1_APC_1_FBXO5_nTermu_ +wt _Cyt__FBXO5_APC_FZR1_Ser182p_ ic_wt_Cyt__FBXO5_APC_FZR1_Ser182p_ +wt _Cyt__FOXM1_DBD_Thr600u_ ic_wt_Cyt__FOXM1_DBD_Thr600u_ +wt _Cyt__FOXM1_DBD_Thr600p_ ic_wt_Cyt__FOXM1_DBD_Thr600p_ +wt _Cyt__WEE1_Ser123u_ ic_wt_Cyt__WEE1_Ser123u_ +wt _Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_ ic_wt_Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_ +wt _Cyt__WEE1_Ser123p_ ic_wt_Cyt__WEE1_Ser123p_ +wt _Cyt__CDC25_pSitesp_ ic_wt_Cyt__CDC25_pSitesp_ +wt _Cyt__CDC25_pSitesu_ ic_wt_Cyt__CDC25_pSitesu_ +wt _Cyt__MASTL_Thr198u_ ic_wt_Cyt__MASTL_Thr198u_ +wt _Cyt__MASTL_Thr198p_ ic_wt_Cyt__MASTL_Thr198p_ +wt _Cyt__ENSA_ARPP19_PPP2R2B_Ser62_Ser67u_ ic_wt_Cyt__ENSA_ARPP19_PPP2R2B_Ser62_Ser67u_ +wt _Cyt__ENSA_ARPP19_PPP2R2B_Ser62_Ser67p_ ic_wt_Cyt__ENSA_ARPP19_PPP2R2B_Ser62_Ser67p_ +wt _Cyt__ENSA_ARPP19_PPP2R2B_1_Ser62_Ser67p__PPP2R2B_ENSA_ARPP19_1_ ic_wt_Cyt__ENSA_ARPP19_PPP2R2B_1_Ser62_Ser67p__PPP2R2B_ENSA_ARPP19_1_ +wt _Cyt__SKP2 ic_wt_Cyt__SKP2 +wt _Cyt__TP53_DBD_Ser15p_ ic_wt_Cyt__TP53_DBD_Ser15p_ +wt _Cyt__FOXO_DBD_ ic_wt_Cyt__FOXO_DBD_ +wt _Num__NUP_pSitesu_ ic_wt_Num__NUP_pSitesu_ +wt _Nuc__CCND ic_wt_Nuc__CCND +wt _Nuc__CCNE_CDKN1A_B_ ic_wt_Nuc__CCNE_CDKN1A_B_ +wt _Nuc__E2F_DBD_RB1_Ser332u_ ic_wt_Nuc__E2F_DBD_RB1_Ser332u_ +wt _Nuc__E2F_DBD_RB1_Ser332p_ ic_wt_Nuc__E2F_DBD_RB1_Ser332p_ +wt _Nuc__CCNA_CDKN1A_B_ ic_wt_Nuc__CCNA_CDKN1A_B_ +wt _Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_ ic_wt_Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_ +wt _Nuc__E2F_DBD_RB1_1_Ser332u__RB1_E2F_1_Ser807_Ser811u_ ic_wt_Nuc__E2F_DBD_RB1_1_Ser332u__RB1_E2F_1_Ser807_Ser811u_ +wt _Nuc__E2F_DBD_RB1_1_Ser332p__RB1_E2F_1_Ser807_Ser811u_ ic_wt_Nuc__E2F_DBD_RB1_1_Ser332p__RB1_E2F_1_Ser807_Ser811u_ +wt _Nuc__RB1_E2F_Ser807_Ser811u_ ic_wt_Nuc__RB1_E2F_Ser807_Ser811u_ +wt _Nuc__RB1_E2F_Ser807_Ser811p_ ic_wt_Nuc__RB1_E2F_Ser807_Ser811p_ +wt _Nuc__PPP2R2B_ENSA_ARPP19_ ic_wt_Nuc__PPP2R2B_ENSA_ARPP19_ +wt _Nuc__APC_FBXO5_FZR1_CDC20_Ser355u_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_Ser355u_ +wt _Nuc__CDC20_APC_ ic_wt_Nuc__CDC20_APC_ +wt _Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355p__CDC20_APC_1_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355p__CDC20_APC_1_ +wt _Nuc__APC_FBXO5_FZR1_CDC20_Ser355p_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_Ser355p_ +wt _Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355u__FZR1_APC_1_FBXO5_nTermu_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355u__FZR1_APC_1_FBXO5_nTermu_ +wt _Nuc__FZR1_APC_FBXO5_nTermu_ ic_wt_Nuc__FZR1_APC_FBXO5_nTermu_ +wt _Nuc__FZR1_APC_FBXO5_nTermp_ ic_wt_Nuc__FZR1_APC_FBXO5_nTermp_ +wt _Nuc__APC_FBXO5_1_FZR1_CDC20_2_Ser355u__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ ic_wt_Nuc__APC_FBXO5_1_FZR1_CDC20_2_Ser355u__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ +wt _Nuc__FBXO5_APC_FZR1_Ser182u_ ic_wt_Nuc__FBXO5_APC_FZR1_Ser182u_ +wt _Nuc__APC_FBXO5_1_FZR1_CDC20_2_Ser355p__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ ic_wt_Nuc__APC_FBXO5_1_FZR1_CDC20_2_Ser355p__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ +wt _Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355p__FZR1_APC_1_FBXO5_nTermu_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355p__FZR1_APC_1_FBXO5_nTermu_ +wt _Nuc__FBXO5_APC_FZR1_Ser182p_ ic_wt_Nuc__FBXO5_APC_FZR1_Ser182p_ +wt _Nuc__FOXM1_DBD_Thr600u_ ic_wt_Nuc__FOXM1_DBD_Thr600u_ +wt _Nuc__FOXM1_DBD_Thr600p_ ic_wt_Nuc__FOXM1_DBD_Thr600p_ +wt _Nuc__CCNB_promoter_FOXM1_1__FOXM1_DBD_1_Thr600p_ ic_wt_Nuc__CCNB_promoter_FOXM1_1__FOXM1_DBD_1_Thr600p_ +wt _Nuc__CCNB_promoter_FOXM1_ ic_wt_Nuc__CCNB_promoter_FOXM1_ +wt _Nuc__CDC20_promoter_FOXM1_ ic_wt_Nuc__CDC20_promoter_FOXM1_ +wt _Nuc__CDC20_promoter_FOXM1_1__FOXM1_DBD_1_Thr600p_ ic_wt_Nuc__CDC20_promoter_FOXM1_1__FOXM1_DBD_1_Thr600p_ +wt _Nuc__WEE1_Ser123u_ ic_wt_Nuc__WEE1_Ser123u_ +wt _Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_ ic_wt_Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_ +wt _Nuc__WEE1_Ser123p_ ic_wt_Nuc__WEE1_Ser123p_ +wt _Nuc__CDC25_pSitesp_ ic_wt_Nuc__CDC25_pSitesp_ +wt _Nuc__CDC25_pSitesu_ ic_wt_Nuc__CDC25_pSitesu_ +wt _Nuc__MASTL_Thr198u_ ic_wt_Nuc__MASTL_Thr198u_ +wt _Nuc__MASTL_Thr198p_ ic_wt_Nuc__MASTL_Thr198p_ +wt _Nuc__ENSA_ARPP19_PPP2R2B_Ser62_Ser67u_ ic_wt_Nuc__ENSA_ARPP19_PPP2R2B_Ser62_Ser67u_ +wt _Nuc__ENSA_ARPP19_PPP2R2B_Ser62_Ser67p_ ic_wt_Nuc__ENSA_ARPP19_PPP2R2B_Ser62_Ser67p_ +wt _Nuc__ENSA_ARPP19_PPP2R2B_1_Ser62_Ser67p__PPP2R2B_ENSA_ARPP19_1_ ic_wt_Nuc__ENSA_ARPP19_PPP2R2B_1_Ser62_Ser67p__PPP2R2B_ENSA_ARPP19_1_ +wt _Nuc__CCNE_promoter_E2F_ ic_wt_Nuc__CCNE_promoter_E2F_ +wt _Nuc__CCNA_promoter_E2F_ ic_wt_Nuc__CCNA_promoter_E2F_ +wt _Nuc__E2F_promoter_E2F_ ic_wt_Nuc__E2F_promoter_E2F_ +wt _Nuc__FBXO5_promoter_E2F_ ic_wt_Nuc__FBXO5_promoter_E2F_ +wt _Nuc__FOXM1_promoter_E2F_ ic_wt_Nuc__FOXM1_promoter_E2F_ +wt _Nuc__CCNE_promoter_E2F_1__E2F_DBD_1_RB1_Ser332u_ ic_wt_Nuc__CCNE_promoter_E2F_1__E2F_DBD_1_RB1_Ser332u_ +wt _Nuc__CCNA_promoter_E2F_1__E2F_DBD_1_RB1_Ser332u_ ic_wt_Nuc__CCNA_promoter_E2F_1__E2F_DBD_1_RB1_Ser332u_ +wt _Nuc__E2F_DBD_1_RB1_Ser332u__E2F_promoter_E2F_1_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332u__E2F_promoter_E2F_1_ +wt _Nuc__E2F_DBD_1_RB1_Ser332u__FBXO5_promoter_E2F_1_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332u__FBXO5_promoter_E2F_1_ +wt _Nuc__E2F_DBD_1_RB1_Ser332u__FOXM1_promoter_E2F_1_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332u__FOXM1_promoter_E2F_1_ +wt _Nuc__CCNE_promoter_E2F_1__E2F_DBD_1_RB1_Ser332p_ ic_wt_Nuc__CCNE_promoter_E2F_1__E2F_DBD_1_RB1_Ser332p_ +wt _Nuc__CCNA_promoter_E2F_1__E2F_DBD_1_RB1_Ser332p_ ic_wt_Nuc__CCNA_promoter_E2F_1__E2F_DBD_1_RB1_Ser332p_ +wt _Nuc__E2F_DBD_1_RB1_Ser332p__E2F_promoter_E2F_1_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332p__E2F_promoter_E2F_1_ +wt _Nuc__E2F_DBD_1_RB1_Ser332p__FBXO5_promoter_E2F_1_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332p__FBXO5_promoter_E2F_1_ +wt _Nuc__E2F_DBD_1_RB1_Ser332p__FOXM1_promoter_E2F_1_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332p__FOXM1_promoter_E2F_1_ +wt _Nuc__SKP2 ic_wt_Nuc__SKP2 +wt _Nuc__TP53_DBD_Ser15p_ ic_wt_Nuc__TP53_DBD_Ser15p_ +wt _Nuc__CDKN1A_promoter_TP53_ ic_wt_Nuc__CDKN1A_promoter_TP53_ +wt _Nuc__FOXO_DBD_ ic_wt_Nuc__FOXO_DBD_ +wt _Nuc__CDKN1B_promoter_FOXO_ ic_wt_Nuc__CDKN1B_promoter_FOXO_ +wt _Nuc__CDKN1A_promoter_TP53_1__TP53_DBD_1_Ser15p_ ic_wt_Nuc__CDKN1A_promoter_TP53_1__TP53_DBD_1_Ser15p_ +wt _Cyt__CDKN1A_CCNE_A_B_Ser130u_ ic_wt_Cyt__CDKN1A_CCNE_A_B_Ser130u_ +wt _Nuc__CDKN1B_promoter_FOXO_1__FOXO_DBD_1_ ic_wt_Nuc__CDKN1B_promoter_FOXO_1__FOXO_DBD_1_ +wt _Cyt__CDKN1B_CCNE_A_Thr187u_ ic_wt_Cyt__CDKN1B_CCNE_A_Thr187u_ +wt _Cyt__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Cyt__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ +wt _Cyt__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Cyt__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ +wt _Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ +wt _Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ +wt _Cyt__CDKN1A_CCNE_A_B_Ser130p_ ic_wt_Cyt__CDKN1A_CCNE_A_B_Ser130p_ +wt _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ ic_wt_Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ +wt _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ ic_wt_Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ +wt _Cyt__CDKN1B_CCNE_A_Thr187p_ ic_wt_Cyt__CDKN1B_CCNE_A_Thr187p_ +wt _Nuc__CDKN1A_CCNE_A_B_Ser130u_ ic_wt_Nuc__CDKN1A_CCNE_A_B_Ser130u_ +wt _Nuc__CDKN1B_CCNE_A_Thr187u_ ic_wt_Nuc__CDKN1B_CCNE_A_Thr187u_ +wt _Nuc__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Nuc__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ +wt _Nuc__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Nuc__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ +wt _Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ +wt _Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ +wt _Nuc__CDKN1A_CCNE_A_B_Ser130p_ ic_wt_Nuc__CDKN1A_CCNE_A_B_Ser130p_ +wt _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ ic_wt_Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ +wt _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ ic_wt_Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ +wt _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ ic_wt_Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ +wt _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ ic_wt_Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ +wt _Nuc__CDKN1B_CCNE_A_Thr187p_ ic_wt_Nuc__CDKN1B_CCNE_A_Thr187p_ +wt _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ ic_wt_Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ +wt _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ ic_wt_Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ diff --git a/v2/Lang_PLOSComputBiol2024/experiments.tsv b/v2/Lang_PLOSComputBiol2024/experiments.tsv new file mode 100644 index 0000000..079cedf --- /dev/null +++ b/v2/Lang_PLOSComputBiol2024/experiments.tsv @@ -0,0 +1,2 @@ +experimentId conditionId time +experiment____wt wt 0 diff --git a/v2/Lang_PLOSComputBiol2024/measurementData_Lang_PLOSComputBiol2024.tsv b/v2/Lang_PLOSComputBiol2024/measurementData_Lang_PLOSComputBiol2024.tsv new file mode 100644 index 0000000..6357401 --- /dev/null +++ b/v2/Lang_PLOSComputBiol2024/measurementData_Lang_PLOSComputBiol2024.tsv @@ -0,0 +1,9601 @@ +experimentId observableId measurement time datasetId +experiment____wt obs_cycA__nuc_median 0.760224341 0.0 Nucleus +experiment____wt obs_cycA__nuc_median 0.619988707 164.6044632 Nucleus +experiment____wt obs_cycA__nuc_median 0.634750419 329.4838944 Nucleus +experiment____wt obs_cycA__nuc_median 0.673130618 494.6393196 Nucleus +experiment____wt obs_cycA__nuc_median 0.556513665 660.071628 Nucleus +experiment____wt obs_cycA__nuc_median 0.413325805 825.7817088 Nucleus +experiment____wt obs_cycA__nuc_median 0.463515393 991.770588 Nucleus +experiment____wt obs_cycA__nuc_median 0.321803694 1158.039086 Nucleus +experiment____wt obs_cycA__nuc_median 1.018552993 1324.58823 Nucleus +experiment____wt obs_cycA__nuc_median 0.618512546 1491.418908 Nucleus +experiment____wt obs_cycA__nuc_median 0.823699383 1658.532146 Nucleus +experiment____wt obs_cycA__nuc_median 0.535847404 1825.928903 Nucleus +experiment____wt obs_cycA__nuc_median 0.420706612 1993.610066 Nucleus +experiment____wt obs_cycA__nuc_median 0.487133977 2161.576595 Nucleus +experiment____wt obs_cycA__nuc_median 0.453920295 2329.829582 Nucleus +experiment____wt obs_cycA__nuc_median 0.46056307 2498.369918 Nucleus +experiment____wt obs_cycA__nuc_median 0.729962885 2667.198629 Nucleus +experiment____wt obs_cycA__nuc_median 0.439896809 2836.316603 Nucleus +experiment____wt obs_cycA__nuc_median 0.569799119 3005.725003 Nucleus +experiment____wt obs_cycA__nuc_median 0.622202998 3175.424651 Nucleus +experiment____wt obs_cycA__nuc_median 0.340993794 3345.41664 Nucleus +experiment____wt obs_cycA__nuc_median 0.407421159 3515.702065 Nucleus +experiment____wt obs_cycA__nuc_median 0.4900863 3686.281747 Nucleus +experiment____wt obs_cycA__nuc_median 0.581608508 3857.156849 Nucleus +experiment____wt obs_cycA__nuc_median 0.494514785 4028.328328 Nucleus +experiment____wt obs_cycA__nuc_median 0.500419528 4199.797278 Nucleus +experiment____wt obs_cycA__nuc_median 0.289328044 4371.564658 Nucleus +experiment____wt obs_cycA__nuc_median 0.283423398 4543.631561 Nucleus +experiment____wt obs_cycA__nuc_median 0.524776144 4715.999014 Nucleus +experiment____wt obs_cycA__nuc_median 0.305565917 4888.668042 Nucleus +experiment____wt obs_cycA__nuc_median 0.296708852 5061.63974 Nucleus +experiment____wt obs_cycA__nuc_median 0.330660663 5234.915203 Nucleus +experiment____wt obs_cycA__nuc_median 0.296708852 5408.495456 Nucleus +experiment____wt obs_cycA__nuc_median 0.29523269 5582.381594 Nucleus +experiment____wt obs_cycA__nuc_median 0.525514273 5756.574643 Nucleus +experiment____wt obs_cycA__nuc_median 0.305565917 5931.075697 Nucleus +experiment____wt obs_cycA__nuc_median 0.42808742 6105.885919 Nucleus +experiment____wt obs_cycA__nuc_median 0.296708852 6281.006335 Nucleus +experiment____wt obs_cycA__nuc_median 0.34689844 6456.438108 Nucleus +experiment____wt obs_cycA__nuc_median 0.407421159 6632.182332 Nucleus +experiment____wt obs_cycA__nuc_median 0.557989827 6808.240102 Nucleus +experiment____wt obs_cycA__nuc_median 0.386754897 6984.612511 Nucleus +experiment____wt obs_cycA__nuc_median 0.320327532 7161.300724 Nucleus +experiment____wt obs_cycA__nuc_median 0.321803694 7338.305833 Nucleus +experiment____wt obs_cycA__nuc_median 0.386754897 7515.629071 Nucleus +experiment____wt obs_cycA__nuc_median 0.34689844 7693.271464 Nucleus +experiment____wt obs_cycA__nuc_median 0.488610139 7871.234242 Nucleus +experiment____wt obs_cycA__nuc_median 0.333612986 8049.518568 Nucleus +experiment____wt obs_cycA__nuc_median 0.354279247 8228.125606 Nucleus +experiment____wt obs_cycA__nuc_median 0.414801966 8407.056449 Nucleus +experiment____wt obs_cycA__nuc_median 0.548394825 8586.312329 Nucleus +experiment____wt 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85409.65133 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.08503858 85605.25166 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.079228465 85801.24051 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.079756654 85997.61937 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.077115709 86194.38975 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.080284843 86391.55337 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.075002953 86589.11165 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.079228465 86787.06625 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.076059331 86985.41879 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.079228465 87184.17079 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.072362007 87383.32396 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.083982167 87582.8798 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.077643898 87782.84001 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.080284843 87983.20625 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.077115709 88183.98016 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.079756654 88385.16337 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.077115709 88586.75766 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.078172087 88788.76455 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.081341222 88991.1858 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.075002953 89194.02319 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.073946574 89397.27831 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.076059331 89600.95299 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.083453978 89805.04894 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.07658752 90009.56781 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.084510391 90214.51152 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.079228465 90419.8817 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.079756654 90625.6802 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.079756654 90831.9088 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.083453978 91038.56921 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.076059331 91245.66341 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.078700276 91453.19311 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.079228465 91661.16023 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.071833818 91869.56648 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.08503858 92078.41384 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.078172087 92287.70416 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.085566769 92497.43929 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.080813032 92707.62114 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.076059331 92918.25162 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.078172087 93129.33265 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.074474764 93340.86615 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.076059331 93552.85409 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.078172087 93765.29834 Cytoplasm 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0.076059331 103128.0139 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.079228465 103362.1311 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.077643898 103596.805 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.079228465 103832.0384 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.083982167 104067.8338 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.075531142 104304.194 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.079492577 104541.1217 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.072362007 104778.6196 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.076059331 105016.6905 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.075531142 105255.3372 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.074474764 105494.5624 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.077115709 105734.3689 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.079228465 105974.7596 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.082925789 106215.7374 Cytoplasm +experiment____wt 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Cytoplasm +experiment____wt obs_pRB__cyt_median 0.073418385 113473.0748 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.080284843 113733.1022 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.078700276 113993.8166 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.079228465 114255.2216 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.077643898 114517.321 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.077115709 114780.1183 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.077643898 115043.6174 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.075531142 115307.8219 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.076059331 115572.7357 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.07077744 115838.3627 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.080284843 116104.7065 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.078700276 116371.7712 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.083453978 116639.5606 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.078172087 116908.0788 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.083453978 117177.3295 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.081341222 117447.3169 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.07658752 117718.045 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.078700276 117989.518 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.080813032 118261.7397 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.075002953 118534.7146 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.077115709 118808.4466 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.079228465 119082.9401 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.076059331 119358.1993 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.080813032 119634.2283 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.074474764 119911.0318 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.078172087 120188.6138 Cytoplasm +experiment____wt obs_pRB__cyt_median 0.080813032 120466.9788 Cytoplasm +experiment____wt obs_pRB__cyt_median 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obs_Skp2__cyt_median 0.220177597 12427.92282 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.2632291 12614.64066 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.217717515 12801.71247 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.274299466 12989.13955 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.230017922 13176.92334 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.260769018 13365.06513 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.273069425 13553.56629 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.239243267 13742.42827 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.276759547 13931.65236 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.225097759 14121.23999 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.261999059 14311.1926 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.258308937 14501.51157 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.258308937 14692.19825 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.217717515 14883.25415 Cytoplasm 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17597.61937 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.273069425 17794.38975 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.271839384 17991.55337 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.231247962 18189.11165 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.231247962 18387.06625 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.211567312 18585.41879 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.292750075 18784.17079 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.261999059 18983.32396 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.227557841 19182.8798 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.270609344 19382.84001 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.227557841 19583.20625 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.214027394 19783.98016 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.275529506 19985.16337 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.215257434 20186.75766 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.270609344 20388.76455 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.273069425 20591.1858 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.268149262 20794.02319 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.258308937 20997.27831 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.270609344 21200.95299 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.237398166 21405.04894 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.279219628 21609.56781 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.239858247 21814.51152 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.276759547 22019.8817 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.270609344 22225.6802 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.230017922 22431.9088 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.270609344 22638.56921 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.266919222 22845.66341 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.277989587 23053.19311 Cytoplasm 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26005.3893 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.230017922 26219.67898 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.238628206 26434.43493 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.277989587 26649.6593 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.280449669 26865.35411 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.289059953 27081.52144 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.274299466 27298.16332 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.276759547 27515.28189 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.259538978 27732.87918 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.222637678 27950.9574 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.275529506 28169.51858 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.26445914 28388.56493 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.2632291 28608.09863 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.225097759 28828.12173 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.215257434 29048.63656 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.269379303 29269.6453 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.217717515 29491.15009 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.276759547 29713.15316 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.212797353 29935.65686 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.265689181 30158.66336 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.228787881 30382.175 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.265689181 30606.19403 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.220177597 30830.72277 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.2632291 31055.76356 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.222637678 31281.31872 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.217717515 31507.39063 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.268149262 31733.98164 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.212797353 31961.09413 Cytoplasm 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35196.80503 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.220177597 35432.03838 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.2263278 35667.83377 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.273069425 35904.194 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.274299466 36141.12168 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.232478003 36378.61962 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.222637678 36616.69054 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.275529506 36855.33718 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.220177597 37094.56235 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.271839384 37334.36892 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.271839384 37574.75962 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.228787881 37815.73741 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.227557841 38057.30507 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.291520034 38299.46549 Cytoplasm +experiment____wt 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75915.62907 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.217717515 76093.27146 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.228787881 76271.23424 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.260769018 76449.51857 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.20664715 76628.12561 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.281679709 76807.05645 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.2632291 76986.31233 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.2632291 77165.89441 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.215257434 77345.80399 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.265689181 77526.04209 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.217717515 77706.61002 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.266919222 77887.50894 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.2263278 78068.74007 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.270609344 78250.30473 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.26445914 78432.20399 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.221407637 78614.43924 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.2263278 78797.01156 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.218947556 78979.9224 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.2632291 79163.17284 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.269379303 79346.76425 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.261999059 79530.6978 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.268149262 79714.97486 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.221407637 79899.59672 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.222637678 80084.56461 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.274299466 80269.87984 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.257078897 80455.54378 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.227557841 80641.55764 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.220177597 80827.92282 Cytoplasm 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83474.68065 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.259538978 83666.47924 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.275529506 83858.65137 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.24477841 84051.1984 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.257078897 84244.12196 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.260769018 84437.42337 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.273069425 84631.10413 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.239858247 84825.16587 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.2263278 85019.60991 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.266919222 85214.43793 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.277989587 85409.65133 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.3025904 85605.25166 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.221407637 85801.24051 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.280449669 85997.61937 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.273069425 86194.38975 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.271839384 86391.55337 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.231247962 86589.11165 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.231247962 86787.06625 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.211567312 86985.41879 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.292750075 87184.17079 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.261999059 87383.32396 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.227557841 87582.8798 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.270609344 87782.84001 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.227557841 87983.20625 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.214027394 88183.98016 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.275529506 88385.16337 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.215257434 88586.75766 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.270609344 88788.76455 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.273069425 88991.1858 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.268149262 89194.02319 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.258308937 89397.27831 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.270609344 89600.95299 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.237398166 89805.04894 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.279219628 90009.56781 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.239858247 90214.51152 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.276759547 90419.8817 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.270609344 90625.6802 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.230017922 90831.9088 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.270609344 91038.56921 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.266919222 91245.66341 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.277989587 91453.19311 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.222637678 91661.16023 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.26445914 91869.56648 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.242318328 92078.41384 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.28290975 92287.70416 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.290289994 92497.43929 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.252158653 92707.62114 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.266919222 92918.25162 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.222637678 93129.33265 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.269379303 93340.86615 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.265689181 93552.85409 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.221407637 93765.29834 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.280449669 93978.201 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.269379303 94191.56399 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.275529506 94405.3893 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.230017922 94619.67898 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.238628206 94834.43493 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.277989587 95049.6593 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.280449669 95265.35411 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.289059953 95481.52144 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.274299466 95698.16332 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.276759547 95915.28189 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.259538978 96132.87918 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.222637678 96350.9574 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.275529506 96569.51858 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.26445914 96788.56493 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.2632291 97008.09863 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.225097759 97228.12173 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.215257434 97448.63656 Cytoplasm 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100588.7306 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.285369831 100816.8933 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.265689181 101045.5848 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.271839384 101274.8075 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.222637678 101504.564 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.270609344 101734.8566 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.225097759 101965.6879 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.218947556 102197.0604 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.292750075 102428.9767 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.276759547 102661.4393 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.223867719 102894.4509 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.215257434 103128.0139 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.270609344 103362.1311 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.271224324 103596.805 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.220177597 103832.0384 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.2263278 104067.8338 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.273069425 104304.194 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.274299466 104541.1217 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.232478003 104778.6196 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.222637678 105016.6905 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.275529506 105255.3372 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.220177597 105494.5624 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.271839384 105734.3689 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.271839384 105974.7596 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.228787881 106215.7374 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.227557841 106457.3051 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.291520034 106699.4655 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.221407637 106942.2217 Cytoplasm 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110405.0451 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.274299466 110657.1023 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.271839384 110909.805 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.274299466 111163.1565 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.270609344 111417.16 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.223867719 111671.8191 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.276759547 111927.1371 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.265689181 112183.1174 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.265689181 112439.7634 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.275529506 112697.0787 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.231247962 112955.0666 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.289059953 113213.7308 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.270609344 113473.0748 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.279219628 113733.1022 Cytoplasm +experiment____wt 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Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.223867719 117718.045 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.261999059 117989.518 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.238628206 118261.7397 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.298900278 118534.7146 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.230017922 118808.4466 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.227557841 119082.9401 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.260769018 119358.1993 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.292750075 119634.2283 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.279219628 119911.0318 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.266919222 120188.6138 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.280449669 120466.9788 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.238628206 120746.1313 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.231247962 121026.0757 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.261999059 121306.8166 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.230017922 121588.3584 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.279219628 121870.7057 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.233708044 122153.8633 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.260769018 122437.8357 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.266919222 122722.6277 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.286599872 123008.2439 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.26445914 123294.6892 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.269379303 123581.9684 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.270609344 123870.0864 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.231247962 124159.0481 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.228787881 124448.8584 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.228787881 124739.5223 Cytoplasm +experiment____wt obs_Skp2__cyt_median 0.266919222 125031.045 Cytoplasm +experiment____wt 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kExImCCNB_CDK1_Thr14_Tyr15p_CDKN1A1__CDKN1A_CCNE_A_B1_Ser130u__1 + _Num__NUP_pSitesu_ + _Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ + Num + + + + + + + + + + + + + + + + + + kExImCDKN1A_CCNE_A_B_Ser130p__1 + _Num__NUP_pSitesu_ + _Nuc__CDKN1A_CCNE_A_B_Ser130p_ + Num + + + + + + + + + + + + + + + + + + kExImCCNA_CDKN1A_B1__CDKN1B_CCNE_A1_Thr187u__1 + _Num__NUP_pSitesu_ + _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + Num + + + + + + + + + + + + + + + + + + kExImCCNE_CDKN1A_B1__CDKN1B_CCNE_A1_Thr187u__1 + _Num__NUP_pSitesu_ + _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + Num + + + + + + + + + + + + + + + + + + kExImCDKN1B_CCNE_A_Thr187p__1 + _Num__NUP_pSitesu_ + _Nuc__CDKN1B_CCNE_A_Thr187p_ + Num + + + + + + + + + + + + + + + + + + kImImCCNA_CDKN1A_B1__CDKN1B_CCNE_A1_Thr187p__1 + _Num__NUP_pSitesu_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + Num + + + + + + + + + + + + + + + + + + kImImCCNE_CDKN1A_B1__CDKN1B_CCNE_A1_Thr187p__1 + _Num__NUP_pSitesu_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + Num + + + + + + + + + + + + + + + + kDeCe + _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + Nuc + + + + + + + + + + + + + + + + + + kPhCeE + _Nuc__CCNE_CDKN1A_B_ + _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + Nuc + + + + + + + + + + + + + + + + kDeCa1 + _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + Nuc + + + + + + + + + + + + + + + + + + kPhCeA + _Nuc__CCNA_CDKN1A_B_ + _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + Nuc + + + + + + + + + + + + + + + + + + kDeCa2 + _Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355u__FZR1_APC_1_FBXO5_nTermu_ + _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + Nuc + + + + + + + + + + + + + + + + + + kDeCa2 + _Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355p__FZR1_APC_1_FBXO5_nTermu_ + _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + Nuc + + + + + + + + + + + + + + + + + + kDeCa3 + _Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355p__CDC20_APC_1_ + _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + Nuc + + + + + + + + + + + + + + + + kDeCDKN1B_1 + _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + Nuc + + + + + + + + + + + + + + + + kDeCDKN1B_1 + _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + Nuc + + + + + + + + + + + + + + + + + + kDeCDKN1B_2 + _Nuc__SKP2 + _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + Nuc + + + + + + + + + + + + + + + + + + kDeCDKN1B_2 + _Nuc__SKP2 + _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + Nuc + + + + + + + + + + + + + + + + + kDiCdkn1bC + _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + Nuc + + + + + + + + + + + + + + + + + kDiCdkn1bC + _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + Nuc + + + + + + + + + + + + + + + + kDpCDKN1B + _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + Nuc + + + + + + + + + + + + + + + + kDpCDKN1B + _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + Nuc + + + + + + + + + + + + + + + + + + kExImCCNA_CDKN1A_B1__CDKN1B_CCNE_A1_Thr187p__1 + _Num__NUP_pSitesu_ + _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + Num + + + + + + + + + + + + + + + + + + kExImCCNE_CDKN1A_B1__CDKN1B_CCNE_A1_Thr187p__1 + _Num__NUP_pSitesu_ + _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + Num + + + + + + + diff --git a/v2/Lang_PLOSComputBiol2024/observables_Lang_PLOSComputBiol2024.tsv b/v2/Lang_PLOSComputBiol2024/observables_Lang_PLOSComputBiol2024.tsv new file mode 100644 index 0000000..42d540a --- /dev/null +++ b/v2/Lang_PLOSComputBiol2024/observables_Lang_PLOSComputBiol2024.tsv @@ -0,0 +1,17 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +obs_cycA__nuc_median oCCNA + sCCNA * (_Nuc__CCNA_CDKN1A_B_ + _Nuc__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_) noiseParameter1 + noiseParameter2_cycA_nuc * (oCCNA + sCCNA * (_Nuc__CCNA_CDKN1A_B_ + _Nuc__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_)) +obs_cycB1__nuc_median oCCNB + sCCNB * (_Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_ + _Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_ + _Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_) noiseParameter1 + noiseParameter2_cycB1_nuc * (oCCNB + sCCNB * (_Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_ + _Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_ + _Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_)) +obs_cycE__nuc_median oCCNE + sCCNE * (_Nuc__CCNE_CDKN1A_B_ + _Nuc__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_) noiseParameter1 + noiseParameter2_cycE_nuc * (oCCNE + sCCNE * (_Nuc__CCNE_CDKN1A_B_ + _Nuc__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_)) +obs_E2F1__nuc_median oE2F + sE2F * (_Nuc__E2F_DBD_RB1_Ser332u_ + _Nuc__E2F_DBD_RB1_Ser332p_ + _Nuc__E2F_DBD_RB1_1_Ser332u__RB1_E2F_1_Ser807_Ser811u_ + _Nuc__E2F_DBD_RB1_1_Ser332p__RB1_E2F_1_Ser807_Ser811u_ + _Nuc__CCNE_promoter_E2F_1__E2F_DBD_1_RB1_Ser332u_ + _Nuc__CCNA_promoter_E2F_1__E2F_DBD_1_RB1_Ser332u_ + _Nuc__E2F_DBD_1_RB1_Ser332u__E2F_promoter_E2F_1_ + _Nuc__E2F_DBD_1_RB1_Ser332u__FBXO5_promoter_E2F_1_ + _Nuc__E2F_DBD_1_RB1_Ser332u__FOXM1_promoter_E2F_1_) noiseParameter1 + noiseParameter2_E2F1_nuc * (oE2F + sE2F * (_Nuc__E2F_DBD_RB1_Ser332u_ + _Nuc__E2F_DBD_RB1_Ser332p_ + _Nuc__E2F_DBD_RB1_1_Ser332u__RB1_E2F_1_Ser807_Ser811u_ + _Nuc__E2F_DBD_RB1_1_Ser332p__RB1_E2F_1_Ser807_Ser811u_ + _Nuc__CCNE_promoter_E2F_1__E2F_DBD_1_RB1_Ser332u_ + _Nuc__CCNA_promoter_E2F_1__E2F_DBD_1_RB1_Ser332u_ + _Nuc__E2F_DBD_1_RB1_Ser332u__E2F_promoter_E2F_1_ + _Nuc__E2F_DBD_1_RB1_Ser332u__FBXO5_promoter_E2F_1_ + _Nuc__E2F_DBD_1_RB1_Ser332u__FOXM1_promoter_E2F_1_)) +obs_pRB__nuc_median oRB1_pSer807Ser811 + sRB1_pSer807Ser811 * (_Nuc__RB1_E2F_Ser807_Ser811p_) noiseParameter1 + noiseParameter2_pRB_nuc * (oRB1_pSer807Ser811 + sRB1_pSer807Ser811 * (_Nuc__RB1_E2F_Ser807_Ser811p_)) +obs_Skp2__nuc_median oSKP2 + sSKP2 * _Nuc__SKP2 noiseParameter1 + noiseParameter2_Skp2_nuc * (oSKP2 + sSKP2 * _Nuc__SKP2) +obs_p21__nuc_median oCDKN1A + sCDKN1A * (_Nuc__CDKN1A_CCNE_A_B_Ser130u_ + _Nuc__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Nuc__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Nuc__CDKN1A_CCNE_A_B_Ser130p_) noiseParameter1 + noiseParameter2_p21_nuc * (oCDKN1A + sCDKN1A * (_Nuc__CDKN1A_CCNE_A_B_Ser130u_ + _Nuc__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Nuc__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Nuc__CDKN1A_CCNE_A_B_Ser130p_)) +obs_p27__nuc_median oCDKN1B + sCDKN1B * (_Nuc__CDKN1B_CCNE_A_Thr187u_ + _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Nuc__CDKN1B_CCNE_A_Thr187p_ + _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_) noiseParameter1 + noiseParameter2_p27_nuc * (oCDKN1B + sCDKN1B * (_Nuc__CDKN1B_CCNE_A_Thr187u_ + _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Nuc__CDKN1B_CCNE_A_Thr187p_ + _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_)) +obs_cycA__cyt_median oCCNA + sCCNA * (_Cyt__CCNA_CDKN1A_B_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_) noiseParameter1 + noiseParameter2_cycA_cyt * (oCCNA + sCCNA * (_Cyt__CCNA_CDKN1A_B_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_)) +obs_cycB1__cyt_median oCCNB + sCCNB * (_Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_ + _Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_ + _Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_) noiseParameter1 + noiseParameter2_cycB1_cyt * (oCCNB + sCCNB * (_Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_ + _Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_ + _Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_)) +obs_cycE__cyt_median oCCNE + sCCNE * (_Cyt__CCNE_CDKN1A_B_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_) noiseParameter1 + noiseParameter2_cycE_cyt * (oCCNE + sCCNE * (_Cyt__CCNE_CDKN1A_B_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_)) +obs_E2F1__cyt_median oE2F + sE2F * (_Cyt__E2F_DBD_RB1_Ser332u_ + _Cyt__E2F_DBD_RB1_Ser332p_ + _Cyt__E2F_DBD_RB1_1_Ser332u__RB1_E2F_1_Ser807_Ser811u_ + _Cyt__E2F_DBD_RB1_1_Ser332p__RB1_E2F_1_Ser807_Ser811u_) noiseParameter1 + noiseParameter2_E2F1_cyt * (oE2F + sE2F * (_Cyt__E2F_DBD_RB1_Ser332u_ + _Cyt__E2F_DBD_RB1_Ser332p_ + _Cyt__E2F_DBD_RB1_1_Ser332u__RB1_E2F_1_Ser807_Ser811u_ + _Cyt__E2F_DBD_RB1_1_Ser332p__RB1_E2F_1_Ser807_Ser811u_)) +obs_pRB__cyt_median oRB1_pSer807Ser811 + sRB1_pSer807Ser811 * (_Cyt__RB1_E2F_Ser807_Ser811p_) noiseParameter1 + noiseParameter2_pRB_cyt * (oRB1_pSer807Ser811 + sRB1_pSer807Ser811 * (_Cyt__RB1_E2F_Ser807_Ser811p_)) +obs_Skp2__cyt_median oSKP2 + sSKP2 * _Cyt__SKP2 noiseParameter1 + noiseParameter2_Skp2_cyt * (oSKP2 + sSKP2 * _Cyt__SKP2) +obs_p21__cyt_median oCDKN1A + sCDKN1A * (_Cyt__CDKN1A_CCNE_A_B_Ser130u_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CDKN1A_CCNE_A_B_Ser130p_) noiseParameter1 + noiseParameter2_p21_cyt * (oCDKN1A + sCDKN1A * (_Cyt__CDKN1A_CCNE_A_B_Ser130u_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CDKN1A_CCNE_A_B_Ser130p_)) +obs_p27__cyt_median oCDKN1B + sCDKN1B * (_Cyt__CDKN1B_CCNE_A_Thr187u_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Cyt__CDKN1B_CCNE_A_Thr187p_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_) noiseParameter1 + noiseParameter2_p27_cyt * (oCDKN1B + sCDKN1B * (_Cyt__CDKN1B_CCNE_A_Thr187u_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Cyt__CDKN1B_CCNE_A_Thr187p_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_)) diff --git a/v2/Lang_PLOSComputBiol2024/parameters_Lang_PLOSComputBiol2024.tsv b/v2/Lang_PLOSComputBiol2024/parameters_Lang_PLOSComputBiol2024.tsv new file mode 100644 index 0000000..65007b2 --- /dev/null +++ b/v2/Lang_PLOSComputBiol2024/parameters_Lang_PLOSComputBiol2024.tsv @@ -0,0 +1,376 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorDistribution priorParameters +kPhRbD 1.3e-16 9.21e-13 1.96e-14 true uniform 1.3e-16;9.21e-13 +kPhRbE 1.15e-14 4.22e-12 1.86e-13 true uniform 1.15e-14;4.22e-12 +kDpRb 0.000139 0.013899951 0.002405223 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+ic_wt_Nuc__CCNA_promoter_E2F_1__E2F_DBD_1_RB1_Ser332p_ 0.0 5007949.799 0.0 false uniform 0.0;5007949.799 +ic_wt_Nuc__E2F_DBD_1_RB1_Ser332p__E2F_promoter_E2F_1_ 0.0 5007949.799 0.0 false uniform 0.0;5007949.799 +ic_wt_Nuc__E2F_DBD_1_RB1_Ser332p__FBXO5_promoter_E2F_1_ 0.0 5007949.799 0.0 false uniform 0.0;5007949.799 +ic_wt_Nuc__E2F_DBD_1_RB1_Ser332p__FOXM1_promoter_E2F_1_ 0.0 5007949.799 0.0 false uniform 0.0;5007949.799 +ic_wt_Nuc__SKP2 13103822582.0 1310000000000.0 41372395495.0 true uniform 13103822582.0;1310000000000.0 +ic_wt_Nuc__TP53_DBD_Ser15p_ 0.0 0.0 0.0 false uniform 0.0;0.0 +ic_wt_Nuc__CDKN1A_promoter_TP53_ 602200.0 60220000.0 6022000.0 false uniform 602200.0;60220000.0 +ic_wt_Nuc__FOXO_DBD_ 181303484.0 18122619294.0 6173058606.0 true uniform 181303484.0;18122619294.0 +ic_wt_Nuc__CDKN1B_promoter_FOXO_ 1777.372886 12044000.0 6022000.0 false uniform 1777.372886;12044000.0 +ic_wt_Nuc__CDKN1A_promoter_TP53_1__TP53_DBD_1_Ser15p_ 0.0 0.0 0.0 false uniform 0.0;0.0 +ic_wt_Cyt__CDKN1A_CCNE_A_B_Ser130u_ 0.0 633363.7098 281884.0711 true uniform 0.0;633363.7098 +ic_wt_Nuc__CDKN1B_promoter_FOXO_1__FOXO_DBD_1_ 0.0 60042262.71 0.0 false uniform 0.0;60042262.71 +ic_wt_Cyt__CDKN1B_CCNE_A_Thr187u_ 15148275.57 1514827557.0 264475492.9 true uniform 15148275.57;1514827557.0 +ic_wt_Cyt__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ 0.0 340688357.1 61459.0657 true uniform 0.0;340688357.1 +ic_wt_Cyt__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ 1048299006.0 104830000000.0 1074843604.0 true uniform 1048299006.0;104830000000.0 +ic_wt_Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ 1425042666.0 142504000000.0 5718340364.0 true uniform 1425042666.0;142504000000.0 +ic_wt_Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ 2502.16018 250216.018 186434.2153 true uniform 2502.16018;250216.018 +ic_wt_Cyt__CDKN1A_CCNE_A_B_Ser130p_ 205.2024231 20520.24231 2624.557098 true uniform 205.2024231;20520.24231 +ic_wt_Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ 941.6172707 94161.72707 25326.16823 true uniform 941.6172707;94161.72707 +ic_wt_Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ 751.7705485 75177.05485 5020.972863 true uniform 751.7705485;75177.05485 +ic_wt_Cyt__CDKN1B_CCNE_A_Thr187p_ 0.0 35806.67302 4.547945652 true uniform 0.0;35806.67302 +ic_wt_Nuc__CDKN1A_CCNE_A_B_Ser130u_ 0.0 19072.97936 4747.631151 true uniform 0.0;19072.97936 +ic_wt_Nuc__CDKN1B_CCNE_A_Thr187u_ 0.0 594266348.5 566732957.0 true uniform 0.0;594266348.5 +ic_wt_Nuc__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ 209159399.0 20915939904.0 8490024601.0 true uniform 209159399.0;20915939904.0 +ic_wt_Nuc__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ 0.0 48482734905.0 43323121252.0 true uniform 0.0;48482734905.0 +ic_wt_Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ 34190595396.0 3419060000000.0 34667688641.0 true uniform 34190595396.0;3419060000000.0 +ic_wt_Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ 0.0 62119560780.0 21615284378.0 true uniform 0.0;62119560780.0 +ic_wt_Nuc__CDKN1A_CCNE_A_B_Ser130p_ 15117189.16 1511718916.0 1151453403.0 true uniform 15117189.16;1511718916.0 +ic_wt_Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ 0.0 494555730.7 0.0 true uniform 0.0;494555730.7 +ic_wt_Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ 0.0 2408376.419 17.76993907 true uniform 0.0;2408376.419 +ic_wt_Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ 0.0 3038851329.0 171438.0491 true uniform 0.0;3038851329.0 +ic_wt_Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ 0.0 8394122.219 27347.64208 true uniform 0.0;8394122.219 +ic_wt_Nuc__CDKN1B_CCNE_A_Thr187p_ 0.0 46250793226.0 5994921130.0 true uniform 0.0;46250793226.0 +ic_wt_Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ 0.0 2329488005.0 12.7397651 true uniform 0.0;2329488005.0 +ic_wt_Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ 0.0 7454379847.0 18.04074869 true uniform 0.0;7454379847.0 +oCCNA 0.0 0.305627054 0.208302803 true laplace 0;1 +oCCNB 0.0 0.534931031 0.31077954 true laplace 0;1 +oCCNE 0.0 0.625025635 0.415265382 true laplace 0;1 +oE2F 0.0 0.710586775 0.24407022 true laplace 0;1 +oRB1_pSer807Ser811 0.0 0.092359914 0.077836825 true laplace 0;1 +oSKP2 0.0 0.325469225 0.249109282 true laplace 0;1 +oCDKN1A 0.0 0.569668525 0.409236791 true laplace 0;1 +oCDKN1B 0.0 0.534762112 0.229182409 true laplace 0;1 +sCCNA 0.0 2e-10 6.56e-11 true laplace 0;0.0000000002 +sCCNB 0.0 2e-10 8.15e-12 true laplace 0;0.0000000002 +sCCNE 0.0 2e-10 2.05e-11 true uniform 0.0;2e-10 +sE2F 0.0 2e-10 1.17e-11 true uniform 0.0;2e-10 +sRB1_pSer807Ser811 0.0 2e-10 9.02e-12 true uniform 0.0;2e-10 +sSKP2 0.0 2e-10 2.19e-11 true uniform 0.0;2e-10 +sCDKN1A 0.0 2e-10 6.22e-12 true uniform 0;0.0000000002 +sCDKN1B 1.99e-12 1.99e-10 2e-10 true uniform 0;0.0000000002 +noiseParameter1 0.0 0.2 0.001627808 true laplace 0; 0.001 +noiseParameter2_cycA_nuc 0.166666667 1.5 0.29487787 true uniform 0.166666667;1.5 +noiseParameter2_cycB1_nuc 0.166666667 1.5 0.212210307 true uniform 0.166666667;1.5 +noiseParameter2_cycE_nuc 0.166666667 1.5 0.177955075 true uniform 0.166666667;1.5 +noiseParameter2_E2F1_nuc 0.166666667 1.5 0.28837414 true uniform 0.166666667;1.5 +noiseParameter2_pRB_nuc 0.166666667 1.5 0.221594515 true uniform 0.166666667;1.5 +noiseParameter2_Skp2_nuc 0.166666667 1.5 0.296500263 true uniform 0.166666667;1.5 +noiseParameter2_p21_nuc 0.166666667 1.5 0.409824698 true uniform 0.166666667;1.5 +noiseParameter2_p27_nuc 0.166666667 1.5 0.287313329 true uniform 0.166666667;1.5 +noiseParameter2_cycA_cyt 0.006172868 1.5 0.009893595 true uniform 0.006172868;1.5 +noiseParameter2_cycB1_cyt 0.055555667 1.5 0.106959034 true uniform 0.055555667;1.5 +noiseParameter2_cycE_cyt 0.018518567 1.5 0.048386095 true uniform 0.018518567;1.5 +noiseParameter2_E2F1_cyt 0.055555667 1.5 0.077572039 true uniform 0.055555667;1.5 +noiseParameter2_pRB_cyt 2.86e-06 0.002084234 0.001950222 true uniform 2.86e-06;0.002084234 +noiseParameter2_Skp2_cyt 0.018518567 1.5 0.023853949 true uniform 0.018518567;1.5 +noiseParameter2_p21_cyt 0.018518567 1.5 0.035103562 true uniform 0.018518567;1.5 +noiseParameter2_p27_cyt 0.006172868 1.5 0.014110668 true uniform 0.006172868;1.5 diff --git a/v2/Laske_PLOSComputBiol2019/Laske_PLOSComputBiol2019.yaml b/v2/Laske_PLOSComputBiol2019/Laske_PLOSComputBiol2019.yaml new file mode 100644 index 0000000..50ea6d5 --- /dev/null +++ b/v2/Laske_PLOSComputBiol2019/Laske_PLOSComputBiol2019.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Laske_PLOSComputBiol2019.tsv +model_files: + model_Laske_PLOSComputBiol2019: + location: model_Laske_PLOSComputBiol2019.xml + language: sbml +measurement_files: +- measurementData_Laske_PLOSComputBiol2019.tsv +condition_files: +- experimentalCondition_Laske_PLOSComputBiol2019.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Laske_PLOSComputBiol2019.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Laske_PLOSComputBiol2019/experimentalCondition_Laske_PLOSComputBiol2019.tsv b/v2/Laske_PLOSComputBiol2019/experimentalCondition_Laske_PLOSComputBiol2019.tsv new file mode 100644 index 0000000..d723f26 --- /dev/null +++ b/v2/Laske_PLOSComputBiol2019/experimentalCondition_Laske_PLOSComputBiol2019.tsv @@ -0,0 +1,7 @@ +conditionId targetId targetValue +virus_infection V_ex 50 +virus_infection_2 V_ex 1 +virus_infection_3 V_ex 50 +virus_infection k_syn_P 64800 +virus_infection_2 k_syn_P 64800 +virus_infection_3 k_syn_P 0 diff --git a/v2/Laske_PLOSComputBiol2019/experiments.tsv b/v2/Laske_PLOSComputBiol2019/experiments.tsv new file mode 100644 index 0000000..2986ef5 --- /dev/null +++ b/v2/Laske_PLOSComputBiol2019/experiments.tsv @@ -0,0 +1,4 @@ +experimentId conditionId time +experiment____virus_infection virus_infection 0 +experiment____virus_infection_2 virus_infection_2 0 +experiment____virus_infection_3 virus_infection_3 0 diff --git a/v2/Laske_PLOSComputBiol2019/measurementData_Laske_PLOSComputBiol2019.tsv b/v2/Laske_PLOSComputBiol2019/measurementData_Laske_PLOSComputBiol2019.tsv new file mode 100644 index 0000000..1cb3089 --- /dev/null +++ b/v2/Laske_PLOSComputBiol2019/measurementData_Laske_PLOSComputBiol2019.tsv @@ -0,0 +1,43 @@ +experimentId observableId measurement time noiseParameters observableParameters datasetId +experiment____virus_infection RM5 16.4862319433747 1.0 sigma_RM5 dataset_RM5 +experiment____virus_infection RM5 137.529004093062 2.0 sigma_RM5 dataset_RM5 +experiment____virus_infection RM5 5927.73630370154 3.0 sigma_RM5 dataset_RM5 +experiment____virus_infection RM5 26070.7777033051 4.0 sigma_RM5 dataset_RM5 +experiment____virus_infection RM5 36165.1722001919 5.0 sigma_RM5 dataset_RM5 +experiment____virus_infection RM5 39708.6354393543 6.0 sigma_RM5 dataset_RM5 +experiment____virus_infection RM5 33557.6057996387 7.0 sigma_RM5 dataset_RM5 +experiment____virus_infection RM5 26851.6819153912 8.0 sigma_RM5 dataset_RM5 +experiment____virus_infection RM5 24129.7114856115 9.0 sigma_RM5 dataset_RM5 +experiment____virus_infection RM5 15503.6668243303 10.0 sigma_RM5 dataset_RM5 +experiment____virus_infection RVSegTot 535.171384487193 1.0 sigma_RV vRNA_offset dataset_RV +experiment____virus_infection RVSegTot 505.340542126865 2.0 sigma_RV vRNA_offset dataset_RV +experiment____virus_infection RVSegTot 2257.56566823967 3.0 sigma_RV vRNA_offset dataset_RV +experiment____virus_infection RVSegTot 13599.6998388987 4.0 sigma_RV vRNA_offset dataset_RV +experiment____virus_infection RVSegTot 34431.2425312543 5.0 sigma_RV vRNA_offset dataset_RV +experiment____virus_infection RVSegTot 52925.7096508491 6.0 sigma_RV vRNA_offset dataset_RV +experiment____virus_infection RVSegTot 64547.3268688838 7.0 sigma_RV vRNA_offset dataset_RV +experiment____virus_infection RVSegTot 74091.3081045583 8.0 sigma_RV vRNA_offset dataset_RV +experiment____virus_infection RVSegTot 88032.0436517163 9.0 sigma_RV vRNA_offset dataset_RV +experiment____virus_infection RVSegTot 97993.174580701 10.0 sigma_RV vRNA_offset dataset_RV +experiment____virus_infection RCSegTot 0.316575722115733 1.0 sigma_RC dataset_RC +experiment____virus_infection RCSegTot 28.2322619773035 2.0 sigma_RC dataset_RC +experiment____virus_infection RCSegTot 304.173443943742 3.0 sigma_RC dataset_RC +experiment____virus_infection RCSegTot 853.489726325741 4.0 sigma_RC dataset_RC +experiment____virus_infection RCSegTot 1059.34292406483 5.0 sigma_RC dataset_RC +experiment____virus_infection RCSegTot 1080.18974477004 6.0 sigma_RC dataset_RC +experiment____virus_infection RCSegTot 923.164390912859 7.0 sigma_RC dataset_RC +experiment____virus_infection RCSegTot 944.367497535591 8.0 sigma_RC dataset_RC +experiment____virus_infection RCSegTot 1058.63298698841 9.0 sigma_RC dataset_RC +experiment____virus_infection RCSegTot 1003.14044835124 10.0 sigma_RC dataset_RC +experiment____virus_infection_2 Vrel 848.298307989294 20.0 sigma_Vrel dataset_Vrel +experiment____virus_infection_2 Vrel 907.923629140452 24.0 sigma_Vrel dataset_Vrel +experiment____virus_infection_2 Vrel 1223.94016428638 28.0 sigma_Vrel dataset_Vrel +experiment____virus_infection_3 IntNucOffset 51.6 0.0 scale_sigma_FracNucInt Int_nuc_off dataset_FracNucInt +experiment____virus_infection_3 FracNucInt_1 42.785 0.25 scale_sigma_FracNucInt Int_nuc_off dataset_FracNucInt +experiment____virus_infection_3 FracNucInt_2 51.7075 0.5 scale_sigma_FracNucInt Int_nuc_off dataset_FracNucInt +experiment____virus_infection_3 FracNucInt_3 53.7125 0.75 scale_sigma_FracNucInt Int_nuc_off dataset_FracNucInt +experiment____virus_infection_3 FracNucInt_4 57.4275 1.0 scale_sigma_FracNucInt Int_nuc_off dataset_FracNucInt +experiment____virus_infection_3 FracNucInt_5 65.885 1.25 scale_sigma_FracNucInt Int_nuc_off dataset_FracNucInt +experiment____virus_infection_3 FracNucInt_6 72.12 1.5 scale_sigma_FracNucInt Int_nuc_off dataset_FracNucInt +experiment____virus_infection_3 FracNucInt_7 69.9933333333333 1.75 scale_sigma_FracNucInt Int_nuc_off dataset_FracNucInt +experiment____virus_infection_3 FracNucInt_8 76.97 2.0 scale_sigma_FracNucInt Int_nuc_off dataset_FracNucInt diff --git a/v2/Laske_PLOSComputBiol2019/model_Laske_PLOSComputBiol2019.xml b/v2/Laske_PLOSComputBiol2019/model_Laske_PLOSComputBiol2019.xml new file mode 100644 index 0000000..4aa6c06 --- /dev/null +++ b/v2/Laske_PLOSComputBiol2019/model_Laske_PLOSComputBiol2019.xml @@ -0,0 +1,3271 @@ + + + + + + + 
Heldt2012 - Influenza Virus Replication 
+The model describes the life cycle of influenza A virus in a mammalian cell including the following steps: attachment of parental virions to the cell membrane, receptor-mediated endocytosis, fusion of the virus envelope with the endosomal membrane, nuclear import of vRNPs, viral transcription and replication, translation of the structural viral proteins, nuclear export of progeny vRNPs and budding of new virions. It also explicitly accounts for the stabilization of cRNA by viral polymerases and NP and the inhibition of vRNP activity by M1 protein binding. In short, the model focuses on the molecular mechanism that controls viral transcription and replication.
+
+This model is described in the article: 
+Modeling the intracellular dynamics of influenza virus replication to understand the control of viral RNA synthesis. 
+Heldt FS, Frensing T, Reichl U. 
+J Virol. 
+
+This model has been adapted to fit the needs for parameter optimisation using pyPESTO by Clemens Peiter. In comparison to the original model, the chemical species names are also the IDs of the species in the SBML file, which simplifies things in the PEtab files. Some species have also been added to simplify PEtab problem specification (e.g., F_rnp_nuc).
+
+The values of certain kinetic parameters have been adjusted to Laske et al. re-estimation of the parameters for human A549 cells.
+
+The original model is hosted on BioModels Database and identified by: MODEL1307270000 .
+ + + + + + + + + + Juty + Nick + + juty@ebi.ac.uk + + EMBL-EBI + + + + + Chelliah + Vijayalakshmi + + viji@ebi.ac.uk + + EMBL-EBI + + + + + Peiter + Clemens + + s6clpeit@uni-bonn.de + + LIMES, University of Bonn, Germany + + + + + Heldt + Frank Stefan + + heldt@mpi-magdeburg.mpg.de + + Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany + + + + + + 2021-04-19T11:32:11Z + + + 2021-04-19T11:32:11Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + P_NP + + + R_V_RdRp + + + k_bind_NP + + + + k_bind_NP + R_V_RdRp + P_NP + + + + + + + + + + + P_NP + + + R_C_RdRp + + + k_bind_NP + + + + k_bind_NP + R_C_RdRp + P_NP + + + + + + + + + + + KmB + + + KmC + + + KmD + + + KmE + + + KmF + + + KmG + + + KmH + + + P_HA + + + P_M1 + + + P_M2 + + + P_NA + + + P_NEP + + + P_NP + + + P_RdRp + + + Vp_cyt_M1 + + + k_rel + + + + + + k_rel + Vp_cyt_M1 + P_RdRp + P_HA + P_NP + P_NA + P_M1 + P_M2 + P_NEP + + + + + + P_RdRp + KmB + + + + P_HA + KmC + + + + P_NP + KmD + + + + P_NA + KmE + + + + P_M1 + KmF + + + + P_M2 + KmG + + + + P_NEP + KmH + + + + + + + + + + + + + P_M1 + + + Vp_nuc + + + k_bind_M1 + + + + k_bind_M1 + Vp_nuc + P_M1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 
virions in the extracellular medium (virions)
+ + + + + + + + + + + + + + + + + + + + + + + 
virions in endosomes (virions)
+ + + + + + + + + + + + + + + + + + + + + + + 
parental vRNPs in the cytoplasm (virions)
+ + + + + + + + + + + + + + + + + + + + + + + 
vRNPs in the nucleus (virions)
+ + + + + + + + + + + + + + + + + + + + + + + 
nascent cRNA (molecules)
+ + + + + + + + + + + + + + + + + + 
complex of viral polymerase and cRNA (molecules)
+ + + + + + + + + + + + + + + + + + 
nascent vRNA (molecules)
+ + + + + + + + + + + + + + + + + + 
complex of viral polymerase and vRNA (molecules)
+ + + + + + + + + 
mRNA of segment 1 (molecules)
+ + + + + + + + + + + + + + + + + + 
mRNA of segment 2 (molecules)
+ + + + + + + + + + + + + + + + + + 
mRNA of segment 3 (molecules)
+ + + + + + + + + + + + + + + + + + 
mRNA of segment 4 (molecules)
+ + + + + + + + + + + + + + + + + + 
mRNA of segment 5 (molecules)
+ + + + + + + + + + + + + + + + + + 
mRNA of segment 6 (molecules)
+ + + + + + + + + + + + + + + + + + 
unspliced mRNA of segment 7 (molecules)
+ + + + + + + + + + + + + + + + + + 
unspliced mRNA of segment 8 (molecules)
+ + + + + + + + + + + + + + + + + + 
PB1 proteins (molecules)
+ + + + + + + + + + + + + + + + + + 
PB2 proteins (molecules)
+ + + + + + + + + + + + + + + + + + 
PA proteins (molecules)
+ + + + + + + + + + + + + + + + + + 
HA proteins (molecules)
+ + + + + + + + + + + + + + + + + + 
NP proteins (molecules)
+ + + + + + + + + + + + + + + + + + 
NA proteins (molecules)
+ + + + + + + + + + + + + + + + + + 
M1 proteins (molecules)
+ + + + + + + + + + + + + + + + + + 
NEP proteins (molecules)
+ + + + + + + + + + + + + + + + + + 
M1-vRNP complexes in the nucleus (virions)
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + 
M1-vRNP complexes in the cytoplasm (virions)
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + 
total amount of released virions (virions)
+ + + + + + + + + + + + + + + + + + 
viral polymerase complex (molecules)
+ + + + + + + + + + + + + + + + + + 
cRNPs (molecules)
+ + + + + + + + + + + + + + + + + + 
virions attached to high-affinity binding sites (virions)
+ + + + + + + + + 
virions attached to low-affinity binding sites (virions)
+ + + + + + + + + 
M2 proteins (molecules)
+ + + + + + + + + + + + + + + + + + 
free low-affinity binding sites (sites)
+ + + + + + + + + + + + + + + + + + 
free high-affinity binding sites (sites)
+ + + + + + + + + + + + + + + + + + 
total amount of cRNA in the cell considering an arbitrary segment (molecules)
+ + + + + + + + + 
total amount of vRNA in the cell considering an arbitrary segments (molecules)
+ + + + + + + + + 
The fraction of RNPs that is nuclear
+ + + + + + + + + 
total amount of cRNA in the cell considering all segments (molecules)
+ + + + + + + + + 
total amount of vRNA in the cell considering all segments (molecules)
+ + + + + + + + + 
nuclear RNPs
+ + + + + + + + + 
cytoplasmic RNPs
+ + + + + + + + + + + 
attachment rate of virus particles to high-affinity binding sites (1/(site*h))
+ + + + + + + + + 
attachment rate of virus particles to low-affinity binding sites (1/(site*h))
+ + + + + + + + + 
dissociation rate of virions from high-affinity binding sites (1/h)
+ + + + + + + + + 
dissociation rate of virions from low-affinity binding sites (1/h)
+ + + + + + + + + 
endocytosis rate of virions bound to high-affinity or low-affinity binding sites (1/h)
+ + + + + + + + + 
degradation rate of virions which do not fuse with the endosomal membrane (1/h)
+ + + + + + + + + 
fusion rate of virions in late endosomes (1/h)
+ + + + + + + + + 
nuclear import rate of cytoplasmic vRNPs which are not bound to M1 (1/h)
+ + + + + + + + + 
Degradation of viral ribonucleoproteins.
+ + + + + + + + + 
synthesis rate of cRNAs (1/h)
+ + + + + + + + + 
binding rate of polymerase complexes to cRNA and vRNA (1/(h*molecule))
+ + + + + + + + + 
binding rate of NP to RdRp-cRNA and RdRp-vRNA complexes (1/(h*molecule))
+ + + + + + + + + 
binding rate of M1 to nuclear vRNPs (1/(h*molecule))
+ + + + + + + + + 
combined rate of NEP binding to M1-vRNP complexes and subsequent transport out of the nucleus (1/(molecule*h))
+ + + + + + + + + 
Degradation of viral RNA in the nucleus.
+ + + + + + + + + 
degradation rate of RdRp-cRNA and RdRp-vRNA complexes (1/h)
+ + + + + + + + + 
synthesis rate of mRNAs (nucleotides/h)
+ + + + + + + + + 
synthesis rate of proteins (nucleotides/h)
+ + + + + + + + + 
release rate of progeny virions from the cell (virions/(molecule*h))
+ + + + + + + + + 
distance between two adjacent ribosomes on an mRNA (nucleotides)
+ + + + + + + + + 
fraction of protein synthesis rate and distance between two adjacent ribosomes (1/h)
+ + + + + + + + + 
length of segment 1's mRNA encoding PB2 (nucleotides)
+ + + + + + + + + 
length of segment 2's mRNA encoding PB1 (nucleotides)
+ + + + + + + + + 
length of segment 3's mRNA encoding PA (nucleotides)
+ + + + + + + + + 
length of segment 4's mRNA encoding HA (nucleotides)
+ + + + + + + + + 
length of segment 5's mRNA encoding HA (nucleotides)
+ + + + + + + + + 
length of segment 6's mRNA encoding HA (nucleotides)
+ + + + + + + + + 
length of segment 7's mRNA encoding HA (nucleotides)
+ + + + + + + + + 
length of segment 8's mRNA encoding HA (nucleotides)
+ + + + + + + + + 
synthesis rate of segment 1's mRNA (1/h)
+ + + + + + + + + 
synthesis rate of segment 2's mRNA (1/h)
+ + + + + + + + + 
synthesis rate of segment 3's mRNA (1/h)
+ + + + + + + + + 
synthesis rate of segment 4's mRNA (1/h)
+ + + + + + + + + 
synthesis rate of segment 5's mRNA (1/h)
+ + + + + + + + + 
synthesis rate of segment 6's mRNA (1/h)
+ + + + + + + + + 
synthesis rate of segment 7's mRNA (1/h)
+ + + + + + + + + 
synthesis rate of segment 8's mRNA (1/h)
+ + + + + + + + + 
degradation rate of mRNA (1/h)
+ + + + + + + + + 
number of P_RdRp in a virion
+ + + + + + + + + 
number of P_HA in a virion
+ + + + + + + + + 
number of P_M1 in a virion
+ + + + + + + + + 
number of P_NA in a virion
+ + + + + + + + + 
number of P_NEP in a virion
+ + + + + + + + + 
number of P_NP in a virion
+ + + + + + + + + 
Michaelis-Menten-like constant vor virus release kinetics
+ + + + + + + + + 
fraction of spliced M2 mRNAs compared to total mRNAs of segment 7 (-)
+ + + + + + + + + 
synthesis rate of M1 proteins (1/h)
+ + + + + + + + + 
synthesis rate of M2 proteins (1/h)
+ + + + + + + + + 
fraction of spliced NEP mRNAs compared to total mRNAs of segment 8 (-)
+ + + + + + + + + 
synthesis rate of NEP proteins (1/h)
+ + + + + + + + + 
number of P_M2 in a virion
+ + + + + + + + + 
equilibrium constant for the attachment of virions to the high-affinity binding sites (1/site)
+ + + + + + + + + 
equilibrium constant for the attachment of virions to the low-affinity binding sites (1/site)
+ + + + + + + + + 
fraction of fusion-competent virions (-)
+ + + + + + + + + 
synthesis rate of vRNAs (1/h)
+ + + + + + + + + 
Michaelis-Menten-like constant for half-maximal virus release; necessary for virus release kinetics
+ + + + + + + + + 
Michaelis-Menten-like constant for half-maximal virus release; necessary for virus release kinetics
+ + + + + + + + + 
Michaelis-Menten-like constant for half-maximal virus release; necessary for virus release kinetics
+ + + + + + + + + 
Michaelis-Menten-like constant for half-maximal virus release; necessary for virus release kinetics
+ + + + + + + + + 
Michaelis-Menten-like constant for half-maximal virus release; necessary for virus release kinetics
+ + + + + + + + + 
Michaelis-Menten-like constant for half-maximal virus release; necessary for virus release kinetics
+ + + + + + + + + 
Michaelis-Menten-like constant for half-maximal virus release; necessary for virus release kinetics
+ + + + + + + + + 
formation rate of functional polymerase complexes from the three subunits (1/(h*molecule^2))
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + D_rib + + + + + F_Spl7 + + + + + F_Spl8 + + + + + F_fus + + + + + K_V_rel + + + + + K_eq_Hi + + + + + K_eq_Lo + + + + + L1 + + + + + L2 + + + + + L3 + + + + + L4 + + + + + L5 + + + + + L6 + + + + + L7 + + + + + L8 + + + + + N_P_HA + + + + + N_P_M1 + + + + + N_P_M2 + + + + + N_P_NA + + + + + N_P_NEP + + + + + N_P_NP + + + + + N_P_RdRp + + + + + k_att_Hi + + + + + k_att_Lo + + + + + k_fus + + + + + k_syn_P + + + + + k_syn_R_M + + + + + + + + + + + ModelValue_79 + ModelValue_84 + + 8 + + + + + + + + + + ModelValue_79 + ModelValue_85 + + 8 + + + + + + + + + + ModelValue_79 + ModelValue_86 + + 8 + + + + + + + + + + ModelValue_79 + ModelValue_88 + + 8 + + + + + + + + + + ModelValue_79 + ModelValue_87 + + 8 + + + + + + + + Cp + R_C_RdRp + R_C + + + + + + + + R_C_total_0 + 8 + + + + + + + + + + 8 + + + V_att_Hi + V_att_Lo + V_end + + + Vp_cyt_M1 + Vp_nuc_M1 + Vp_cyt + Vp_nuc + R_V + + + + + + + + R_V_total_0 + 8 + + + + + + + + Vp_nuc_M1 + Vp_nuc + + + + + + + + + + 8 + V_end + + Vp_cyt + Vp_cyt_M1 + + + + + + + + + + RNP_nuc + + + RNP_nuc + RNP_cyt + + + 100 + + + + + + + + ModelValue_63 + ModelValue_114 + + + + + + + + ModelValue_64 + ModelValue_115 + + + + + + + + + + + + 1 + ModelValue_116 + + ModelValue_116 + + ModelValue_69 + + + + + + + + ModelValue_80 + ModelValue_82 + + + + + + + + + + ModelValue_79 + ModelValue_89 + + 8 + + + + + + + + + + ModelValue_79 + ModelValue_90 + + 8 + + + + + + + + + + ModelValue_79 + ModelValue_91 + + 8 + + + + + + + + + + ModelValue_80 + ModelValue_82 + + + + 1 + ModelValue_108 + + + + + + + + + + + ModelValue_80 + ModelValue_82 + + ModelValue_108 + + + + + + + + + + ModelValue_80 + ModelValue_82 + + ModelValue_111 + + + + + + + + ModelValue_107 + ModelValue_101 + + + + + + + + ModelValue_107 + ModelValue_102 + + + + + + + + ModelValue_107 + ModelValue_106 + + + + + + + + ModelValue_107 + ModelValue_104 + + + + + + + + ModelValue_107 + ModelValue_103 + + + + + + + + ModelValue_107 + ModelValue_113 + + + + + + + + ModelValue_107 + ModelValue_105 + + + + + + + + + + + + + + + + + + + + compartment + k_att_Hi + V_ex + B_att_Hi + + + + + + + + + + + + + + + + + + + compartment + k_dis_Hi + V_att_Hi + + + + + + + + + + + + + + + + + + + compartment + k_end + V_att_Hi + + + + + + + + + + + + + + + compartment + k_deg_end + V_end + + + + + + + + + + + + + + + + + + compartment + k_fus + V_end + + + + + + + + + + + + + + + + + + compartment + k_imp + Vp_cyt + + + + + + + + + + + + + + + + + + + compartment + k_syn_R_C + Vp_nuc + + + + + + + + + + + + + + + compartment + k_deg_R + R_C + + + + + + + + + + + + + + + + + + + compartment + k_bind_RdRp + R_C + P_RdRp + + + + + + + + + + + + + + + compartment + k_deg_R_RdRp + R_C_RdRp + + + + + + + + + + + + + + + + + + + compartment + + Rate_Law_for_binding_of_viral_proteins_1 + P_NP + R_C_RdRp + k_bind_NP + + + + + + + + + + + + + + + + + + + + compartment + k_syn_R_V + Cp + + + + + + + + + + + + + + + compartment + k_deg_Rnp + Cp + + + + + + + + + + + + + + + + + + + compartment + k_bind_RdRp + R_V + P_RdRp + + + + + + + + + + + + + + + compartment + k_deg_R + R_V + + + + + + + + 
Actual reaction:
+R_V_RdRp + 71 * P_NP -> Vp_nuc
+ + + + + + + + + + + + + + + + compartment + + Rate_Law_for_binding_of_viral_proteins_2 + P_NP + R_V_RdRp + k_bind_NP + + + + + + + + + + + + + + + + compartment + k_deg_Rnp + Vp_nuc + + + + + + + + + + + + + + + + + + + compartment + k_syn_R_M1_rel + Vp_nuc + + + + + + + + + + + + + + + + + + + compartment + k_syn_R_M2_rel + Vp_nuc + + + + + + + + + + + + + + + + + + + compartment + k_syn_R_M3_rel + Vp_nuc + + + + + + + + + + + + + + + + + + + compartment + k_syn_R_M4_rel + Vp_nuc + + + + + + + + + + + + + + + + + + + compartment + k_syn_R_M5_rel + Vp_nuc + + + + + + + + + + + + + + + + + + + compartment + k_syn_R_M6_rel + Vp_nuc + + + + + + + + + + + + + + + + + + + compartment + k_syn_R_M7_rel + Vp_nuc + + + + + + + + + + + + + + + + + + + compartment + k_syn_R_M8_rel + Vp_nuc + + + + + + + + + + + + + + + + + + + compartment + k_syn_P_rel + R_M2 + + + + + + + + + + + + + + + + + + + compartment + k_syn_P_rel + R_M1 + + + + + + + + + + + + + + + + + + + compartment + k_syn_P_rel + R_M3 + + + + + + + + + + + + + + + + + + + compartment + k_syn_P_rel + R_M4 + + + + + + + + + + + + + + + + + + + compartment + k_syn_P_rel + R_M5 + + + + + + + + + + + + + + + + + + + compartment + k_syn_P_rel + R_M6 + + + + + + + + + + + + + + + + + + + compartment + k_syn_P_M1_rel + R_M7 + + + + + + + + + + + + + + + + + + + compartment + k_syn_P_NEP_rel + R_M8 + + + + + + + + + + + + + + + compartment + k_deg_R_M + R_M1 + + + + + + + + + + + + + + + compartment + k_deg_R_M + R_M2 + + + + + + + + + + + + + + + compartment + k_deg_R_M + R_M3 + + + + + + + + + + + + + + + compartment + k_deg_R_M + R_M4 + + + + + + + + + + + + + + + compartment + k_deg_R_M + R_M5 + + + + + + + + + + + + + + + compartment + k_deg_R_M + R_M6 + + + + + + + + + + + + + + + compartment + k_deg_R_M + R_M7 + + + + + + + + + + + + + + + compartment + k_deg_R_M + R_M8 + + + + + + + + + + + + + + + + + + + + compartment + k_RdRp + P_B1 + P_B2 + P_PA + + + + + + + + 
Actual reaction:
+Vp_nuc + 8 * P_M1 -> Vp_nuc_M1
+ + + + + + + + + + + + + + + + compartment + + Rate_Law_for_binding_of_viral_proteins_3 + P_M1 + Vp_nuc + k_bind_M1 + + + + + + + + + + + + + + + + + + + + compartment + k_exp_Vp_nuc_M1 + Vp_nuc_M1 + P_NEP + + + + + + + + 
Actual reaction:
+8 * Vp_cyt_M1 + 37 * P_RdRp + 433 * P_NP + 2932 * P_M1 + 157 * P_NEP + 500 * P_HA + 100 * P_NA + 40 * P_M2 -> V_rel
+ + + + + + + + + + + + + + + + + + + + + + compartment + + Rate_Law_for_Vp_cyt_M1_Virion_release_1 + KmB + KmC + KmD + KmE + KmF + KmG + KmH + P_HA + P_M1 + P_M2 + P_NA + P_NEP + P_NP + P_RdRp + Vp_cyt_M1 + k_rel + + + + + + + + + + + + + + + + + + + + compartment + k_att_Lo + V_ex + B_att_Lo + + + + + + + + + + + + + + + + + + + compartment + k_syn_P_M2_rel + R_M7 + + + + + + + + + + + + + + + + + + + compartment + k_dis_Lo + V_att_Lo + + + + + + + + + + + + + + + + + + + compartment + k_end + V_att_Lo + + + + + + + + + + + + + + + compartment + k_deg_Rnp + Vp_nuc_M1 + + + + + + + + + + + + + + + compartment + k_deg_R_RdRp + R_V_RdRp + + + + + + + + + + + + + + + compartment + k_deg_Rnp + Vp_cyt_M1 + + + + + + + diff --git a/v2/Laske_PLOSComputBiol2019/observables_Laske_PLOSComputBiol2019.tsv b/v2/Laske_PLOSComputBiol2019/observables_Laske_PLOSComputBiol2019.tsv new file mode 100644 index 0000000..aec74dd --- /dev/null +++ b/v2/Laske_PLOSComputBiol2019/observables_Laske_PLOSComputBiol2019.tsv @@ -0,0 +1,14 @@ +observableId observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +RM5 R_M5 noiseParameter1_RM5 noiseParameter1_RM5 +RVSegTot observableParameter1_RVSegTot + R_V_seg_tot noiseParameter1_RVSegTot observableParameter1_RVSegTot noiseParameter1_RVSegTot +RCSegTot R_C_seg_tot noiseParameter1_RCSegTot noiseParameter1_RCSegTot +Vrel V_rel noiseParameter1_Vrel noiseParameter1_Vrel +IntNucOffset observableParameter1_IntNucOffset 13.0334748500416 * noiseParameter1_IntNucOffset observableParameter1_IntNucOffset noiseParameter1_IntNucOffset +FracNucInt_1 F_rnp_nuc + observableParameter1_FracNucInt_1 3.10956052629092 * noiseParameter1_FracNucInt_1 observableParameter1_FracNucInt_1 noiseParameter1_FracNucInt_1 +FracNucInt_2 F_rnp_nuc + observableParameter1_FracNucInt_2 3.44650910342625 * noiseParameter1_FracNucInt_2 observableParameter1_FracNucInt_2 noiseParameter1_FracNucInt_2 +FracNucInt_3 F_rnp_nuc + observableParameter1_FracNucInt_3 1.96540708251497 * noiseParameter1_FracNucInt_3 observableParameter1_FracNucInt_3 noiseParameter1_FracNucInt_3 +FracNucInt_4 F_rnp_nuc + observableParameter1_FracNucInt_4 3.03676774438437 * noiseParameter1_FracNucInt_4 observableParameter1_FracNucInt_4 noiseParameter1_FracNucInt_4 +FracNucInt_5 F_rnp_nuc + observableParameter1_FracNucInt_5 4.00311961683219 * noiseParameter1_FracNucInt_5 observableParameter1_FracNucInt_5 noiseParameter1_FracNucInt_5 +FracNucInt_6 F_rnp_nuc + observableParameter1_FracNucInt_6 4.8783911282307 * noiseParameter1_FracNucInt_6 observableParameter1_FracNucInt_6 noiseParameter1_FracNucInt_6 +FracNucInt_7 F_rnp_nuc + observableParameter1_FracNucInt_7 3.96353798182046 * noiseParameter1_FracNucInt_7 observableParameter1_FracNucInt_7 noiseParameter1_FracNucInt_7 +FracNucInt_8 F_rnp_nuc + observableParameter1_FracNucInt_8 4.8820897165046 * noiseParameter1_FracNucInt_8 observableParameter1_FracNucInt_8 noiseParameter1_FracNucInt_8 diff --git a/v2/Laske_PLOSComputBiol2019/parameters_Laske_PLOSComputBiol2019.tsv b/v2/Laske_PLOSComputBiol2019/parameters_Laske_PLOSComputBiol2019.tsv new file mode 100644 index 0000000..6869cc7 --- /dev/null +++ b/v2/Laske_PLOSComputBiol2019/parameters_Laske_PLOSComputBiol2019.tsv @@ -0,0 +1,14 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorParameters +k_imp k_{Imp} 1e-10 10000000000 0.296 true +k_syn_R_M R^{Syn}_{R_M} 1e-10 10000000000 30600.0 true +k_syn_R_C {R^{Syn}}_{R_C} 1e-10 10000000000 1.53 true +k_syn_R_V R^{Syn}_{R_V} 1e-10 10000000000 100.93 true +k_bind_M1 k^{Bind}_{M1} 1e-10 10000000000 1.82e-06 true +k_rel k^{Release} 1e-10 10000000000 0.0011 true +vRNA_offset vRNA_{offset} 1e-10 10000000000 535.0 true +Int_nuc_off Int^{nuc}_offset 1e-10 10000000000 45.8 true +scale_sigma_FracNucInt Stdev frac^{Int}_{nuc} 0.001 1000 1.0 true +sigma_RM5 Stdev R_{M5} 0.001 1000 1.0 true +sigma_RV Stdev R^{SegTot}_{V} 0.001 1000 1.0 true +sigma_RC Stdev R^{SegTot}_{C} 0.001 1000 1.0 true +sigma_Vrel Stdev V_{rel} 0.001 1000 1.0 true diff --git a/v2/Lucarelli_CellSystems2018/Lucarelli_CellSystems2018.yaml b/v2/Lucarelli_CellSystems2018/Lucarelli_CellSystems2018.yaml new file mode 100644 index 0000000..02c3129 --- /dev/null +++ b/v2/Lucarelli_CellSystems2018/Lucarelli_CellSystems2018.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Lucarelli_CellSystems2018.tsv +model_files: + model_Lucarelli_CellSystems2018: + location: model_Lucarelli_CellSystems2018.xml + language: sbml +measurement_files: +- measurementData_Lucarelli_CellSystems2018.tsv +condition_files: +- experimentalCondition_Lucarelli_CellSystems2018.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Lucarelli_CellSystems2018.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Lucarelli_CellSystems2018/experimentalCondition_Lucarelli_CellSystems2018.tsv b/v2/Lucarelli_CellSystems2018/experimentalCondition_Lucarelli_CellSystems2018.tsv new file mode 100644 index 0000000..1e9604d --- /dev/null +++ b/v2/Lucarelli_CellSystems2018/experimentalCondition_Lucarelli_CellSystems2018.tsv @@ -0,0 +1,65 @@ +conditionId targetId targetValue +model1_data1 init_S2 S2tot +model1_data2 init_S2 S2tot +model1_data3 init_S2 S2tot +model1_data4 init_S2 S2tot +model1_data5 init_S2 S2tot +model1_data6 init_S2 S2tot +model1_data7 init_S2 S2tot +model1_data8 init_S2 142.34 +model1_data9 init_S2 142.34 +model1_data10 init_S2 142.34 +model1_data11 init_S2 284.68 +model1_data12 init_S2 142.34 +model1_data13 init_S2 142.34 +model1_data14 init_S2 142.34 +model1_data15 init_S2 284.68 +model1_data16 init_S2 142.34 +model1_data1 init_S3 S3tot +model1_data2 init_S3 S3tot +model1_data3 init_S3 S3tot +model1_data4 init_S3 S3tot +model1_data5 init_S3 S3tot +model1_data6 init_S3 S3tot +model1_data7 init_S3 S3tot +model1_data8 init_S3 14.234 +model1_data9 init_S3 14.234 +model1_data10 init_S3 227.744 +model1_data11 init_S3 14.234 +model1_data12 init_S3 14.234 +model1_data13 init_S3 14.234 +model1_data14 init_S3 227.744 +model1_data15 init_S3 14.234 +model1_data16 init_S3 S3tot +model1_data1 init_S4 S4tot +model1_data2 init_S4 S4tot +model1_data3 init_S4 S4tot +model1_data4 init_S4 S4tot +model1_data5 init_S4 S4tot +model1_data6 init_S4 S4tot +model1_data7 init_S4 S4tot +model1_data8 init_S4 208.41 +model1_data9 init_S4 69.47 +model1_data10 init_S4 69.47 +model1_data11 init_S4 69.47 +model1_data12 init_S4 208.41 +model1_data13 init_S4 69.47 +model1_data14 init_S4 69.47 +model1_data15 init_S4 69.47 +model1_data16 init_S4 69.47 +model1_data1 init_TGFb 0.0 +model1_data2 init_TGFb 0.1 +model1_data3 init_TGFb 1.0 +model1_data4 init_TGFb 1.0 +model1_data5 init_TGFb 0.0 +model1_data6 init_TGFb 1.0 +model1_data7 init_TGFb 0.0 +model1_data8 init_TGFb 0.0 +model1_data9 init_TGFb 0.0 +model1_data10 init_TGFb 0.0 +model1_data11 init_TGFb 0.0 +model1_data12 init_TGFb 1.0 +model1_data13 init_TGFb 1.0 +model1_data14 init_TGFb 1.0 +model1_data15 init_TGFb 1.0 +model1_data16 init_TGFb 1.0 diff --git a/v2/Lucarelli_CellSystems2018/experiments.tsv b/v2/Lucarelli_CellSystems2018/experiments.tsv new file mode 100644 index 0000000..9bdf295 --- /dev/null +++ b/v2/Lucarelli_CellSystems2018/experiments.tsv @@ -0,0 +1,17 @@ +experimentId conditionId time +experiment____model1_data1 model1_data1 0 +experiment____model1_data10 model1_data10 0 +experiment____model1_data11 model1_data11 0 +experiment____model1_data12 model1_data12 0 +experiment____model1_data13 model1_data13 0 +experiment____model1_data14 model1_data14 0 +experiment____model1_data15 model1_data15 0 +experiment____model1_data16 model1_data16 0 +experiment____model1_data2 model1_data2 0 +experiment____model1_data3 model1_data3 0 +experiment____model1_data4 model1_data4 0 +experiment____model1_data5 model1_data5 0 +experiment____model1_data6 model1_data6 0 +experiment____model1_data7 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b/v2/Lucarelli_CellSystems2018/model_Lucarelli_CellSystems2018.xml @@ -0,0 +1,1791 @@ + + + + + + 
PEtab implementation of the model from Lucarelli et al. (2018), Cell Syst. 2018 Jan 24;6(1):75-89.e11
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ppS2_ppS3_ppS3 + + 1 + + + + + + + + + + + + + + + cell + geneJ + geneJ_turn + + + + + + + + + + + + + + + + + + cell + + + + + geneK_turn + + + geneK_act2 + ppS2_S4_S4 + + + + geneK_act1 + ppS2_ppS3_S4 + + + + geneK_act3 + ppS2_ppS3_ppS3 + + + + + + + geneK_inh2 + ppS2_S4_S4 + + + + geneK_inh1 + ppS2_ppS3_S4 + + + + geneK_inh3 + ppS2_ppS3_ppS3 + + 1 + + + + + + + + + + + + + + + cell + geneK + geneK_turn + + + + + + + + + + + + + + + + + + cell + + + + + geneL_turn + + + geneL_act2 + ppS2_S4_S4 + + + + geneL_act1 + ppS2_ppS3_S4 + + + + geneL_act3 + ppS2_ppS3_ppS3 + + + + + + + geneL_inh2 + ppS2_S4_S4 + + + + geneL_inh1 + ppS2_ppS3_S4 + + + + geneL_inh3 + ppS2_ppS3_ppS3 + + 1 + + + + + + + + + + + + + + + cell + geneL + geneL_turn + + + + + + + diff --git a/v2/Lucarelli_CellSystems2018/observables_Lucarelli_CellSystems2018.tsv b/v2/Lucarelli_CellSystems2018/observables_Lucarelli_CellSystems2018.tsv new file mode 100644 index 0000000..e3a17d1 --- /dev/null +++ b/v2/Lucarelli_CellSystems2018/observables_Lucarelli_CellSystems2018.tsv @@ -0,0 +1,66 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +Bmp4_gene_expression_OE_nExpID100 Bmp4 geneH + 0.000001 sd_Bmp4_nExpID100 +Cxcl15_gene_expression_OE_nExpID100 Cxcl15 geneI + 0.000001 sd_Cxcl15_nExpID100 +Dnmt3a_gene_expression_OE_nExpID100 Dnmt3a geneC + 0.000001 sd_Dnmt3a_nExpID100 +Dusp5_gene_expression_OE_nExpID100 Dusp5 geneJ + 0.000001 sd_Dusp5_nExpID100 +Jun_gene_expression_OE_nExpID100 Jun geneE + 0.000001 sd_Jun_nExpID100 +Klf10_gene_expression_OE_nExpID100 Klf10 geneG + 0.000001 sd_Klf10_nExpID100 +Pdk4_gene_expression_OE_nExpID100 Pdk4 geneL + 0.000001 sd_Pdk4_nExpID100 +S23IP_S2_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 S23IP_S2 (100*(S2 + S2_S4_S4))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) 5 +S23IP_S2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_S2 (100*(S2 + S2_S4_S4))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) 5 +S23IP_S3_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 S23IP_S3 (100*S3)/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 5 +S23IP_S3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_S3 (100*S3)/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 5 +S23IP_pS2_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 S23IP_pS2 (100*pS2)/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) 5 +S23IP_pS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_pS2 (100*pS2)/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) 5 +S23IP_pS3_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 S23IP_pS3 (100*pS3)/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 5 +S23IP_pS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_pS3 (100*pS3)/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 5 +S23IP_ppS2_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 S23IP_ppS2 (100*(ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) 5 +S23IP_ppS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_ppS2 (100*(ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) 5 +S23IP_ppS3_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 S23IP_ppS3 (100*(ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 5 +S23IP_ppS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_ppS3 (100*(ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 5 +S23IP_tS2_MSPL2_PL_PN_molecules_per_cell_hepa16_nExpID1 S23IP_tS2 S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3 15 +S23IP_tS2_MSPL2_PL_PN_molecules_per_cell_hepa16_ratios_nExpID10 S23IP_tS2 (100*(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + S3 + S2_S4_S4 + pS2 + pS3 + ppS2 + ppS3 + ppS2_S4_S4 + ppS3_S4_S4 + 2*ppS2_ppS2_S4 + 2*ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 1 +S23IP_tS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_tS2 (100*(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + S3 + 3*S2_S4_S4 + pS2 + pS3 + ppS2 + ppS3 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 4*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 5 +S23IP_tS3_MSPL2_PL_PN_molecules_per_cell_hepa16_ratios_nExpID10 S23IP_tS3 (100*(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S2 + S3 + S2_S4_S4 + pS2 + pS3 + ppS2 + ppS3 + ppS2_S4_S4 + ppS3_S4_S4 + 2*ppS2_ppS2_S4 + 2*ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 1 +S23IP_tS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_tS3 (100*(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S2 + S3 + 3*S2_S4_S4 + pS2 + pS3 + ppS2 + ppS3 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 4*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 5 +S23IP_tS4_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_tS4 (100*(2*S2_S4_S4 + 2*ppS2_S4_S4 + 2*ppS3_S4_S4 + ppS2_ppS2_S4 + 2*ppS2_ppS3_S4 + ppS3_ppS3_S4))/(S2 + S3 + 3*S2_S4_S4 + pS2 + pS3 + ppS2 + ppS3 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 4*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 5 +S2IP_S2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_S2 (100*(S2 + S2_S4_S4))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) 5 +S2IP_S2_MSPL2_complexes_all_hepa16_time_course_nExpID6 S2IP_S2 (100*(S2 + S2_S4_S4))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) 5 +S2IP_S3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_S3 0 5 +S2IP_pS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_pS2 (100*pS2)/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) 5 +S2IP_pS2_MSPL2_complexes_all_hepa16_time_course_nExpID6 S2IP_pS2 (100*pS2)/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) 5 +S2IP_pS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_pS3 0 5 +S2IP_ppS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_ppS2 (100*(ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) 5 +S2IP_ppS2_MSPL2_complexes_all_hepa16_time_course_nExpID6 S2IP_ppS2 (100*(ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) 5 +S2IP_ppS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_ppS3 100 5 +S2IP_tS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_tS2 (100*(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + 3*S2_S4_S4 + pS2 + ppS2 + 3*ppS2_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3) 5 +S2IP_tS2_MSPL2_complexes_all_hepa16_time_course_nExpID6 S2IP_tS2 (100*(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + 3*S2_S4_S4 + pS2 + ppS2 + 3*ppS2_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3) 5 +S2IP_tS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_tS3 (100*(ppS2_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3))/(S2 + 3*S2_S4_S4 + pS2 + ppS2 + 3*ppS2_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3) 5 +S2IP_tS3_MSPL2_complexes_all_hepa16_time_course_nExpID6 S2IP_tS3 (100*(ppS2_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3))/(S2 + 3*S2_S4_S4 + pS2 + ppS2 + 3*ppS2_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3) 5 +S2IP_tS4_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_tS4 (100*(2*ppS2_S4_S4 + ppS2_ppS2_S4 + ppS2_ppS3_S4))/(S2 + 3*S2_S4_S4 + pS2 + ppS2 + 3*ppS2_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3) 5 +S2IP_tS4_MSPL2_complexes_all_hepa16_time_course_nExpID6 S2IP_tS4 (100*(2*ppS2_S4_S4 + ppS2_ppS2_S4 + ppS2_ppS3_S4))/(S2 + 3*S2_S4_S4 + pS2 + ppS2 + 3*ppS2_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3) 5 +S3IP_S2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_S2 0 5 +S3IP_S3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_S3 (100*S3)/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 5 +S3IP_pS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_pS2 0 5 +S3IP_pS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_pS3 (100*pS3)/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 5 +S3IP_ppS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_ppS2 100 5 +S3IP_ppS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_ppS3 (100*(ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 5 +S3IP_tS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_tS2 (100*(ppS2_ppS3_S4 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S3 + pS3 + ppS3 + 3*ppS3_S4_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 5 +S3IP_tS2_MSPL2_complexes_all_hepa16_time_course_nExpID6 S3IP_tS2 (100*(ppS2_ppS3_S4 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S3 + pS3 + ppS3 + 3*ppS3_S4_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 5 +S3IP_tS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_tS3 (100*(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S3 + pS3 + ppS3 + 3*ppS3_S4_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 5 +S3IP_tS3_MSPL2_complexes_all_hepa16_time_course_nExpID6 S3IP_tS3 (100*(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S3 + pS3 + ppS3 + 3*ppS3_S4_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 5 +S3IP_tS4_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_tS4 (100*(2*ppS3_S4_S4 + ppS2_ppS3_S4 + ppS3_ppS3_S4))/(S3 + pS3 + ppS3 + 3*ppS3_S4_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 5 +S3IP_tS4_MSPL2_complexes_all_hepa16_time_course_nExpID6 S3IP_tS4 (100*(2*ppS3_S4_S4 + ppS2_ppS3_S4 + ppS3_ppS3_S4))/(S3 + pS3 + ppS3 + 3*ppS3_S4_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) 5 +S4IP_tS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S4IP_tS2 (100*(S2_S4_S4 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4))/(S4 + 3*S2_S4_S4 + 3*S4_S4_S4 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4) 5 +S4IP_tS2_MSPL2_complexes_all_hepa16_time_course_nExpID6 S4IP_tS2 (100*(S2_S4_S4 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4))/(S4 + 3*S2_S4_S4 + 3*S4_S4_S4 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4) 5 +S4IP_tS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S4IP_tS3 (100*(ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4))/(S4 + 3*S2_S4_S4 + 3*S4_S4_S4 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4) 5 +S4IP_tS3_MSPL2_complexes_all_hepa16_time_course_nExpID6 S4IP_tS3 (100*(ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4))/(S4 + 3*S2_S4_S4 + 3*S4_S4_S4 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4) 5 +S4IP_tS4_MSPL2_PL_PN_molecules_per_cell_hepa16_nExpID1 S4IP_tS4 S4 + 2*S2_S4_S4 + 3*S4_S4_S4 + 2*ppS2_S4_S4 + 2*ppS3_S4_S4 + ppS2_ppS2_S4 + ppS2_ppS3_S4 + ppS3_ppS3_S4 15 +S4IP_tS4_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S4IP_tS4 (100*(S4 + 2*S2_S4_S4 + 3*S4_S4_S4 + 2*ppS2_S4_S4 + 2*ppS3_S4_S4 + ppS2_ppS2_S4 + ppS2_ppS3_S4 + ppS3_ppS3_S4))/(S4 + 3*S2_S4_S4 + 3*S4_S4_S4 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4) 5 +S4IP_tS4_MSPL2_complexes_all_hepa16_time_course_nExpID6 S4IP_tS4 (100*(S4 + 2*S2_S4_S4 + 3*S4_S4_S4 + 2*ppS2_S4_S4 + 2*ppS3_S4_S4 + ppS2_ppS2_S4 + ppS2_ppS3_S4 + ppS3_ppS3_S4))/(S4 + 3*S2_S4_S4 + 3*S4_S4_S4 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4) 5 +Ski_gene_expression_OE_nExpID100 Ski geneA + 0.000001 sd_Ski_nExpID100 +Skil_gene_expression_OE_nExpID100 Skil geneB + 0.000001 sd_Skil_nExpID100 +Smad7_gene_expression_OE_nExpID100 Smad7 geneF + 0.000001 sd_Smad7_nExpID100 +Sox4_gene_expression_OE_nExpID100 Sox4 geneD + 0.000001 sd_Sox4_nExpID100 +TGFbR_PL_PN_TGFbR_hepa16_nExpID11 TGFbR Rec + TGFb_pRec 0.092 +Tgfa_gene_expression_OE_nExpID100 Tgfa geneK + 0.000001 sd_Tgfa_nExpID100 diff --git a/v2/Lucarelli_CellSystems2018/parameters_Lucarelli_CellSystems2018.tsv b/v2/Lucarelli_CellSystems2018/parameters_Lucarelli_CellSystems2018.tsv new file mode 100644 index 0000000..181e72d --- /dev/null +++ b/v2/Lucarelli_CellSystems2018/parameters_Lucarelli_CellSystems2018.tsv @@ -0,0 +1,118 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorParameters +Rec_act Rec_{act} 1e-05 1000 0.005969840220269 true +S2tot S2tot 1e-05 1000 142.781779487328 true +S3tot S3tot 1e-05 1000 16.2589451746389 true +S4tot S4tot 1e-05 1000 67.0231777556657 true +S_dephos S_{dephos} 1e-05 1000 0.27814192587492 true +S_dephosphos S_{dephosphos} 1e-05 1000 0.047612869772851 true +S_phos S_{phos} 1e-05 1000 0.377121036829566 true +geneA_act1 geneA_{act1} 1e-05 1000 0.014141482569873 true +geneA_act2 geneA_{act2} 1e-05 1000 0.000804762503775 true +geneA_act3 geneA_{act3} 0.0 1000 0.0 false +geneA_inh1 geneA_{inh1} 0.0 1000 0.0 false +geneA_inh2 geneA_{inh2} 1e-05 1000 0.046327226117843 true +geneA_inh3 geneA_{inh3} 1e-05 1000 0.026267107319375 true +geneA_turn geneA_{turn} 1e-05 1000 0.00457249551772 true +geneB_act1 geneB_{act1} 1e-05 1000 0.459613121530843 true +geneB_act2 geneB_{act2} 1e-05 1000 0.073383419339726 true +geneB_act3 geneB_{act3} 1e-05 1000 0.030882914826193 true +geneB_inh1 geneB_{inh1} 0.0 1000 0.0 false +geneB_inh2 geneB_{inh2} 1e-05 1000 0.741363220477926 true +geneB_inh3 geneB_{inh3} 1e-05 1000 0.408770024042632 true +geneB_turn geneB_{turn} 1e-05 1000 0.011249707694988 true +geneC_act1 geneC_{act1} 1e-05 1000 0.007148127389081 true +geneC_act2 geneC_{act2} 0.0 1000 0.0 false +geneC_act3 geneC_{act3} 0.0 1000 0.0 false +geneC_inh1 geneC_{inh1} 0.0 1000 0.0 false +geneC_inh2 geneC_{inh2} 1e-05 1000 0.018280189253089 true +geneC_inh3 geneC_{inh3} 1e-05 1000 0.035357897325705 true +geneC_turn geneC_{turn} 1e-05 1000 0.003788712045359 true +geneD_act1 geneD_{act1} 1e-05 1000 0.011196450539858 true +geneD_act2 geneD_{act2} 1e-05 1000 0.000274226711471 true +geneD_act3 geneD_{act3} 0.0 1000 0.0 false +geneD_inh1 geneD_{inh1} 0.0 1000 0.0 false +geneD_inh2 geneD_{inh2} 1e-05 1000 0.087254446388786 true +geneD_inh3 geneD_{inh3} 1e-05 1000 0.101513276183648 true +geneD_turn geneD_{turn} 1e-05 1000 0.000808762955598 true +geneE_act1 geneE_{act1} 0.0 1000 0.0 false +geneE_act2 geneE_{act2} 1e-05 1000 1.00646343942677 true +geneE_act3 geneE_{act3} 1e-05 1000 5.99313266073915 true +geneE_inh1 geneE_{inh1} 1e-05 1000 8.07491215308045 true +geneE_inh2 geneE_{inh2} 1e-05 1000 1.41088296804943 true +geneE_inh3 geneE_{inh3} 1e-05 1000 9.6007014049458 true +geneE_turn geneE_{turn} 1e-05 1000 0.123153223674769 true +geneF_act1 geneF_{act1} 1e-05 1000 997.409937077934 true +geneF_act2 geneF_{act2} 1e-05 1000 0.202918268796874 true +geneF_act3 geneF_{act3} 1e-05 1000 20.6601154704175 true +geneF_inh1 geneF_{inh1} 1e-05 1000 3.61748263470294 true +geneF_inh2 geneF_{inh2} 0.0 1000 0.0 false +geneF_inh3 geneF_{inh3} 0.0 1000 0.0 false +geneF_turn geneF_{turn} 1e-05 1000 36.7828145068642 true +geneG_act1 geneG_{act1} 1e-05 1000 631.448426386524 true +geneG_act2 geneG_{act2} 1e-05 1000 55.8423040781623 true +geneG_act3 geneG_{act3} 0.0 1000 0.0 false +geneG_inh1 geneG_{inh1} 0.0 1000 0.0 false +geneG_inh2 geneG_{inh2} 1e-05 1000 0.017226968457893 true +geneG_inh3 geneG_{inh3} 1e-05 1000 0.000789710736856 true +geneG_turn geneG_{turn} 1e-05 1000 298.52886647117 true +geneH_act1 geneH_{act1} 0.0 1000 0.0 false +geneH_act2 geneH_{act2} 1e-05 1000 89.4094400577504 true +geneH_act3 geneH_{act3} 1e-05 1000 999.941275471262 true +geneH_inh1 geneH_{inh1} 1e-05 1000 999.998157205339 true +geneH_inh2 geneH_{inh2} 1e-05 1000 18.9335116736955 true +geneH_inh3 geneH_{inh3} 1e-05 1000 218.414317332393 true +geneH_turn geneH_{turn} 1e-05 1000 0.992432086986075 true +geneI_act1 geneI_{act1} 1e-05 1000 9.30363565946309 true +geneI_act2 geneI_{act2} 0.0 1000 0.0 false +geneI_act3 geneI_{act3} 0.0 1000 0.0 false +geneI_inh1 geneI_{inh1} 0.0 1000 0.0 false +geneI_inh2 geneI_{inh2} 1e-05 1000 318.827113851182 true +geneI_inh3 geneI_{inh3} 1e-05 1000 999.984313802586 true +geneI_turn geneI_{turn} 1e-05 1000 0.003283125626569 true +geneJ_act1 geneJ_{act1} 0.0 1000 0.0 false +geneJ_act2 geneJ_{act2} 0.0 1000 0.0 false +geneJ_act3 geneJ_{act3} 0.0 1000 0.0 false +geneJ_inh1 geneJ_{inh1} 1e-05 1000 0.477105124254686 true +geneJ_inh2 geneJ_{inh2} 1e-05 1000 0.009916494960393 true +geneJ_inh3 geneJ_{inh3} 1e-05 1000 0.008538578630726 true +geneJ_turn geneJ_{turn} 1e-05 1000 0.014037170066501 true +geneK_act1 geneK_{act1} 1e-05 1000 0.012554063210037 true +geneK_act2 geneK_{act2} 1e-05 1000 0.000277659442546 true +geneK_act3 geneK_{act3} 0.0 1000 0.0 false +geneK_inh1 geneK_{inh1} 0.0 1000 0.0 false +geneK_inh2 geneK_{inh2} 1e-05 1000 1.35229129075373 true +geneK_inh3 geneK_{inh3} 1e-05 1000 2.43517542511281 true +geneK_turn geneK_{turn} 1e-05 1000 0.003604029209818 true +geneL_act1 geneL_{act1} 0.0 1000 0.0 false +geneL_act2 geneL_{act2} 1e-05 1000 0.000469494240947 true +geneL_act3 geneL_{act3} 0.0 1000 0.0 false +geneL_inh1 geneL_{inh1} 1e-05 1000 1.29355064932496 true +geneL_inh2 geneL_{inh2} 1e-05 1000 0.062052638950287 true +geneL_inh3 geneL_{inh3} 1e-05 1000 0.134647700641231 true +geneL_turn geneL_{turn} 1e-05 1000 0.014959914457387 true +init_Rec init_{Rec} 1e-05 1000 1.83573022281688 true +k_223 K_{223} 0.0 3 0.0 false +k_224 K_{224} 0.0 3 0.0 false +k_233 K_{233} 1e-08 1000 0.142085879395794 true +k_234 K_{234} 1e-08 1000 0.000388982466668 true +k_244 K_{244} 1e-08 1000 8.39675013568961e-06 true +k_334 K_{334} 0.0 3 0.0 false +k_344 K_{344} 0.0 3 0.0 false +k_on_u k_{on,u} 0.0 3 0.0 false +kdiss_SS kdiss_{SS} 0.0 3 0.0 false +khomo2 khomo2 0.0 3 0.0 false +khomo3 khomo3 0.0 3 0.0 false +khomo4 khomo4 0.0 3 0.0 false +pRec_degind pRec_{degind} 1e-05 1000 0.04135528194872 true +sd_Bmp4_nExpID100 \sigma_{Bmp4,nExpID100} 1e-05 1000 0.137157454763382 true +sd_Cxcl15_nExpID100 \sigma_{Cxcl15,nExpID100} 1e-05 1000 0.13079064242208 true +sd_Dnmt3a_nExpID100 \sigma_{Dnmt3a,nExpID100} 1e-05 1000 0.094144201838107 true +sd_Dusp5_nExpID100 \sigma_{Dusp5,nExpID100} 1e-05 1000 0.102712401706984 true +sd_Jun_nExpID100 \sigma_{Jun,nExpID100} 1e-05 1000 0.160218041756984 true +sd_Klf10_nExpID100 \sigma_{Klf10,nExpID100} 1e-05 1000 0.114163398031463 true +sd_Pdk4_nExpID100 \sigma_{Pdk4,nExpID100} 1e-05 1000 0.071815166180012 true +sd_Ski_nExpID100 \sigma_{Ski,nExpID100} 1e-05 1000 0.099395735077609 true +sd_Skil_nExpID100 \sigma_{Skil,nExpID100} 1e-05 1000 0.170117118767879 true +sd_Smad7_nExpID100 \sigma_{Smad7,nExpID100} 1e-05 1000 0.068439045180716 true +sd_Sox4_nExpID100 \sigma_{Sox4,nExpID100} 1e-05 1000 0.12283736185634 true +sd_Tgfa_nExpID100 \sigma_{Tgfa,nExpID100} 1e-05 1000 0.075061798783051 true diff --git a/v2/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020.yaml b/v2/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020.yaml new file mode 100644 index 0000000..d931fc7 --- /dev/null +++ b/v2/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Okuonghae_ChaosSolitonsFractals2020.tsv +model_files: + model_Okuonghae_ChaosSolitonsFractals2020: + location: model_Okuonghae_ChaosSolitonsFractals2020.xml + language: sbml +measurement_files: +- measurementData_Okuonghae_ChaosSolitonsFractals2020.tsv +condition_files: +- experimentalConditions_Okuonghae_ChaosSolitonsFractals2020.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Okuonghae_ChaosSolitonsFractals2020.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Okuonghae_ChaosSolitonsFractals2020/experimentalConditions_Okuonghae_ChaosSolitonsFractals2020.tsv b/v2/Okuonghae_ChaosSolitonsFractals2020/experimentalConditions_Okuonghae_ChaosSolitonsFractals2020.tsv new file mode 100644 index 0000000..3d1bb68 --- /dev/null +++ b/v2/Okuonghae_ChaosSolitonsFractals2020/experimentalConditions_Okuonghae_ChaosSolitonsFractals2020.tsv @@ -0,0 +1,3 @@ +conditionId targetId targetValue +cond1 delta 0 +cond1 eps 0 diff --git a/v2/Okuonghae_ChaosSolitonsFractals2020/experiments.tsv b/v2/Okuonghae_ChaosSolitonsFractals2020/experiments.tsv new file mode 100644 index 0000000..6376640 --- /dev/null +++ b/v2/Okuonghae_ChaosSolitonsFractals2020/experiments.tsv @@ -0,0 +1,2 @@ +experimentId conditionId time +experiment____cond1 cond1 0 diff --git a/v2/Okuonghae_ChaosSolitonsFractals2020/measurementData_Okuonghae_ChaosSolitonsFractals2020.tsv b/v2/Okuonghae_ChaosSolitonsFractals2020/measurementData_Okuonghae_ChaosSolitonsFractals2020.tsv new file mode 100644 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a/v2/Okuonghae_ChaosSolitonsFractals2020/parameters_Okuonghae_ChaosSolitonsFractals2020.tsv b/v2/Okuonghae_ChaosSolitonsFractals2020/parameters_Okuonghae_ChaosSolitonsFractals2020.tsv new file mode 100644 index 0000000..78c8831 --- /dev/null +++ b/v2/Okuonghae_ChaosSolitonsFractals2020/parameters_Okuonghae_ChaosSolitonsFractals2020.tsv @@ -0,0 +1,17 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorParameters +alpha alpha 1e-05 1000 0.5 true +d_0 d_0 1e-05 1000 0.015 true +d_D d_D 1e-05 1000 0.015 true +gamma_0 gamma_0 1e-05 1000 0.13978 true +gamma_a gamma_a 1e-05 1000 0.13978 true +gamma_i gamma_i 1e-05 1000 0.06666667 true +nu nu 1e-05 1000 0.5 true +psi psi 1e-05 1000 0.0135 true +sigma sigma 1e-05 1000 0.1923077 true +theta theta 1e-13 1000 2e-12 true +asymptomatic_start asymptomatic_start 1.0 10000 188.0 true +symptomatic_start symptomatic_start 1.0 10000 212.0 true +exposed_start exposed_start 1.0 1000 441.0 true +transmission_rate_effective transmissionRate_effective 1e-05 1000 0.4236 true +sd_Cumulative sd_Cumulative 1e-05 1000 1.0 true +sd_ActiveCases sd_ActiveCases 1e-05 1000 1.0 true diff --git a/v2/Oliveira_NatCommun2021/Oliveira_NatCommun2021.yaml b/v2/Oliveira_NatCommun2021/Oliveira_NatCommun2021.yaml new file mode 100644 index 0000000..4583709 --- /dev/null +++ b/v2/Oliveira_NatCommun2021/Oliveira_NatCommun2021.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Oliveira_NatCommun2021.tsv +model_files: + Oliveira_NatCommun2021_model: + location: Oliveira_NatCommun2021_model.xml + language: sbml +measurement_files: +- measurementData_Oliveira_NatCommun2021.tsv +condition_files: +- experimentalConditions_Oliveira_NatCommun2021.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Oliveira_NatCommun2021.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml b/v2/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml new file mode 100644 index 0000000..2c6b751 --- /dev/null +++ b/v2/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml @@ -0,0 +1,1444 @@ + + + + + + + 
Oliveira, Nature 2021.
+
+https://www.nature.com/articles/s41467-020-19798-3.
+
+COVID-19  is  affecting  healthcare  resources  worldwide,  with  lower  and  middle-income countries being particularly disadvantaged to mitigate the challenges imposed by the disease, including the availability of a sufficient number of infirmary/ICU hospital beds, ventilators, and medical supplies. Here, we use mathematical modelling to study the dynamics of COVID-19 in Bahia, a state in northeastern Brazil, considering the influences of asymptomatic/non-detected cases, hospitalizations, and mortality. The impacts of policies on the transmission rate  were  also  examined.  Our  results  underscore  the  difficulties  in  maintaining  a  fully operational health infrastructure amidst the pandemic. Lowering the transmission rate is paramount to this objective, but current local efforts, leading to a 36% decrease, remain insufficient to prevent systemic collapse at peak demand, which could be accomplished using periodic interventions. Non-detected cases contribute to a ∽55% increase inR0. Finally, we discuss our results in light of epidemiological data that became available after the initial analyses.
+
+To model with a two-step transmission rate, set 'beta_2_multiplier' = 0. To model with a three-step transmission rate, set 'beta_2_multiplier' = 1. 
+
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+++ b/v2/Oliveira_NatCommun2021/experiments.tsv @@ -0,0 +1,2 @@ +experimentId conditionId time +experiment____interior interior 0 diff --git a/v2/Oliveira_NatCommun2021/measurementData_Oliveira_NatCommun2021.tsv b/v2/Oliveira_NatCommun2021/measurementData_Oliveira_NatCommun2021.tsv new file mode 100644 index 0000000..55b5303 --- /dev/null +++ b/v2/Oliveira_NatCommun2021/measurementData_Oliveira_NatCommun2021.tsv @@ -0,0 +1,121 @@ +experimentId observableId measurement time noiseParameters datasetId +experiment____interior cumulative_cases 1 0 sd_cumulative_cases dataset_ +experiment____interior cumulative_deaths 0 0 sd_cumulative_deaths dataset_ +experiment____interior cumulative_cases 2 1 sd_cumulative_cases dataset_ +experiment____interior cumulative_deaths 0 1 sd_cumulative_deaths dataset_ +experiment____interior cumulative_cases 2 2 sd_cumulative_cases dataset_ +experiment____interior cumulative_deaths 0 2 sd_cumulative_deaths dataset_ +experiment____interior cumulative_cases 2 3 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cumulative_cases 1077 55 sd_cumulative_cases dataset_ +experiment____interior cumulative_deaths 39 55 sd_cumulative_deaths dataset_ +experiment____interior cumulative_cases 1139 56 sd_cumulative_cases dataset_ +experiment____interior cumulative_deaths 41 56 sd_cumulative_deaths dataset_ +experiment____interior cumulative_cases 1209 57 sd_cumulative_cases dataset_ +experiment____interior cumulative_deaths 45 57 sd_cumulative_deaths dataset_ +experiment____interior cumulative_cases 1313 58 sd_cumulative_cases dataset_ +experiment____interior cumulative_deaths 48 58 sd_cumulative_deaths dataset_ +experiment____interior cumulative_cases 1357 59 sd_cumulative_cases dataset_ +experiment____interior cumulative_deaths 50 59 sd_cumulative_deaths dataset_ diff --git a/v2/Oliveira_NatCommun2021/observables_Oliveira_NatCommun2021.tsv b/v2/Oliveira_NatCommun2021/observables_Oliveira_NatCommun2021.tsv new file mode 100644 index 0000000..b63e7b7 --- /dev/null +++ b/v2/Oliveira_NatCommun2021/observables_Oliveira_NatCommun2021.tsv @@ -0,0 +1,3 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +cumulative_deaths cumulative_deaths Deaths noiseParameter1_cumulative_deaths normal noiseParameter1_cumulative_deaths +cumulative_cases cumulative_cases Cumulative_cases noiseParameter1_cumulative_cases normal noiseParameter1_cumulative_cases diff --git a/v2/Oliveira_NatCommun2021/parameters_Oliveira_NatCommun2021.tsv b/v2/Oliveira_NatCommun2021/parameters_Oliveira_NatCommun2021.tsv new file mode 100644 index 0000000..5bef9cc --- /dev/null +++ b/v2/Oliveira_NatCommun2021/parameters_Oliveira_NatCommun2021.tsv @@ -0,0 +1,25 @@ +parameterId lowerBound upperBound nominalValue estimate priorParameters +p_symp_rate 0.2 false +kappa 0.25 false +gamma_a 0.28571429 false +gamma_s 0.25 false +xi 0.53 false +mu_h 0.15 false +mu_u 0.4 false +omega_h 0.14 false +omega_u 0.29 false +beta_0 1e-08 2.0 0.97 true +beta_1 1e-08 2.0 0.57 true +beta_2 1e-08 2.0 0.57 true +t_1 9.0 40.0 29.0 true +t_2 40.0 191.0 100.0 true +delta_ 1e-08 0.75 0.62 true +h_hosp_rate 0.05 0.25 0.2 true +gamma_h 0.0833333333 0.25 0.1 true +gamma_u 0.0833333333 0.3333333333 0.1 true +sd_cumulative_deaths 1.0 false +sd_cumulative_cases 1.0 false +population 12098867.0 false +exposed_init_concentration 1e-12 1.0 6.37e-08 true +asymptomatic_init_concentration 1e-12 1.0 6.3e-07 true +symptomatic_init_concentration 1e-12 1.0 3.32e-07 true diff --git a/v2/Perelson_Science1996/Perelson_Science1996.yaml b/v2/Perelson_Science1996/Perelson_Science1996.yaml new file mode 100644 index 0000000..a4e578d --- /dev/null +++ b/v2/Perelson_Science1996/Perelson_Science1996.yaml @@ -0,0 +1,16 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Perelson_Science1996.tsv +model_files: + model_Perelson_Science1996: + location: model_Perelson_Science1996.xml + language: sbml +measurement_files: +- measurementData_Perelson_Science1996.tsv +condition_files: +- experimentalCondition_Perelson_Science1996.tsv +experiment_files: [] +observable_files: +- observables_Perelson_Science1996.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Perelson_Science1996/experimentalCondition_Perelson_Science1996.tsv b/v2/Perelson_Science1996/experimentalCondition_Perelson_Science1996.tsv new file mode 100644 index 0000000..730c58d --- /dev/null +++ b/v2/Perelson_Science1996/experimentalCondition_Perelson_Science1996.tsv @@ -0,0 +1 @@ +conditionId targetId targetValue diff --git a/v2/Perelson_Science1996/measurementData_Perelson_Science1996.tsv b/v2/Perelson_Science1996/measurementData_Perelson_Science1996.tsv new file mode 100644 index 0000000..a3a3a83 --- /dev/null +++ b/v2/Perelson_Science1996/measurementData_Perelson_Science1996.tsv @@ -0,0 +1,17 @@ +experimentId observableId measurement time observableParameters noiseParameters + task0_model0_perelson1_V 1029000.0 0.0 sd_task0_model0_perelson1_V + task0_model0_perelson1_V 1087000.0 0.105 sd_task0_model0_perelson1_V + task0_model0_perelson1_V 2158000.0 0.169 sd_task0_model0_perelson1_V + task0_model0_perelson1_V 1860000.0 0.282 sd_task0_model0_perelson1_V + task0_model0_perelson1_V 2195000.0 0.492 sd_task0_model0_perelson1_V + task0_model0_perelson1_V 1567000.0 0.757 sd_task0_model0_perelson1_V + task0_model0_perelson1_V 3208000.0 1.029 sd_task0_model0_perelson1_V + task0_model0_perelson1_V 2293000.0 1.253 sd_task0_model0_perelson1_V + task0_model0_perelson1_V 1342000.0 1.533 sd_task0_model0_perelson1_V + task0_model0_perelson1_V 1197000.0 1.75 sd_task0_model0_perelson1_V + task0_model0_perelson1_V 987100.0 2.038 sd_task0_model0_perelson1_V + task0_model0_perelson1_V 697300.0 3.013 sd_task0_model0_perelson1_V + task0_model0_perelson1_V 503800.0 3.987 sd_task0_model0_perelson1_V + task0_model0_perelson1_V 282200.0 4.968 sd_task0_model0_perelson1_V + task0_model0_perelson1_V 172700.0 5.972 sd_task0_model0_perelson1_V + task0_model0_perelson1_V 91618.242 6.973 sd_task0_model0_perelson1_V diff --git a/v2/Perelson_Science1996/model_Perelson_Science1996.xml b/v2/Perelson_Science1996/model_Perelson_Science1996.xml new file mode 100644 index 0000000..88a1625 --- /dev/null +++ b/v2/Perelson_Science1996/model_Perelson_Science1996.xml @@ -0,0 +1,136 @@ + + + + + + 
PEtab implementation of the model from Perelson et al. (1996), Science  15 Mar 1996: Vol. 271, Issue 5255, pp. 1582-1586
+ + + + + + + + + + Perelson + Alan + + + + + + 2019-11-29T09:41:48Z + + + 2019-11-29T09:41:48Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + K0 + T0 + Vin + + + + + + + + + + + + + delta + Tstar + + + + + + + + + + + + + + c + Vin + + + + + + + + + + + + + + c + Vni + + + + + + + + + + + + + + + + + delta + NN + Tstar + + + + + + + diff --git a/v2/Perelson_Science1996/observables_Perelson_Science1996.tsv b/v2/Perelson_Science1996/observables_Perelson_Science1996.tsv new file mode 100644 index 0000000..eca383f --- /dev/null +++ b/v2/Perelson_Science1996/observables_Perelson_Science1996.tsv @@ -0,0 +1,2 @@ +observableId observableFormula observableName noiseDistribution noiseFormula observablePlaceholders noisePlaceholders +task0_model0_perelson1_V V noiseParameter1_task0_model0_perelson1_V noiseParameter1_task0_model0_perelson1_V diff --git a/v2/Perelson_Science1996/parameters_Perelson_Science1996.tsv b/v2/Perelson_Science1996/parameters_Perelson_Science1996.tsv new file mode 100644 index 0000000..269beba --- /dev/null +++ b/v2/Perelson_Science1996/parameters_Perelson_Science1996.tsv @@ -0,0 +1,7 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorParameters +NN NN 1e-05 100000 480.000000026982 false +T0 T0 1e-05 100000 11000.0000010581 false +c c 1e-05 100000 2.06000000014632 true +delta delta 1e-05 100000 0.529999999999037 true +K0 K0 1e-05 100000 3.89999999976204e-07 false +sd_task0_model0_perelson1_V sigma_task0_model0_perelson1_V 1e-10 10000000000 100000.0 true diff --git a/v2/Rahman_MBS2016/Rahman_MBS2016.yaml b/v2/Rahman_MBS2016/Rahman_MBS2016.yaml new file mode 100644 index 0000000..5efee36 --- /dev/null +++ b/v2/Rahman_MBS2016/Rahman_MBS2016.yaml @@ -0,0 +1,16 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Rahman_MBS2016.tsv +model_files: + model_Rahman_MBS2016: + location: model_Rahman_MBS2016.xml + language: sbml +measurement_files: +- measurementData_Rahman_MBS2016.tsv +condition_files: +- experimentalCondition_Rahman_MBS2016.tsv +experiment_files: [] +observable_files: +- observables_Rahman_MBS2016.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Rahman_MBS2016/experimentalCondition_Rahman_MBS2016.tsv b/v2/Rahman_MBS2016/experimentalCondition_Rahman_MBS2016.tsv new file mode 100644 index 0000000..730c58d --- /dev/null +++ b/v2/Rahman_MBS2016/experimentalCondition_Rahman_MBS2016.tsv @@ -0,0 +1 @@ +conditionId targetId targetValue diff --git a/v2/Rahman_MBS2016/measurementData_Rahman_MBS2016.tsv b/v2/Rahman_MBS2016/measurementData_Rahman_MBS2016.tsv new file mode 100644 index 0000000..6bb8cd1 --- /dev/null +++ b/v2/Rahman_MBS2016/measurementData_Rahman_MBS2016.tsv @@ -0,0 +1,24 @@ +experimentId observableId measurement time observableParameters noiseParameters datasetId + observable_prevalence 0.3 0 1 model1_data1_prevalence + observable_prevalence 0.6 1 1 model1_data1_prevalence + observable_prevalence 1.1 2 1 model1_data1_prevalence + observable_prevalence 2.0 3 1 model1_data1_prevalence + observable_prevalence 3.3 4 1 model1_data1_prevalence + observable_prevalence 5.0 5 1 model1_data1_prevalence + observable_prevalence 7.0 6 1 model1_data1_prevalence + observable_prevalence 9.2 7 1 model1_data1_prevalence + observable_prevalence 11.3 8 1 model1_data1_prevalence + observable_prevalence 13.2 9 1 model1_data1_prevalence + observable_prevalence 14.9 10 1 model1_data1_prevalence + observable_prevalence 16.2 11 1 model1_data1_prevalence + observable_prevalence 17.1 12 1 model1_data1_prevalence + observable_prevalence 17.8 13 1 model1_data1_prevalence + observable_prevalence 18.3 14 1 model1_data1_prevalence + observable_prevalence 18.5 15 1 model1_data1_prevalence + observable_prevalence 18.7 16 1 model1_data1_prevalence + observable_prevalence 18.8 17 1 model1_data1_prevalence + observable_prevalence 18.9 18 1 model1_data1_prevalence + observable_prevalence 18.9 19 1 model1_data1_prevalence + observable_prevalence 18.9 20 1 model1_data1_prevalence + observable_prevalence 18.8 21 1 model1_data1_prevalence + observable_prevalence 18.9 22 1 model1_data1_prevalence diff --git a/v2/Rahman_MBS2016/model_Rahman_MBS2016.xml b/v2/Rahman_MBS2016/model_Rahman_MBS2016.xml new file mode 100644 index 0000000..c9d49af --- /dev/null +++ b/v2/Rahman_MBS2016/model_Rahman_MBS2016.xml @@ -0,0 +1,435 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + infected_normal_transmission_rate_relative + infected_moderate_transmission_rate + + + + + + + + infected_weak_transmission_rate_relative + infected_moderate_transmission_rate + + + + + + + + 0.04 + infected_moderate_transmission_rate + + + + + + + + + + + + + + infected_normal_transmission_rate + infected_normal + + + + infected_moderate_transmission_rate + infected_moderate + + + + infected_weak_transmission_rate + infected_weak + + + + treated_transmission_rate + + + treated_normal + treated_moderate + treated_weak + + + + + + susceptible + infected_normal + infected_moderate + infected_weak + treated_normal + treated_moderate + treated_weak + + + + + + + + + 1 + + behavioural_change_rate + + + infected_normal + infected_moderate + infected_weak + treated_normal + treated_moderate + treated_weak + + + + + + + + + + + + + 1 + + + susceptible + + + susceptible + infected_normal + infected_moderate + infected_weak + treated_normal + treated_moderate + treated_weak + + + + 100 + + + + + + + + + + + + recruitment_rate + + + + + + + + + + + + + + + force_of_infection + susceptible + + + + + + + + + + + + + + + + infected_normal_worsen_rate + infected_normal + + + + + + + + + + + + + + + + infected_moderate_worsen_rate + infected_moderate + + + + + + + + + + + + + + + + treated_weak_improve_rate + treated_weak + + + + + + + + + + + + + + + + treated_moderate_improve_rate + treated_moderate + + + + + + + + + + + + + + + + infected_normal_treatment_rate + infected_normal + + + + + + + + + + + + + + + + infected_moderate_treatment_rate + infected_moderate + + + + + + + + + + + + + + + + infected_weak_treatment_rate + infected_weak + + + + + + + + + + + + + susceptible_death_rate + susceptible + + + + + + + + + + + + + infected_normal_death_rate + infected_normal + + + + + + + + + + + + + infected_moderate_death_rate + infected_moderate + + + + + + + + + + + + + infected_weak_death_rate + infected_weak + + + + + + + + + + + + + treated_normal_death_rate + treated_normal + + + + + + + + + + + + + treated_moderate_death_rate + treated_moderate + + + + + + + + + + + + + treated_weak_death_rate + treated_weak + + + + + + + diff --git a/v2/Rahman_MBS2016/observables_Rahman_MBS2016.tsv b/v2/Rahman_MBS2016/observables_Rahman_MBS2016.tsv new file mode 100644 index 0000000..81f62b7 --- /dev/null +++ b/v2/Rahman_MBS2016/observables_Rahman_MBS2016.tsv @@ -0,0 +1,2 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +observable_prevalence prevalence prevalence noiseParameter1_observable_prevalence noiseParameter1_observable_prevalence diff --git a/v2/Rahman_MBS2016/parameters_Rahman_MBS2016.tsv b/v2/Rahman_MBS2016/parameters_Rahman_MBS2016.tsv new file mode 100644 index 0000000..9c79855 --- /dev/null +++ b/v2/Rahman_MBS2016/parameters_Rahman_MBS2016.tsv @@ -0,0 +1,10 @@ +parameterId lowerBound upperBound nominalValue estimate priorParameters +infected_normal_transmission_rate_relative 0.1 1000.0 427.47 true +infected_moderate_transmission_rate 0.0001 1.0 0.0029273 true +infected_weak_transmission_rate_relative 0.1 1000.0 992.96 true +infected_weak_treatment_rate 0.0001 1.0 0.0001 true +infected_normal_worsen_rate 0.0001 1.0 0.66545 true +infected_moderate_worsen_rate 0.0001 1.0 0.0079757 true +treated_moderate_improve_rate 0.0001 1.0 0.13636 true +treated_weak_improve_rate 0.0001 1.0 0.77557 true +behavioural_change_rate 1e-09 1e-05 1.338e-07 true diff --git a/v2/Raia_CancerResearch2011/Raia_CancerResearch2011.yaml b/v2/Raia_CancerResearch2011/Raia_CancerResearch2011.yaml new file mode 100644 index 0000000..c71cb07 --- /dev/null +++ b/v2/Raia_CancerResearch2011/Raia_CancerResearch2011.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Raia_CancerResearch2011.tsv +model_files: + model_Raia_CancerResearch2011: + location: model_Raia_CancerResearch2011.xml + language: sbml +measurement_files: +- measurementData_Raia_CancerResearch2011.tsv +condition_files: +- experimentalCondition_Raia_CancerResearch2011.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Raia_CancerResearch2011.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Raia_CancerResearch2011/experimentalCondition_Raia_CancerResearch2011.tsv b/v2/Raia_CancerResearch2011/experimentalCondition_Raia_CancerResearch2011.tsv new file mode 100644 index 0000000..8ee865a --- /dev/null +++ b/v2/Raia_CancerResearch2011/experimentalCondition_Raia_CancerResearch2011.tsv @@ -0,0 +1,5 @@ +conditionId targetId targetValue +model1_data1 il13_level 0 +model1_data2 il13_level 20 +model1_data3 il13_level 4 +model1_data4 il13_level 80 diff --git a/v2/Raia_CancerResearch2011/experiments.tsv b/v2/Raia_CancerResearch2011/experiments.tsv new file mode 100644 index 0000000..c8b3857 --- /dev/null +++ b/v2/Raia_CancerResearch2011/experiments.tsv @@ -0,0 +1,5 @@ +experimentId conditionId time +experiment____model1_data1 model1_data1 0 +experiment____model1_data2 model1_data2 0 +experiment____model1_data3 model1_data3 0 +experiment____model1_data4 model1_data4 0 diff --git a/v2/Raia_CancerResearch2011/measurementData_Raia_CancerResearch2011.tsv b/v2/Raia_CancerResearch2011/measurementData_Raia_CancerResearch2011.tsv new file mode 100644 index 0000000..f093b22 --- /dev/null +++ b/v2/Raia_CancerResearch2011/measurementData_Raia_CancerResearch2011.tsv @@ -0,0 +1,206 @@ +experimentId observableId measurement time observableParameters noiseParameters observableTransformation noiseDistribution datasetId +experiment____model1_data1 observable_RecSurf 1.289752779 0.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data1_RecSurf +experiment____model1_data1 observable_RecSurf 1.57854438 10.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data1_RecSurf +experiment____model1_data1 observable_RecSurf 1.515091272 20.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data1_RecSurf +experiment____model1_data1 observable_RecSurf 1.50496416 30.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data1_RecSurf +experiment____model1_data1 observable_RecSurf 1.617802874 60.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data1_RecSurf +experiment____model1_data1 observable_RecSurf 1.572371701 90.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data1_RecSurf +experiment____model1_data1 observable_RecSurf 1.430619477 120.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data1_RecSurf +experiment____model1_data1 observable_IL13_cell 0.615740257 0.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data1_IL13_cell +experiment____model1_data1 observable_IL13_cell 0.295868505 15.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data1_IL13_cell +experiment____model1_data1 observable_IL13_cell 0.322285203 30.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data1_IL13_cell +experiment____model1_data1 observable_IL13_cell 0.169527777 60.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data1_IL13_cell +experiment____model1_data1 observable_IL13_cell 0.257966287 90.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data1_IL13_cell +experiment____model1_data1 observable_IL13_cell 0.231549589 120.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data1_IL13_cell +experiment____model1_data1 observable_SOCS3mRNA 1.562357019 0.0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data1_SOCS3mRNA +experiment____model1_data1 observable_SOCS3mRNA 0.992868163 20.0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data1_SOCS3mRNA +experiment____model1_data1 observable_SOCS3mRNA 14.83449477 30.0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data1_SOCS3mRNA +experiment____model1_data1 observable_SOCS3mRNA 11.675177 40.0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data1_SOCS3mRNA +experiment____model1_data1 observable_SOCS3mRNA 11.62681448 60.0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data1_SOCS3mRNA +experiment____model1_data1 observable_SOCS3mRNA 5.710282463 80.0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data1_SOCS3mRNA +experiment____model1_data1 observable_SOCS3mRNA 1.24343046 90.0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data1_SOCS3mRNA +experiment____model1_data1 observable_SOCS3mRNA 0.659244766 100.0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data1_SOCS3mRNA +experiment____model1_data1 observable_SOCS3mRNA 14.54733886 120.0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data1_SOCS3mRNA +experiment____model1_data1 observable_CD274mRNA 0.01 30.0 scaling_CD274mRNA sd_CD274mRNA_abs;sd_CD274mRNA_rel lin normal model1_data1_CD274mRNA +experiment____model1_data1 observable_CD274mRNA 0.042114502 60.0 scaling_CD274mRNA sd_CD274mRNA_abs;sd_CD274mRNA_rel lin normal model1_data1_CD274mRNA +experiment____model1_data1 observable_CD274mRNA 0.01 90.0 scaling_CD274mRNA sd_CD274mRNA_abs;sd_CD274mRNA_rel lin normal model1_data1_CD274mRNA +experiment____model1_data1 observable_CD274mRNA 0.009833619 120.0 scaling_CD274mRNA sd_CD274mRNA_abs;sd_CD274mRNA_rel lin normal model1_data1_CD274mRNA +experiment____model1_data1 observable_SOCS3 8.334077674 0.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data1_SOCS3 +experiment____model1_data1 observable_SOCS3 6.442655791 20.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data1_SOCS3 +experiment____model1_data1 observable_SOCS3 7.624794468 40.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data1_SOCS3 +experiment____model1_data1 observable_SOCS3 8.688719277 60.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data1_SOCS3 +experiment____model1_data1 observable_SOCS3 13.29906012 90.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data1_SOCS3 +experiment____model1_data1 observable_SOCS3 16.43172761 120.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data1_SOCS3 +experiment____model1_data2 observable_IL13_cell 3.974680793 5.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +experiment____model1_data2 observable_IL13_cell 4.129735323 10.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +experiment____model1_data2 observable_IL13_cell 5.016417523 15.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +experiment____model1_data2 observable_IL13_cell 4.932573221 20.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +experiment____model1_data2 observable_IL13_cell 6.024846242 30.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +experiment____model1_data2 observable_IL13_cell 6.352183583 40.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +experiment____model1_data2 observable_IL13_cell 5.878980129 50.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +experiment____model1_data2 observable_IL13_cell 5.07614223 60.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +experiment____model1_data2 observable_IL13_cell 6.210911678 80.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +experiment____model1_data2 observable_IL13_cell 5.946744701 100.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +experiment____model1_data2 observable_IL13_cell 5.094519064 120.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +experiment____model1_data2 observable_pIL4Ra 0.185418978 0.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +experiment____model1_data2 observable_pIL4Ra 0.442239546 4.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +experiment____model1_data2 observable_pIL4Ra 1.63082953 5.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +experiment____model1_data2 observable_pIL4Ra 1.926293409 7.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +experiment____model1_data2 observable_pIL4Ra 1.40013759 10.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +experiment____model1_data2 observable_pIL4Ra 2.223954642 15.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +experiment____model1_data2 observable_pIL4Ra 2.258737723 20.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +experiment____model1_data2 observable_pIL4Ra 1.541743723 30.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +experiment____model1_data2 observable_pIL4Ra 1.659951486 40.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +experiment____model1_data2 observable_pIL4Ra 2.283486889 45.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +experiment____model1_data2 observable_pIL4Ra 1.364989369 60.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +experiment____model1_data2 observable_pJAK2 0.221391383 0.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +experiment____model1_data2 observable_pJAK2 0.689572875 4.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +experiment____model1_data2 observable_pJAK2 1.278252103 5.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +experiment____model1_data2 observable_pJAK2 1.688749897 7.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +experiment____model1_data2 observable_pJAK2 1.388817503 10.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +experiment____model1_data2 observable_pJAK2 2.02085372 15.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +experiment____model1_data2 observable_pJAK2 2.10261027 20.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +experiment____model1_data2 observable_pJAK2 1.642938963 25.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +experiment____model1_data2 observable_pJAK2 2.055630098 30.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +experiment____model1_data2 observable_pJAK2 1.764426702 40.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +experiment____model1_data2 observable_pJAK2 1.81682256 45.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +experiment____model1_data2 observable_pJAK2 1.099656357 50.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +experiment____model1_data2 observable_pJAK2 1.480674485 60.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +experiment____model1_data2 observable_pJAK2 1.584028801 80.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +experiment____model1_data2 observable_pJAK2 0.922925871 100.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +experiment____model1_data2 observable_pJAK2 1.204385534 120.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +experiment____model1_data2 observable_SOCS3mRNA 1.399863921 0.0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data2_SOCS3mRNA +experiment____model1_data2 observable_SOCS3mRNA 15.59376831 20.0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data2_SOCS3mRNA +experiment____model1_data2 observable_SOCS3mRNA 29.66110989 30.0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data2_SOCS3mRNA +experiment____model1_data2 observable_SOCS3mRNA 250.7513584 40.0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data2_SOCS3mRNA +experiment____model1_data2 observable_SOCS3mRNA 208.0216845 60.0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data2_SOCS3mRNA +experiment____model1_data2 observable_SOCS3mRNA 719.6189149 80.0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data2_SOCS3mRNA +experiment____model1_data2 observable_SOCS3mRNA 1154.942401 90.0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data2_SOCS3mRNA +experiment____model1_data2 observable_SOCS3mRNA 504.6313426 100.0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data2_SOCS3mRNA +experiment____model1_data2 observable_SOCS3mRNA 1017.019576 120.0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data2_SOCS3mRNA +experiment____model1_data2 observable_CD274mRNA 0.01 30.0 scaling_CD274mRNA sd_CD274mRNA_abs;sd_CD274mRNA_rel lin normal model1_data2_CD274mRNA +experiment____model1_data2 observable_CD274mRNA 0.67477531 60.0 scaling_CD274mRNA sd_CD274mRNA_abs;sd_CD274mRNA_rel lin normal model1_data2_CD274mRNA +experiment____model1_data2 observable_CD274mRNA 2.304976603 90.0 scaling_CD274mRNA sd_CD274mRNA_abs;sd_CD274mRNA_rel lin normal model1_data2_CD274mRNA +experiment____model1_data2 observable_CD274mRNA 1.774992771 120.0 scaling_CD274mRNA sd_CD274mRNA_abs;sd_CD274mRNA_rel lin normal model1_data2_CD274mRNA +experiment____model1_data2 observable_SOCS3 35.10201482 0.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data2_SOCS3 +experiment____model1_data2 observable_SOCS3 23.88158667 20.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data2_SOCS3 +experiment____model1_data2 observable_SOCS3 79.71985958 40.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data2_SOCS3 +experiment____model1_data2 observable_SOCS3 148.678 60.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data2_SOCS3 +experiment____model1_data2 observable_SOCS3 259.1129009 80.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data2_SOCS3 +experiment____model1_data2 observable_SOCS3 271.9076533 90.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data2_SOCS3 +experiment____model1_data2 observable_SOCS3 255.3756956 100.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data2_SOCS3 +experiment____model1_data2 observable_SOCS3 204.4612162 120.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data2_SOCS3 +experiment____model1_data2 observable_pSTAT5 1.716733095 0.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +experiment____model1_data2 observable_pSTAT5 9.772025181 5.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +experiment____model1_data2 observable_pSTAT5 32.81159437 10.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +experiment____model1_data2 observable_pSTAT5 50.80322648 15.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +experiment____model1_data2 observable_pSTAT5 68.99256124 20.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +experiment____model1_data2 observable_pSTAT5 107.9066904 25.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +experiment____model1_data2 observable_pSTAT5 111.5714137 30.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +experiment____model1_data2 observable_pSTAT5 106.7423055 35.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +experiment____model1_data2 observable_pSTAT5 104.28 40.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +experiment____model1_data2 observable_pSTAT5 125.2740088 45.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +experiment____model1_data2 observable_pSTAT5 115.7026455 50.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +experiment____model1_data2 observable_pSTAT5 128.2373073 60.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +experiment____model1_data2 observable_pSTAT5 123.2374928 70.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +experiment____model1_data2 observable_pSTAT5 89.65411083 80.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +experiment____model1_data2 observable_pSTAT5 65.83056831 90.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +experiment____model1_data2 observable_pSTAT5 108.2978696 100.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +experiment____model1_data2 observable_pSTAT5 80.75011175 120.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +experiment____model1_data3 observable_RecSurf 1.40469351 0.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data3_RecSurf +experiment____model1_data3 observable_RecSurf 1.36298049 10.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data3_RecSurf +experiment____model1_data3 observable_RecSurf 1.333586237 20.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data3_RecSurf +experiment____model1_data3 observable_RecSurf 1.210536056 30.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data3_RecSurf +experiment____model1_data3 observable_RecSurf 1.256908767 60.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data3_RecSurf +experiment____model1_data3 observable_RecSurf 1.255595571 90.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data3_RecSurf +experiment____model1_data3 observable_RecSurf 1.230653226 120.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data3_RecSurf +experiment____model1_data3 observable_IL13_cell 1.185996361 5.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +experiment____model1_data3 observable_IL13_cell 1.458203202 10.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +experiment____model1_data3 observable_IL13_cell 1.797026064 15.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +experiment____model1_data3 observable_IL13_cell 1.783243439 20.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +experiment____model1_data3 observable_IL13_cell 2.295497663 30.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +experiment____model1_data3 observable_IL13_cell 2.470077578 40.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +experiment____model1_data3 observable_IL13_cell 2.514871109 50.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +experiment____model1_data3 observable_IL13_cell 2.656143014 60.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +experiment____model1_data3 observable_IL13_cell 2.955915105 80.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +experiment____model1_data3 observable_IL13_cell 3.199408144 100.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +experiment____model1_data3 observable_IL13_cell 2.6205379 120.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +experiment____model1_data3 observable_pIL4Ra 0.338107913 0.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +experiment____model1_data3 observable_pIL4Ra 1.084337349 4.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +experiment____model1_data3 observable_pIL4Ra 0.539111503 5.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +experiment____model1_data3 observable_pIL4Ra 0.299787385 7.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +experiment____model1_data3 observable_pIL4Ra 0.845156744 10.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +experiment____model1_data3 observable_pIL4Ra 1.175990856 15.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +experiment____model1_data3 observable_pIL4Ra 1.35788895 17.5 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +experiment____model1_data3 observable_pIL4Ra 1.442254159 20.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +experiment____model1_data3 observable_pIL4Ra 1.123066049 22.5 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +experiment____model1_data3 observable_pIL4Ra 1.551873086 25.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +experiment____model1_data3 observable_pIL4Ra 1.147885063 30.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +experiment____model1_data3 observable_pIL4Ra 0.995444907 35.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +experiment____model1_data3 observable_pIL4Ra 1.242317637 40.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +experiment____model1_data3 observable_pIL4Ra 1.28102483 45.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +experiment____model1_data3 observable_pIL4Ra 1.194533888 50.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +experiment____model1_data3 observable_pIL4Ra 1.133331567 60.0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +experiment____model1_data3 observable_pJAK2 0.187105104 0.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 0.533560311 2.5 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 0.645132088 4.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 0.639432248 5.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 0.245165007 7.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 0.152528245 7.5 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 0.834682988 10.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 1.45841689 12.5 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 1.288880253 15.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 1.275386838 17.5 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 1.432895442 20.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 0.842800855 25.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 1.36716485 30.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 1.753162054 35.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 1.434440914 40.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 1.036951691 45.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 1.150316562 50.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 1.37390999 60.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 1.216679546 75.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 1.490035697 90.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 0.365588806 105.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pJAK2 0.66753154 120.0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +experiment____model1_data3 observable_pSTAT5 1.598406966 0.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +experiment____model1_data3 observable_pSTAT5 2.012148639 5.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +experiment____model1_data3 observable_pSTAT5 7.644693901 10.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +experiment____model1_data3 observable_pSTAT5 30.339995 15.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +experiment____model1_data3 observable_pSTAT5 34.49644889 20.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +experiment____model1_data3 observable_pSTAT5 54.73958911 25.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +experiment____model1_data3 observable_pSTAT5 48.86794422 30.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +experiment____model1_data3 observable_pSTAT5 57.76829847 35.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +experiment____model1_data3 observable_pSTAT5 68.400004 40.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +experiment____model1_data3 observable_pSTAT5 57.5319745 45.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +experiment____model1_data3 observable_pSTAT5 84.08635186 50.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +experiment____model1_data3 observable_pSTAT5 80.47435164 60.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +experiment____model1_data3 observable_pSTAT5 66.61604471 70.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +experiment____model1_data3 observable_pSTAT5 57.65815916 80.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +experiment____model1_data3 observable_pSTAT5 52.79857246 100.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +experiment____model1_data3 observable_pSTAT5 56.17671662 120.0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +experiment____model1_data4 observable_RecSurf 1.321308168 0.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data4_RecSurf +experiment____model1_data4 observable_RecSurf 1.179069779 10.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data4_RecSurf +experiment____model1_data4 observable_RecSurf 1.042164123 20.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data4_RecSurf +experiment____model1_data4 observable_RecSurf 1.056526564 30.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data4_RecSurf +experiment____model1_data4 observable_RecSurf 1.056091246 60.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data4_RecSurf +experiment____model1_data4 observable_RecSurf 1.078735295 90.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data4_RecSurf +experiment____model1_data4 observable_RecSurf 0.929233191 120.0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data4_RecSurf +experiment____model1_data4 observable_IL13_cell 9.781760071 5.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +experiment____model1_data4 observable_IL13_cell 9.951745778 10.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +experiment____model1_data4 observable_IL13_cell 10.67418503 15.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +experiment____model1_data4 observable_IL13_cell 11.24846107 20.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +experiment____model1_data4 observable_IL13_cell 12.74732152 30.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +experiment____model1_data4 observable_IL13_cell 12.39816169 40.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +experiment____model1_data4 observable_IL13_cell 10.96936291 50.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +experiment____model1_data4 observable_IL13_cell 8.286345273 60.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +experiment____model1_data4 observable_IL13_cell 11.34493944 80.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +experiment____model1_data4 observable_IL13_cell 11.19792478 100.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +experiment____model1_data4 observable_IL13_cell 10.55243851 120.0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +experiment____model1_data4 observable_SOCS3 6.04829306 0.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data4_SOCS3 +experiment____model1_data4 observable_SOCS3 6.231540693 20.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data4_SOCS3 +experiment____model1_data4 observable_SOCS3 87.45060405 40.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data4_SOCS3 +experiment____model1_data4 observable_SOCS3 103.2714398 60.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data4_SOCS3 +experiment____model1_data4 observable_SOCS3 221.7408479 80.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data4_SOCS3 +experiment____model1_data4 observable_SOCS3 262.8501062 100.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data4_SOCS3 +experiment____model1_data4 observable_SOCS3 140.7680663 120.0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data4_SOCS3 diff --git a/v2/Raia_CancerResearch2011/model_Raia_CancerResearch2011.xml b/v2/Raia_CancerResearch2011/model_Raia_CancerResearch2011.xml new file mode 100644 index 0000000..5455306 --- /dev/null +++ b/v2/Raia_CancerResearch2011/model_Raia_CancerResearch2011.xml @@ -0,0 +1,441 @@ + + + + + + 
PEtab implementation of the model from Raia et al. (2011), Cancer Res February 1 2011 (71) (3) 693-704
+ + + + + + + + + + Raia + Valentina + + + + + + 2019-11-29T09:41:48Z + + + 2019-11-29T09:41:48Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + init_Rec_i + + + + + + + + + + + + + + + + cyt + 2.265 + il13_level + Kon_IL13Rec + Rec + + + + + + + + + + + + + + + + cyt + Rec + Rec_intern + + + + + + + + + + + + + + + + cyt + Rec_i + Rec_recycle + + + + + + + + + + + + + + + + + + + cyt + IL13_Rec + Rec_phosphorylation + pJAK2 + + + + + + + + + + + + + + + + + + + + cyt + + + + + IL13_Rec + JAK2 + JAK2_phosphorylation + + + + + + JAK2_p_inhibition + SOCS3 + + 1 + + + + + + + + + + + + + + + + + + + + + + cyt + + + + + JAK2 + JAK2_phosphorylation + p_IL13_Rec + + + + + + JAK2_p_inhibition + SOCS3 + + 1 + + + + + + + + + + + + + + + + + + cyt + pRec_intern + p_IL13_Rec + + + + + + + + + + + + + cyt + pRec_degradation + p_IL13_Rec_i + + + + + + + + + + + + + + + + cyt + 91 + pJAK2 + pJAK2_dephosphorylation + + + + + + + + + + + + + + + + + + + cyt + STAT5 + STAT5_phosphorylation + pJAK2 + + + + + + + + + + + + + + + + cyt + 91 + pSTAT5 + pSTAT5_dephosphorylation + + + + + + + + + + + + + + + + cyt + 2.265 + il13_level + DecoyR + DecoyR_binding + + + + + + + + + + + + + + + + nuc + SOCS3mRNA_production + pSTAT5 + + + + + + + + + + + + + + + + cyt + + + + + SOCS3mRNA + SOCS3_translation + + + + SOCS3mRNA + SOCS3_accumulation + + + + + + + + + + + + + + + cyt + SOCS3 + SOCS3_degradation + + + + + + + + + + + + + + + + nuc + CD274mRNA_production + pSTAT5 + + + + + + + diff --git a/v2/Raia_CancerResearch2011/observables_Raia_CancerResearch2011.tsv b/v2/Raia_CancerResearch2011/observables_Raia_CancerResearch2011.tsv new file mode 100644 index 0000000..09ceafc --- /dev/null +++ b/v2/Raia_CancerResearch2011/observables_Raia_CancerResearch2011.tsv @@ -0,0 +1,9 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +observable_CD274mRNA CD274mRNA * observableParameter1_observable_CD274mRNA noiseParameter1_observable_CD274mRNA + noiseParameter2_observable_CD274mRNA * (CD274mRNA * observableParameter1_observable_CD274mRNA) observableParameter1_observable_CD274mRNA noiseParameter1_observable_CD274mRNA;noiseParameter2_observable_CD274mRNA +observable_IL13_cell observableParameter1_observable_IL13_cell * (IL13_Rec + IL13_DecoyR + p_IL13_Rec + p_IL13_Rec_i) noiseParameter1_observable_IL13_cell + noiseParameter2_observable_IL13_cell * (observableParameter1_observable_IL13_cell * (IL13_Rec + IL13_DecoyR + p_IL13_Rec + p_IL13_Rec_i)) observableParameter1_observable_IL13_cell noiseParameter1_observable_IL13_cell;noiseParameter2_observable_IL13_cell +observable_RecSurf IL13_Rec + Rec + p_IL13_Rec noiseParameter1_observable_RecSurf + noiseParameter2_observable_RecSurf * (IL13_Rec + Rec + p_IL13_Rec) noiseParameter1_observable_RecSurf;noiseParameter2_observable_RecSurf +observable_SOCS3 SOCS3 noiseParameter1_observable_SOCS3 + noiseParameter2_observable_SOCS3 * SOCS3 noiseParameter1_observable_SOCS3;noiseParameter2_observable_SOCS3 +observable_SOCS3mRNA SOCS3mRNA * observableParameter1_observable_SOCS3mRNA noiseParameter1_observable_SOCS3mRNA + noiseParameter2_observable_SOCS3mRNA * (SOCS3mRNA * observableParameter1_observable_SOCS3mRNA) observableParameter1_observable_SOCS3mRNA noiseParameter1_observable_SOCS3mRNA;noiseParameter2_observable_SOCS3mRNA +observable_pIL4Ra observableParameter1_observable_pIL4Ra * (p_IL13_Rec + p_IL13_Rec_i) noiseParameter1_observable_pIL4Ra + noiseParameter2_observable_pIL4Ra * (observableParameter1_observable_pIL4Ra * (p_IL13_Rec + p_IL13_Rec_i)) observableParameter1_observable_pIL4Ra noiseParameter1_observable_pIL4Ra;noiseParameter2_observable_pIL4Ra +observable_pJAK2 pJAK2 * observableParameter1_observable_pJAK2 noiseParameter1_observable_pJAK2 + noiseParameter2_observable_pJAK2 * (pJAK2 * observableParameter1_observable_pJAK2) observableParameter1_observable_pJAK2 noiseParameter1_observable_pJAK2;noiseParameter2_observable_pJAK2 +observable_pSTAT5 pSTAT5 noiseParameter1_observable_pSTAT5 + noiseParameter2_observable_pSTAT5 * pSTAT5 noiseParameter1_observable_pSTAT5;noiseParameter2_observable_pSTAT5 diff --git a/v2/Raia_CancerResearch2011/parameters_Raia_CancerResearch2011.tsv b/v2/Raia_CancerResearch2011/parameters_Raia_CancerResearch2011.tsv new file mode 100644 index 0000000..e9c70a0 --- /dev/null +++ b/v2/Raia_CancerResearch2011/parameters_Raia_CancerResearch2011.tsv @@ -0,0 +1,40 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorParameters +CD274mRNA_production CD274mRNA_{production} 1e-05 1000 0.021208853684209 true +DecoyR_binding DecoyR_{binding} 1e-05 1000 0.003851039137402 true +JAK2_p_inhibition JAK2_{p,inhibition} 1e-05 1000 0.078140000505809 true +JAK2_phosphorylation JAK2_{phosphorylation} 1e-05 1000 1.01721171826747 true +Kon_IL13Rec Kon_{IL13Rec} 1e-05 1000 0.002278141087201 true +Rec_intern Rec_{intern} 1e-05 1000 0.344129281159739 true +Rec_phosphorylation Rec_{phosphorylation} 1e-05 1000 999.999816483984 true +Rec_recycle Rec_{recycle} 1e-05 1000 0.00209774906794 true +SOCS3_accumulation SOCS3_{accumulation} 1e-05 1000 451.777901711184 true +SOCS3_degradation SOCS3_{degradation} 1e-05 1000 0.043380223348167 true +SOCS3_translation SOCS3_{translation} 1e-05 1000 15.7186888386006 true +SOCS3mRNA_production SOCS3mRNA_{production} 1e-05 1000 0.14337151776186 true +STAT5_phosphorylation STAT5_{phosphorylation} 1e-05 1000 0.01948207479306 true +init_Rec_i init_{Rec,i} 1e-05 1000 235.058493601113 true +pJAK2_dephosphorylation pJAK2_{dephosphorylation} 1e-05 1000 0.000175894009439 true +pRec_degradation pRec_{degradation} 1e-05 1000 0.209573978543856 true +pRec_intern pRec_{intern} 1e-05 1000 0.585271535297764 true +pSTAT5_dephosphorylation pSTAT5_{dephosphorylation} 1e-05 1000 0.000274832319318 true +scaling_CD274mRNA scaling_{CD274mRNA} 1e-05 1000 0.00815283660871 true +scaling_IL13_cell scaling_{IL13,cell} 1e-05 1000 5.50098613841361 true +scaling_SOCS3mRNA scaling_{SOCS3mRNA} 1e-05 1000 0.581287913862507 true +scaling_pIL4Ra scaling_{pIL4Ra} 1e-05 1000 2.9757729322919 true +scaling_pJAK2 scaling_{pJAK2} 1e-05 1000 0.857246885626022 true +sd_SOCS3mRNA_abs sd_SOCS3mRNA_abs 1e-05 1000 9.2 true +sd_RecSurf_abs sd_RecSurf_abs 1e-05 1000 1e-05 true +sd_pSTAT5_rel sd_pSTAT5_rel 1e-05 1000 0.18 true +sd_IL13_cell_rel sd_IL13_cell_rel 1e-05 1000 0.065 true +sd_RecSurf_rel sd_RecSurf_rel 1e-05 1000 0.078 true +sd_pJAK2_abs sd_pJAK2_abs 1e-05 1000 0.32 true +sd_pIL4Ra_abs sd_pIL4Ra_abs 1e-05 1000 0.62 true +sd_CD274mRNA_rel sd_CD274mRNA_rel 1e-05 1000 0.61 true +sd_SOCS3mRNA_rel sd_SOCS3mRNA_rel 1e-05 1000 0.52 true +sd_pIL4Ra_rel sd_pIL4Ra_rel 1e-05 1000 1.1e-05 true +sd_IL13_cell_abs sd_IL13_cell_abs 1e-05 1000 0.28 true +sd_SOCS3_rel sd_SOCS3_rel 1e-05 1000 0.18 true +sd_CD274mRNA_abs sd_CD274mRNA_abs 1e-05 1000 0.024 true +sd_pSTAT5_abs sd_pSTAT5_abs 1e-05 1000 1.4 true +sd_SOCS3_abs sd_SOCS3_abs 1e-05 1000 15.0 true +sd_pJAK2_rel sd_pJAK2_rel 1e-05 1000 1e-05 true diff --git a/v2/Raimundez_PCB2020/Raimundez_PCB2020.yaml b/v2/Raimundez_PCB2020/Raimundez_PCB2020.yaml new file mode 100644 index 0000000..0d5eac5 --- /dev/null +++ b/v2/Raimundez_PCB2020/Raimundez_PCB2020.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Raimundez_PCB2020.tsv +model_files: + model_Raimundez_PCB2020: + location: model_Raimundez_PCB2020.xml + language: sbml +measurement_files: +- measurementData_Raimundez_PCB2020.tsv +condition_files: +- experimentalCondition_Raimundez_PCB2020.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Raimundez_PCB2020.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Raimundez_PCB2020/experimentalCondition_Raimundez_PCB2020.tsv b/v2/Raimundez_PCB2020/experimentalCondition_Raimundez_PCB2020.tsv new file mode 100644 index 0000000..d5d3ee2 --- /dev/null +++ b/v2/Raimundez_PCB2020/experimentalCondition_Raimundez_PCB2020.tsv @@ -0,0 +1,1393 @@ +conditionId targetId targetValue +model1_data1 CET_level 0.0 +model1_data2 CET_level 0.0 +model1_data3 CET_level 0.0 +model1_data4 CET_level 0.0 +model1_data5 CET_level 0.0 +model1_data6 CET_level 0.0 +model1_data7 CET_level 0.0 +model1_data8 CET_level 1.0 +model1_data9 CET_level 50.0 +model1_data10 CET_level 0.0 +model1_data11 CET_level 1.0 +model1_data12 CET_level 50.0 +model1_data13 CET_level 0.0 +model1_data14 CET_level 0.1 +model1_data15 CET_level 1.0 +model1_data16 CET_level 0.0 +model1_data17 CET_level 0.1 +model1_data18 CET_level 1.0 +model1_data19 CET_level 0.0 +model1_data20 CET_level 1.0 +model1_data21 CET_level 50.0 +model1_data22 CET_level 0.0 +model1_data23 CET_level 1.0 +model1_data24 CET_level 50.0 +model1_data25 CET_level 0.0 +model1_data26 CET_level 0.1 +model1_data27 CET_level 1.0 +model1_data28 CET_level 0.0 +model1_data29 CET_level 0.1 +model1_data30 CET_level 1.0 +model1_data31 CET_level 0.0 +model1_data32 CET_level 0.05 +model1_data33 CET_level 0.1 +model1_data34 CET_level 1.0 +model1_data35 CET_level 10.0 +model1_data36 CET_level 0.0 +model1_data37 CET_level 0.05 +model1_data38 CET_level 0.1 +model1_data39 CET_level 1.0 +model1_data40 CET_level 10.0 +model1_data41 CET_level 0.0 +model1_data42 CET_level 0.05 +model1_data43 CET_level 0.1 +model1_data44 CET_level 1.0 +model1_data45 CET_level 10.0 +model1_data46 CET_level 0.0 +model1_data47 CET_level 0.05 +model1_data48 CET_level 0.1 +model1_data49 CET_level 1.0 +model1_data50 CET_level 10.0 +model1_data51 CET_level 0.0 +model1_data52 CET_level 0.05 +model1_data53 CET_level 0.1 +model1_data54 CET_level 1.0 +model1_data55 CET_level 10.0 +model1_data56 CET_level 0.0 +model1_data57 CET_level 0.05 +model1_data58 CET_level 0.1 +model1_data59 CET_level 1.0 +model1_data60 CET_level 10.0 +model1_data61 CET_level 0.0 +model1_data62 CET_level 0.05 +model1_data63 CET_level 0.1 +model1_data64 CET_level 1.0 +model1_data65 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b/v2/Raimundez_PCB2020/observables_Raimundez_PCB2020.tsv @@ -0,0 +1,80 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +EGFR_ID10_HS746T_FM_EGF_CET EGFR_ID10_HS746T_FM_EGF_CET observableParameter1_EGFR_ID10_HS746T_FM_EGF_CET*(EGFR + EGFR_EGF + EGFR_CET + 2*EGFR_EGF_2 + EGFR_MMET_METinh + MMET_EGFR + 2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_EGFR_ID10_HS746T_FM_EGF_CET observableParameter1_EGFR_ID10_HS746T_FM_EGF_CET noiseParameter1_EGFR_ID10_HS746T_FM_EGF_CET +EGFR_ID10_HS746T_FM_EGF EGFR_ID10_HS746T_FM_EGF observableParameter1_EGFR_ID10_HS746T_FM_EGF*(EGFR + EGFR_EGF + EGFR_CET + 2*EGFR_EGF_2 + EGFR_MMET_METinh + MMET_EGFR + 2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_EGFR_ID10_HS746T_FM_EGF observableParameter1_EGFR_ID10_HS746T_FM_EGF noiseParameter1_EGFR_ID10_HS746T_FM_EGF +EGFR_ID12_MKN1_FM_HM EGFR_ID12_MKN1_FM_HM observableParameter1_EGFR_ID12_MKN1_FM_HM*(EGFR + EGFR_EGF + EGFR_CET + 2*EGFR_EGF_2 + EGFR_MMET_METinh + MMET_EGFR + 2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_EGFR_ID12_MKN1_FM_HM observableParameter1_EGFR_ID12_MKN1_FM_HM noiseParameter1_EGFR_ID12_MKN1_FM_HM +EGFR_ID3_HS746T_FM EGFR_ID3_HS746T_FM observableParameter1_EGFR_ID3_HS746T_FM*(EGFR + EGFR_EGF + EGFR_CET + 2*EGFR_EGF_2 + EGFR_MMET_METinh + MMET_EGFR + 2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_EGFR_ID3_HS746T_FM observableParameter1_EGFR_ID3_HS746T_FM noiseParameter1_EGFR_ID3_HS746T_FM +EGFR_ID3_MKN1_FM EGFR_ID3_MKN1_FM observableParameter1_EGFR_ID3_MKN1_FM*(EGFR + EGFR_EGF + EGFR_CET + 2*EGFR_EGF_2 + EGFR_MMET_METinh + MMET_EGFR + 2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_EGFR_ID3_MKN1_FM observableParameter1_EGFR_ID3_MKN1_FM noiseParameter1_EGFR_ID3_MKN1_FM +EGFR_ID4_HS746T_HM_3min EGFR_ID4_HS746T_HM_3min observableParameter1_EGFR_ID4_HS746T_HM_3min*(EGFR + EGFR_EGF + EGFR_CET + 2*EGFR_EGF_2 + EGFR_MMET_METinh + MMET_EGFR + 2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_EGFR_ID4_HS746T_HM_3min observableParameter1_EGFR_ID4_HS746T_HM_3min noiseParameter1_EGFR_ID4_HS746T_HM_3min +EGFR_ID4_MKN1_HM_3min EGFR_ID4_MKN1_HM_3min observableParameter1_EGFR_ID4_MKN1_HM_3min*(EGFR + EGFR_EGF + EGFR_CET + 2*EGFR_EGF_2 + EGFR_MMET_METinh + MMET_EGFR + 2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_EGFR_ID4_MKN1_HM_3min observableParameter1_EGFR_ID4_MKN1_HM_3min noiseParameter1_EGFR_ID4_MKN1_HM_3min +MMET_ID10_HS746T_FM_EGF_CET MMET_ID10_HS746T_FM_EGF_CET observableParameter1_MMET_ID10_HS746T_FM_EGF_CET*(EGFR_MMET_METinh + MMET + 2*MMET_2 + MMET_EGFR + MMET_METinh + 2*MMET_METinh_2 + 2*MMET_MMET_METinh + 2*pMMET_2 + 2*pMMET_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_MMET_ID10_HS746T_FM_EGF_CET observableParameter1_MMET_ID10_HS746T_FM_EGF_CET noiseParameter1_MMET_ID10_HS746T_FM_EGF_CET +MMET_ID10_HS746T_FM_EGF MMET_ID10_HS746T_FM_EGF observableParameter1_MMET_ID10_HS746T_FM_EGF*(EGFR_MMET_METinh + MMET + 2*MMET_2 + MMET_EGFR + MMET_METinh + 2*MMET_METinh_2 + 2*MMET_MMET_METinh + 2*pMMET_2 + 2*pMMET_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_MMET_ID10_HS746T_FM_EGF observableParameter1_MMET_ID10_HS746T_FM_EGF noiseParameter1_MMET_ID10_HS746T_FM_EGF +pAKT_ID12_MKN1_FM_HM pAKT_ID12_MKN1_FM_HM pAKT*observableParameter1_pAKT_ID12_MKN1_FM_HM noiseParameter1_pAKT_ID12_MKN1_FM_HM observableParameter1_pAKT_ID12_MKN1_FM_HM noiseParameter1_pAKT_ID12_MKN1_FM_HM +pAKT_ID2_HS746T_HM pAKT_ID2_HS746T_HM pAKT*observableParameter1_pAKT_ID2_HS746T_HM noiseParameter1_pAKT_ID2_HS746T_HM observableParameter1_pAKT_ID2_HS746T_HM noiseParameter1_pAKT_ID2_HS746T_HM +pAKT_ID2_MKN1_HM pAKT_ID2_MKN1_HM pAKT*observableParameter1_pAKT_ID2_MKN1_HM noiseParameter1_pAKT_ID2_MKN1_HM observableParameter1_pAKT_ID2_MKN1_HM noiseParameter1_pAKT_ID2_MKN1_HM +pAKT_ID5_MKN1_FM_15min pAKT_ID5_MKN1_FM_15min pAKT*observableParameter1_pAKT_ID5_MKN1_FM_15min noiseParameter1_pAKT_ID5_MKN1_FM_15min observableParameter1_pAKT_ID5_MKN1_FM_15min noiseParameter1_pAKT_ID5_MKN1_FM_15min +pAKT_ID5_MKN1_FM_1min pAKT_ID5_MKN1_FM_1min pAKT*observableParameter1_pAKT_ID5_MKN1_FM_1min noiseParameter1_pAKT_ID5_MKN1_FM_1min observableParameter1_pAKT_ID5_MKN1_FM_1min noiseParameter1_pAKT_ID5_MKN1_FM_1min +pAKT_ID5_MKN1_FM_240min pAKT_ID5_MKN1_FM_240min pAKT*observableParameter1_pAKT_ID5_MKN1_FM_240min noiseParameter1_pAKT_ID5_MKN1_FM_240min observableParameter1_pAKT_ID5_MKN1_FM_240min noiseParameter1_pAKT_ID5_MKN1_FM_240min +pAKT_ID5_MKN1_FM_3min pAKT_ID5_MKN1_FM_3min pAKT*observableParameter1_pAKT_ID5_MKN1_FM_3min noiseParameter1_pAKT_ID5_MKN1_FM_3min observableParameter1_pAKT_ID5_MKN1_FM_3min noiseParameter1_pAKT_ID5_MKN1_FM_3min +pAKT_ID7_HS746T_FM_15min pAKT_ID7_HS746T_FM_15min pAKT*observableParameter1_pAKT_ID7_HS746T_FM_15min noiseParameter1_pAKT_ID7_HS746T_FM_15min observableParameter1_pAKT_ID7_HS746T_FM_15min noiseParameter1_pAKT_ID7_HS746T_FM_15min +pAKT_ID7_HS746T_FM_1min pAKT_ID7_HS746T_FM_1min pAKT*observableParameter1_pAKT_ID7_HS746T_FM_1min noiseParameter1_pAKT_ID7_HS746T_FM_1min observableParameter1_pAKT_ID7_HS746T_FM_1min noiseParameter1_pAKT_ID7_HS746T_FM_1min +pAKT_ID7_HS746T_FM_240min pAKT_ID7_HS746T_FM_240min pAKT*observableParameter1_pAKT_ID7_HS746T_FM_240min noiseParameter1_pAKT_ID7_HS746T_FM_240min observableParameter1_pAKT_ID7_HS746T_FM_240min noiseParameter1_pAKT_ID7_HS746T_FM_240min +pAKT_ID7_HS746T_FM_3min pAKT_ID7_HS746T_FM_3min pAKT*observableParameter1_pAKT_ID7_HS746T_FM_3min noiseParameter1_pAKT_ID7_HS746T_FM_3min observableParameter1_pAKT_ID7_HS746T_FM_3min noiseParameter1_pAKT_ID7_HS746T_FM_3min +pAKT_ID8_HS746T_HM_15min pAKT_ID8_HS746T_HM_15min pAKT*observableParameter1_pAKT_ID8_HS746T_HM_15min noiseParameter1_pAKT_ID8_HS746T_HM_15min observableParameter1_pAKT_ID8_HS746T_HM_15min noiseParameter1_pAKT_ID8_HS746T_HM_15min +pAKT_ID8_HS746T_HM_1min pAKT_ID8_HS746T_HM_1min pAKT*observableParameter1_pAKT_ID8_HS746T_HM_1min noiseParameter1_pAKT_ID8_HS746T_HM_1min observableParameter1_pAKT_ID8_HS746T_HM_1min noiseParameter1_pAKT_ID8_HS746T_HM_1min +pAKT_ID8_HS746T_HM_240min pAKT_ID8_HS746T_HM_240min pAKT*observableParameter1_pAKT_ID8_HS746T_HM_240min noiseParameter1_pAKT_ID8_HS746T_HM_240min observableParameter1_pAKT_ID8_HS746T_HM_240min noiseParameter1_pAKT_ID8_HS746T_HM_240min +pAKT_ID8_HS746T_HM_3min pAKT_ID8_HS746T_HM_3min pAKT*observableParameter1_pAKT_ID8_HS746T_HM_3min noiseParameter1_pAKT_ID8_HS746T_HM_3min observableParameter1_pAKT_ID8_HS746T_HM_3min noiseParameter1_pAKT_ID8_HS746T_HM_3min +pAKT_ID9_HS746T_FM pAKT_ID9_HS746T_FM pAKT*observableParameter1_pAKT_ID9_HS746T_FM noiseParameter1_pAKT_ID9_HS746T_FM observableParameter1_pAKT_ID9_HS746T_FM noiseParameter1_pAKT_ID9_HS746T_FM +pAKT_ID9_HS746T_HM_30EGF pAKT_ID9_HS746T_HM_30EGF pAKT*observableParameter1_pAKT_ID9_HS746T_HM_30EGF noiseParameter1_pAKT_ID9_HS746T_HM_30EGF observableParameter1_pAKT_ID9_HS746T_HM_30EGF noiseParameter1_pAKT_ID9_HS746T_HM_30EGF +pAKT_ID9_HS746T_HM_5EGF pAKT_ID9_HS746T_HM_5EGF pAKT*observableParameter1_pAKT_ID9_HS746T_HM_5EGF noiseParameter1_pAKT_ID9_HS746T_HM_5EGF observableParameter1_pAKT_ID9_HS746T_HM_5EGF noiseParameter1_pAKT_ID9_HS746T_HM_5EGF +pEGFR_ID10_HS746T_FM_EGF_CET pEGFR_ID10_HS746T_FM_EGF_CET observableParameter1_pEGFR_ID10_HS746T_FM_EGF_CET*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID10_HS746T_FM_EGF_CET observableParameter1_pEGFR_ID10_HS746T_FM_EGF_CET noiseParameter1_pEGFR_ID10_HS746T_FM_EGF_CET +pEGFR_ID10_HS746T_FM_EGF pEGFR_ID10_HS746T_FM_EGF observableParameter1_pEGFR_ID10_HS746T_FM_EGF*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID10_HS746T_FM_EGF observableParameter1_pEGFR_ID10_HS746T_FM_EGF noiseParameter1_pEGFR_ID10_HS746T_FM_EGF +pEGFR_ID12_MKN1_FM_HM pEGFR_ID12_MKN1_FM_HM observableParameter1_pEGFR_ID12_MKN1_FM_HM*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID12_MKN1_FM_HM observableParameter1_pEGFR_ID12_MKN1_FM_HM noiseParameter1_pEGFR_ID12_MKN1_FM_HM +pEGFR_ID2_HS746T_HM pEGFR_ID2_HS746T_HM observableParameter1_pEGFR_ID2_HS746T_HM*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID2_HS746T_HM observableParameter1_pEGFR_ID2_HS746T_HM noiseParameter1_pEGFR_ID2_HS746T_HM +pEGFR_ID2_MKN1_HM pEGFR_ID2_MKN1_HM observableParameter1_pEGFR_ID2_MKN1_HM*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID2_MKN1_HM observableParameter1_pEGFR_ID2_MKN1_HM noiseParameter1_pEGFR_ID2_MKN1_HM +pEGFR_ID3_HS746T_FM pEGFR_ID3_HS746T_FM observableParameter1_pEGFR_ID3_HS746T_FM*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID3_HS746T_FM observableParameter1_pEGFR_ID3_HS746T_FM noiseParameter1_pEGFR_ID3_HS746T_FM +pEGFR_ID3_MKN1_FM pEGFR_ID3_MKN1_FM observableParameter1_pEGFR_ID3_MKN1_FM*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID3_MKN1_FM observableParameter1_pEGFR_ID3_MKN1_FM noiseParameter1_pEGFR_ID3_MKN1_FM +pEGFR_ID4_HS746T_HM_3min pEGFR_ID4_HS746T_HM_3min observableParameter1_pEGFR_ID4_HS746T_HM_3min*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID4_HS746T_HM_3min observableParameter1_pEGFR_ID4_HS746T_HM_3min noiseParameter1_pEGFR_ID4_HS746T_HM_3min +pEGFR_ID4_MKN1_HM_3min pEGFR_ID4_MKN1_HM_3min observableParameter1_pEGFR_ID4_MKN1_HM_3min*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID4_MKN1_HM_3min observableParameter1_pEGFR_ID4_MKN1_HM_3min noiseParameter1_pEGFR_ID4_MKN1_HM_3min +pEGFR_ID5_MKN1_FM_15min pEGFR_ID5_MKN1_FM_15min observableParameter1_pEGFR_ID5_MKN1_FM_15min*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID5_MKN1_FM_15min observableParameter1_pEGFR_ID5_MKN1_FM_15min noiseParameter1_pEGFR_ID5_MKN1_FM_15min +pEGFR_ID5_MKN1_FM_1min pEGFR_ID5_MKN1_FM_1min observableParameter1_pEGFR_ID5_MKN1_FM_1min*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID5_MKN1_FM_1min observableParameter1_pEGFR_ID5_MKN1_FM_1min noiseParameter1_pEGFR_ID5_MKN1_FM_1min +pEGFR_ID5_MKN1_FM_240min pEGFR_ID5_MKN1_FM_240min observableParameter1_pEGFR_ID5_MKN1_FM_240min*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID5_MKN1_FM_240min observableParameter1_pEGFR_ID5_MKN1_FM_240min noiseParameter1_pEGFR_ID5_MKN1_FM_240min +pEGFR_ID5_MKN1_FM_3min pEGFR_ID5_MKN1_FM_3min observableParameter1_pEGFR_ID5_MKN1_FM_3min*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID5_MKN1_FM_3min observableParameter1_pEGFR_ID5_MKN1_FM_3min noiseParameter1_pEGFR_ID5_MKN1_FM_3min +pEGFR_ID6_MKN1_HM_15min pEGFR_ID6_MKN1_HM_15min observableParameter1_pEGFR_ID6_MKN1_HM_15min*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID6_MKN1_HM_15min observableParameter1_pEGFR_ID6_MKN1_HM_15min noiseParameter1_pEGFR_ID6_MKN1_HM_15min +pEGFR_ID6_MKN1_HM_1min pEGFR_ID6_MKN1_HM_1min observableParameter1_pEGFR_ID6_MKN1_HM_1min*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID6_MKN1_HM_1min observableParameter1_pEGFR_ID6_MKN1_HM_1min noiseParameter1_pEGFR_ID6_MKN1_HM_1min +pEGFR_ID6_MKN1_HM_240min pEGFR_ID6_MKN1_HM_240min observableParameter1_pEGFR_ID6_MKN1_HM_240min*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID6_MKN1_HM_240min observableParameter1_pEGFR_ID6_MKN1_HM_240min noiseParameter1_pEGFR_ID6_MKN1_HM_240min +pEGFR_ID6_MKN1_HM_3min pEGFR_ID6_MKN1_HM_3min observableParameter1_pEGFR_ID6_MKN1_HM_3min*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID6_MKN1_HM_3min observableParameter1_pEGFR_ID6_MKN1_HM_3min noiseParameter1_pEGFR_ID6_MKN1_HM_3min +pEGFR_ID7_HS746T_FM_15min pEGFR_ID7_HS746T_FM_15min observableParameter1_pEGFR_ID7_HS746T_FM_15min*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID7_HS746T_FM_15min observableParameter1_pEGFR_ID7_HS746T_FM_15min noiseParameter1_pEGFR_ID7_HS746T_FM_15min +pEGFR_ID7_HS746T_FM_1min pEGFR_ID7_HS746T_FM_1min observableParameter1_pEGFR_ID7_HS746T_FM_1min*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID7_HS746T_FM_1min observableParameter1_pEGFR_ID7_HS746T_FM_1min noiseParameter1_pEGFR_ID7_HS746T_FM_1min +pEGFR_ID7_HS746T_FM_240min pEGFR_ID7_HS746T_FM_240min observableParameter1_pEGFR_ID7_HS746T_FM_240min*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID7_HS746T_FM_240min observableParameter1_pEGFR_ID7_HS746T_FM_240min noiseParameter1_pEGFR_ID7_HS746T_FM_240min +pEGFR_ID7_HS746T_FM_3min pEGFR_ID7_HS746T_FM_3min observableParameter1_pEGFR_ID7_HS746T_FM_3min*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID7_HS746T_FM_3min observableParameter1_pEGFR_ID7_HS746T_FM_3min noiseParameter1_pEGFR_ID7_HS746T_FM_3min +pEGFR_ID8_HS746T_HM_15min pEGFR_ID8_HS746T_HM_15min observableParameter1_pEGFR_ID8_HS746T_HM_15min*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID8_HS746T_HM_15min observableParameter1_pEGFR_ID8_HS746T_HM_15min noiseParameter1_pEGFR_ID8_HS746T_HM_15min +pEGFR_ID8_HS746T_HM_1min pEGFR_ID8_HS746T_HM_1min observableParameter1_pEGFR_ID8_HS746T_HM_1min*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID8_HS746T_HM_1min observableParameter1_pEGFR_ID8_HS746T_HM_1min noiseParameter1_pEGFR_ID8_HS746T_HM_1min +pEGFR_ID8_HS746T_HM_240min pEGFR_ID8_HS746T_HM_240min observableParameter1_pEGFR_ID8_HS746T_HM_240min*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID8_HS746T_HM_240min observableParameter1_pEGFR_ID8_HS746T_HM_240min noiseParameter1_pEGFR_ID8_HS746T_HM_240min +pEGFR_ID8_HS746T_HM_3min pEGFR_ID8_HS746T_HM_3min observableParameter1_pEGFR_ID8_HS746T_HM_3min*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID8_HS746T_HM_3min observableParameter1_pEGFR_ID8_HS746T_HM_3min noiseParameter1_pEGFR_ID8_HS746T_HM_3min +pEGFR_ID9_HS746T_FM pEGFR_ID9_HS746T_FM observableParameter1_pEGFR_ID9_HS746T_FM*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID9_HS746T_FM observableParameter1_pEGFR_ID9_HS746T_FM noiseParameter1_pEGFR_ID9_HS746T_FM +pEGFR_ID9_HS746T_HM_30EGF pEGFR_ID9_HS746T_HM_30EGF observableParameter1_pEGFR_ID9_HS746T_HM_30EGF*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID9_HS746T_HM_30EGF observableParameter1_pEGFR_ID9_HS746T_HM_30EGF noiseParameter1_pEGFR_ID9_HS746T_HM_30EGF +pEGFR_ID9_HS746T_HM_5EGF pEGFR_ID9_HS746T_HM_5EGF observableParameter1_pEGFR_ID9_HS746T_HM_5EGF*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID9_HS746T_HM_5EGF observableParameter1_pEGFR_ID9_HS746T_HM_5EGF noiseParameter1_pEGFR_ID9_HS746T_HM_5EGF +pEGFR_ID9b_MKN1_HM_1EGF pEGFR_ID9b_MKN1_HM_1EGF observableParameter1_pEGFR_ID9b_MKN1_HM_1EGF*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID9b_MKN1_HM_1EGF observableParameter1_pEGFR_ID9b_MKN1_HM_1EGF noiseParameter1_pEGFR_ID9b_MKN1_HM_1EGF +pEGFR_ID9b_MKN1_HM_5EGF pEGFR_ID9b_MKN1_HM_5EGF observableParameter1_pEGFR_ID9b_MKN1_HM_5EGF*(2*pEGFR_EGF_2 + 2*pEGFR_EGF_2_i + pMMET_pEGFR + pMMET_pEGFR_i) noiseParameter1_pEGFR_ID9b_MKN1_HM_5EGF observableParameter1_pEGFR_ID9b_MKN1_HM_5EGF noiseParameter1_pEGFR_ID9b_MKN1_HM_5EGF +pMAPK_ID10_HS746T_FM_EGF_CET pMAPK_ID10_HS746T_FM_EGF_CET pMAPK*observableParameter1_pMAPK_ID10_HS746T_FM_EGF_CET noiseParameter1_pMAPK_ID10_HS746T_FM_EGF_CET observableParameter1_pMAPK_ID10_HS746T_FM_EGF_CET noiseParameter1_pMAPK_ID10_HS746T_FM_EGF_CET +pMAPK_ID10_HS746T_FM_EGF pMAPK_ID10_HS746T_FM_EGF pMAPK*observableParameter1_pMAPK_ID10_HS746T_FM_EGF noiseParameter1_pMAPK_ID10_HS746T_FM_EGF observableParameter1_pMAPK_ID10_HS746T_FM_EGF noiseParameter1_pMAPK_ID10_HS746T_FM_EGF +pMAPK_ID12_MKN1_FM_HM pMAPK_ID12_MKN1_FM_HM pMAPK*observableParameter1_pMAPK_ID12_MKN1_FM_HM noiseParameter1_pMAPK_ID12_MKN1_FM_HM observableParameter1_pMAPK_ID12_MKN1_FM_HM noiseParameter1_pMAPK_ID12_MKN1_FM_HM +pMAPK_ID2_HS746T_HM pMAPK_ID2_HS746T_HM pMAPK*observableParameter1_pMAPK_ID2_HS746T_HM noiseParameter1_pMAPK_ID2_HS746T_HM observableParameter1_pMAPK_ID2_HS746T_HM noiseParameter1_pMAPK_ID2_HS746T_HM +pMAPK_ID2_MKN1_HM pMAPK_ID2_MKN1_HM pMAPK*observableParameter1_pMAPK_ID2_MKN1_HM noiseParameter1_pMAPK_ID2_MKN1_HM observableParameter1_pMAPK_ID2_MKN1_HM noiseParameter1_pMAPK_ID2_MKN1_HM +pMAPK_ID5_MKN1_FM_15min pMAPK_ID5_MKN1_FM_15min pMAPK*observableParameter1_pMAPK_ID5_MKN1_FM_15min noiseParameter1_pMAPK_ID5_MKN1_FM_15min observableParameter1_pMAPK_ID5_MKN1_FM_15min noiseParameter1_pMAPK_ID5_MKN1_FM_15min +pMAPK_ID5_MKN1_FM_1min pMAPK_ID5_MKN1_FM_1min pMAPK*observableParameter1_pMAPK_ID5_MKN1_FM_1min noiseParameter1_pMAPK_ID5_MKN1_FM_1min observableParameter1_pMAPK_ID5_MKN1_FM_1min noiseParameter1_pMAPK_ID5_MKN1_FM_1min +pMAPK_ID5_MKN1_FM_240min pMAPK_ID5_MKN1_FM_240min pMAPK*observableParameter1_pMAPK_ID5_MKN1_FM_240min noiseParameter1_pMAPK_ID5_MKN1_FM_240min observableParameter1_pMAPK_ID5_MKN1_FM_240min noiseParameter1_pMAPK_ID5_MKN1_FM_240min +pMAPK_ID5_MKN1_FM_3min pMAPK_ID5_MKN1_FM_3min pMAPK*observableParameter1_pMAPK_ID5_MKN1_FM_3min noiseParameter1_pMAPK_ID5_MKN1_FM_3min observableParameter1_pMAPK_ID5_MKN1_FM_3min noiseParameter1_pMAPK_ID5_MKN1_FM_3min +pMAPK_ID7_HS746T_FM_15min pMAPK_ID7_HS746T_FM_15min pMAPK*observableParameter1_pMAPK_ID7_HS746T_FM_15min noiseParameter1_pMAPK_ID7_HS746T_FM_15min observableParameter1_pMAPK_ID7_HS746T_FM_15min noiseParameter1_pMAPK_ID7_HS746T_FM_15min +pMAPK_ID7_HS746T_FM_1min pMAPK_ID7_HS746T_FM_1min pMAPK*observableParameter1_pMAPK_ID7_HS746T_FM_1min noiseParameter1_pMAPK_ID7_HS746T_FM_1min observableParameter1_pMAPK_ID7_HS746T_FM_1min noiseParameter1_pMAPK_ID7_HS746T_FM_1min +pMAPK_ID7_HS746T_FM_240min pMAPK_ID7_HS746T_FM_240min pMAPK*observableParameter1_pMAPK_ID7_HS746T_FM_240min noiseParameter1_pMAPK_ID7_HS746T_FM_240min observableParameter1_pMAPK_ID7_HS746T_FM_240min noiseParameter1_pMAPK_ID7_HS746T_FM_240min +pMAPK_ID7_HS746T_FM_3min pMAPK_ID7_HS746T_FM_3min pMAPK*observableParameter1_pMAPK_ID7_HS746T_FM_3min noiseParameter1_pMAPK_ID7_HS746T_FM_3min observableParameter1_pMAPK_ID7_HS746T_FM_3min noiseParameter1_pMAPK_ID7_HS746T_FM_3min +pMAPK_ID8_HS746T_HM_15min pMAPK_ID8_HS746T_HM_15min pMAPK*observableParameter1_pMAPK_ID8_HS746T_HM_15min noiseParameter1_pMAPK_ID8_HS746T_HM_15min observableParameter1_pMAPK_ID8_HS746T_HM_15min noiseParameter1_pMAPK_ID8_HS746T_HM_15min +pMAPK_ID8_HS746T_HM_1min pMAPK_ID8_HS746T_HM_1min pMAPK*observableParameter1_pMAPK_ID8_HS746T_HM_1min noiseParameter1_pMAPK_ID8_HS746T_HM_1min observableParameter1_pMAPK_ID8_HS746T_HM_1min noiseParameter1_pMAPK_ID8_HS746T_HM_1min +pMAPK_ID8_HS746T_HM_240min pMAPK_ID8_HS746T_HM_240min pMAPK*observableParameter1_pMAPK_ID8_HS746T_HM_240min noiseParameter1_pMAPK_ID8_HS746T_HM_240min observableParameter1_pMAPK_ID8_HS746T_HM_240min noiseParameter1_pMAPK_ID8_HS746T_HM_240min +pMAPK_ID8_HS746T_HM_3min pMAPK_ID8_HS746T_HM_3min pMAPK*observableParameter1_pMAPK_ID8_HS746T_HM_3min noiseParameter1_pMAPK_ID8_HS746T_HM_3min observableParameter1_pMAPK_ID8_HS746T_HM_3min noiseParameter1_pMAPK_ID8_HS746T_HM_3min +pMAPK_ID9_HS746T_FM pMAPK_ID9_HS746T_FM pMAPK*observableParameter1_pMAPK_ID9_HS746T_FM noiseParameter1_pMAPK_ID9_HS746T_FM observableParameter1_pMAPK_ID9_HS746T_FM noiseParameter1_pMAPK_ID9_HS746T_FM +pMAPK_ID9_HS746T_HM_30EGF pMAPK_ID9_HS746T_HM_30EGF pMAPK*observableParameter1_pMAPK_ID9_HS746T_HM_30EGF noiseParameter1_pMAPK_ID9_HS746T_HM_30EGF observableParameter1_pMAPK_ID9_HS746T_HM_30EGF noiseParameter1_pMAPK_ID9_HS746T_HM_30EGF +pMAPK_ID9_HS746T_HM_5EGF pMAPK_ID9_HS746T_HM_5EGF pMAPK*observableParameter1_pMAPK_ID9_HS746T_HM_5EGF noiseParameter1_pMAPK_ID9_HS746T_HM_5EGF observableParameter1_pMAPK_ID9_HS746T_HM_5EGF noiseParameter1_pMAPK_ID9_HS746T_HM_5EGF +pMAPK_ID9b_MKN1_HM_1EGF pMAPK_ID9b_MKN1_HM_1EGF pMAPK*observableParameter1_pMAPK_ID9b_MKN1_HM_1EGF noiseParameter1_pMAPK_ID9b_MKN1_HM_1EGF observableParameter1_pMAPK_ID9b_MKN1_HM_1EGF noiseParameter1_pMAPK_ID9b_MKN1_HM_1EGF +pMAPK_ID9b_MKN1_HM_5EGF pMAPK_ID9b_MKN1_HM_5EGF pMAPK*observableParameter1_pMAPK_ID9b_MKN1_HM_5EGF noiseParameter1_pMAPK_ID9b_MKN1_HM_5EGF observableParameter1_pMAPK_ID9b_MKN1_HM_5EGF noiseParameter1_pMAPK_ID9b_MKN1_HM_5EGF diff --git a/v2/Raimundez_PCB2020/parameters_Raimundez_PCB2020.tsv b/v2/Raimundez_PCB2020/parameters_Raimundez_PCB2020.tsv new file mode 100644 index 0000000..92405cd --- /dev/null +++ b/v2/Raimundez_PCB2020/parameters_Raimundez_PCB2020.tsv @@ -0,0 +1,150 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorDistribution priorParameters +AKTtotal__MKN1_fm AKTtotal__MKN1_fm 1e-05 1000 1.0 false uniform 1e-05;1000 +KD_EGFR_CET KD_EGFR_CET 0.001 1000 0.218012149340634 true log10-normal -0.4089;0.2 +KD_EGFR_EGF KD_EGFR_EGF 0.001 1000 0.320759905034371 true log10-normal 0.3010;0.2 +KD_METinh KD_METinh 1e-05 1000 0.041936901194249 true uniform 1e-05;1000 +MAPKtotal__MKN1_fm MAPKtotal__MKN1_fm 1e-05 1000 1.0 false uniform 1e-05;1000 +MPI3Ktotal__MKN1_fm MPI3Ktotal__MKN1_fm 1e-05 1000 1.0 false uniform 1e-05;1000 +PI3Ktotal__HS746T_fm PI3Ktotal__HS746T_fm 1e-05 1000 1.0 false uniform 1e-05;1000 +RAStotal__MKN1_fm RAStotal__MKN1_fm 1e-05 1000 1.0 false uniform 1e-05;1000 +d_AKTtotal__MKN1_2_HS746T d_AKTtotal__MKN1_2_HS746T -3.0 3 0.0 true laplace 0;3 +d_AKTtotal__fm_2_hm d_AKTtotal__fm_2_hm -3.0 3 0.822922669170335 true laplace 0;3 +d_MAPKtotal__MKN1_2_HS746T d_MAPKtotal__MKN1_2_HS746T -3.0 3 0.0 true laplace 0;3 +d_MAPKtotal__fm_2_hm d_MAPKtotal__fm_2_hm -3.0 3 0.427450996540987 true laplace 0;3 +d_MPI3Ktotal__fm_2_hm d_MPI3Ktotal__fm_2_hm -3.0 3 -1.54468079589527 true laplace 0;3 +d_PI3Ktotal__fm_2_hm d_PI3Ktotal__fm_2_hm -3.0 3 -0.53183572852766 true laplace 0;3 +d_RAStotal__MKN1_2_HS746T d_RAStotal__MKN1_2_HS746T -3.0 3 -1.06e-22 true laplace 0;3 +d_RAStotal__fm_2_hm d_RAStotal__fm_2_hm -3.0 3 -0.538190130449678 true laplace 0;3 +d_ka_AKT__MKN1_2_HS746T d_ka_AKT__MKN1_2_HS746T -3.0 3 0.0 false laplace 0;3 +d_ka_MAPK__MKN1_2_HS746T d_ka_MAPK__MKN1_2_HS746T -3.0 3 0.0 false laplace 0;3 +d_ka_RAS__basal__MKN1_2_HS746T d_ka_RAS__basal__MKN1_2_HS746T -3.0 3 0.0 false laplace 0;3 +d_ka_RAS__pEGFR_EGF_2__MKN1_2_HS746T d_ka_RAS__pEGFR_EGF_2__MKN1_2_HS746T -3.0 3 0.0 false laplace 0;3 +d_kdeg_membran__MKN1_2_HS746T d_kdeg_membran__MKN1_2_HS746T -3.0 3 -0.599975506316473 true laplace 0;3 +d_kdeg_pEGFR_EGF_2_i__MKN1_2_HS746T d_kdeg_pEGFR_EGF_2_i__MKN1_2_HS746T -3.0 3 2.99999999999997 true laplace 0;3 +d_kexp_pEGFR_EGF_2_i__MKN1_2_HS746T d_kexp_pEGFR_EGF_2_i__MKN1_2_HS746T -3.0 3 -0.23823693668421 true laplace 0;3 +d_ki_AKT__MKN1_2_HS746T d_ki_AKT__MKN1_2_HS746T -3.0 3 0.0 false laplace 0;3 +d_ki_PI3K__MKN1_2_HS746T d_ki_PI3K__MKN1_2_HS746T -3.0 3 0.0 false laplace 0;3 +d_ki_RAS__MKN1_2_HS746T d_ki_RAS__MKN1_2_HS746T -3.0 3 0.0 false laplace 0;3 +d_kimp_pEGFR_EGF_2__MKN1_2_HS746T d_kimp_pEGFR_EGF_2__MKN1_2_HS746T -3.0 3 -1.74579260575349 true laplace 0;3 +d_ksyn_EGFR__MKN1_2_HS746T d_ksyn_EGFR__MKN1_2_HS746T -3.0 3 -2.99999999999997 true laplace 0;3 +d_ksyn_EGFR__fm_2_hm d_ksyn_EGFR__fm_2_hm -3.0 3 -0.087595179128819 true laplace 0;3 +d_ksyn_MMET__fm_2_hm d_ksyn_MMET__fm_2_hm -3.0 3 -0.518888973548685 true laplace 0;3 +ka_AKT__MKN1 ka_AKT__MKN1 1e-05 1000 443.101158324899 true uniform 1e-05;1000 +ka_MAPK__MKN1 ka_MAPK__MKN1 1e-05 1000 999.999999999942 true uniform 1e-05;1000 +ka_PI3K__basal ka_PI3K__basal 1e-05 1000 0.000364915071486 true uniform 1e-05;1000 +ka_PI3K__pEGFR_EGF_2 ka_PI3K__pEGFR_EGF_2 1e-05 1000 0.00170094333324 true uniform 1e-05;1000 +ka_RAS__basal__MKN1 ka_RAS__basal__MKN1 1e-05 1000 0.000214463346879 true uniform 1e-05;1000 +ka_RAS__pEGFR_EGF_2__MKN1 ka_RAS__pEGFR_EGF_2__MKN1 1e-05 1000 1.47e-05 true uniform 1e-05;1000 +kbin_EGFR_CET kbin_EGFR_CET 1e-05 1000 0.585302658299007 true uniform 1e-05;1000 +kbin_EGFR_EGF kbin_EGFR_EGF 1e-05 1000 8.88174858370342 true uniform 1e-05;1000 +kdeg_membran__MKN1 kdeg_membran__MKN1 1e-05 1000 0.00225906406532 true uniform 1e-05;1000 +kdeg_pEGFR_EGF_2_i__MKN1 kdeg_pEGFR_EGF_2_i__MKN1 1e-05 1000 0.06679561220892 true uniform 1e-05;1000 +kdim_EGFR_EGF kdim_EGFR_EGF 1e-05 1000 0.03239486876776 true uniform 1e-05;1000 +kdim_MMET kdim_MMET 1e-05 1000 2.61e-05 true uniform 1e-05;1000 +kdim_MMET_EGFR kdim_MMET_EGFR 1e-05 1000 0.001882197025602 true uniform 1e-05;1000 +kdim_MMETinh kdim_MMETinh 1e-05 1000 0.031271407854883 true uniform 1e-05;1000 +kexp_pEGFR_EGF_2_i__MKN1 kexp_pEGFR_EGF_2_i__MKN1 1e-05 1000 0.75168312329534 true uniform 1e-05;1000 +ki_AKT__MKN1 ki_AKT__MKN1 1e-05 1000 18.4692967396058 true log10-normal 1.9542;0.2 +ki_MAPK ki_MAPK 1e-05 1000 2.17715931380425 true uniform 1e-05;1000 +ki_PI3K__MKN1 ki_PI3K__MKN1 1e-05 1000 1.31587984277014 true uniform 1e-05;1000 +ki_RAS__MKN1 ki_RAS__MKN1 1e-05 1000 0.326956568863966 true uniform 1e-05;1000 +kimp_pEGFR_EGF_2__MKN1 kimp_pEGFR_EGF_2__MKN1 0.001 1000 0.746870204508838 true log10-normal -0.6021;0.2 +kpho_EGFR_EGF kpho_EGFR_EGF 1e-05 1000 1.34412787040515 true uniform 1e-05;1000 +kpho_MMET kpho_MMET 1e-05 1000 2.54267401784407 true uniform 1e-05;1000 +kpho_MMET_EGFR kpho_MMET_EGFR 1e-05 1000 4.56300939074226 true uniform 1e-05;1000 +ksyn_EGFR__MKN1_fm ksyn_EGFR__MKN1_fm 1e-05 1000 1.0 false uniform 1e-05;1000 +ksyn_MMET__HS746T_fm ksyn_MMET__HS746T_fm 1e-05 1000 0.026350805070197 true uniform 1e-05;1000 +s_EGFR_ID10_HS746T_FM_EGF s_EGFR_ID10_HS746T_FM_EGF 1e-05 1000 0.022641950376667 true uniform 1e-05;1000 +s_EGFR_ID10_HS746T_FM_EGF_CET s_EGFR_ID10_HS746T_FM_EGF_CET 1e-05 1000 0.017375365285149 true uniform 1e-05;1000 +s_EGFR_ID12_MKN1_FM_HM s_EGFR_ID12_MKN1_FM_HM 1e-05 1000 0.001218038538687 true uniform 1e-05;1000 +s_EGFR_ID3_HS746T_FM s_EGFR_ID3_HS746T_FM 1e-05 1000 0.020211329370285 true uniform 1e-05;1000 +s_EGFR_ID3_MKN1_FM s_EGFR_ID3_MKN1_FM 1e-05 1000 0.002751326970535 true uniform 1e-05;1000 +s_EGFR_ID4_HS746T_HM_3min s_EGFR_ID4_HS746T_HM_3min 1e-05 1000 0.018855356689418 true uniform 1e-05;1000 +s_EGFR_ID4_MKN1_HM_3min s_EGFR_ID4_MKN1_HM_3min 1e-05 1000 0.002875316021922 true uniform 1e-05;1000 +s_MMET_ID10_HS746T_FM_EGF s_MMET_ID10_HS746T_FM_EGF 1e-05 1000 0.04315183185774 true uniform 1e-05;1000 +s_MMET_ID10_HS746T_FM_EGF_CET s_MMET_ID10_HS746T_FM_EGF_CET 1e-05 1000 0.042269564075267 true uniform 1e-05;1000 +s_pAKT_ID12_MKN1_FM_HM s_pAKT_ID12_MKN1_FM_HM 1e-05 1000 0.420517003782066 true uniform 1e-05;1000 +s_pAKT_ID2_HS746T_HM s_pAKT_ID2_HS746T_HM 1e-05 1000 2.80501982215997 true uniform 1e-05;1000 +s_pAKT_ID2_MKN1_HM s_pAKT_ID2_MKN1_HM 1e-05 1000 0.440718151667128 true uniform 1e-05;1000 +s_pAKT_ID5_MKN1_FM_15min s_pAKT_ID5_MKN1_FM_15min 1e-05 1000 0.897109959177639 true uniform 1e-05;1000 +s_pAKT_ID5_MKN1_FM_1min s_pAKT_ID5_MKN1_FM_1min 1e-05 1000 1.21777522131166 true uniform 1e-05;1000 +s_pAKT_ID5_MKN1_FM_240min s_pAKT_ID5_MKN1_FM_240min 1e-05 1000 0.926211879108071 true uniform 1e-05;1000 +s_pAKT_ID5_MKN1_FM_3min s_pAKT_ID5_MKN1_FM_3min 1e-05 1000 1.11236399961917 true uniform 1e-05;1000 +s_pAKT_ID7_HS746T_FM_15min s_pAKT_ID7_HS746T_FM_15min 1e-05 1000 2.65760715254029 true uniform 1e-05;1000 +s_pAKT_ID7_HS746T_FM_1min s_pAKT_ID7_HS746T_FM_1min 1e-05 1000 2.41227143035468 true uniform 1e-05;1000 +s_pAKT_ID7_HS746T_FM_240min s_pAKT_ID7_HS746T_FM_240min 1e-05 1000 2.07673186014235 true uniform 1e-05;1000 +s_pAKT_ID7_HS746T_FM_3min s_pAKT_ID7_HS746T_FM_3min 1e-05 1000 2.2574031908575 true uniform 1e-05;1000 +s_pAKT_ID8_HS746T_HM_15min s_pAKT_ID8_HS746T_HM_15min 1e-05 1000 1.81277662024661 true uniform 1e-05;1000 +s_pAKT_ID8_HS746T_HM_1min s_pAKT_ID8_HS746T_HM_1min 1e-05 1000 2.23462136505094 true uniform 1e-05;1000 +s_pAKT_ID8_HS746T_HM_240min s_pAKT_ID8_HS746T_HM_240min 1e-05 1000 1.97275879564736 true uniform 1e-05;1000 +s_pAKT_ID8_HS746T_HM_3min s_pAKT_ID8_HS746T_HM_3min 1e-05 1000 1.76182210051087 true uniform 1e-05;1000 +s_pAKT_ID9_HS746T_FM s_pAKT_ID9_HS746T_FM 1e-05 1000 1.46317324180354 true uniform 1e-05;1000 +s_pAKT_ID9_HS746T_HM_30EGF s_pAKT_ID9_HS746T_HM_30EGF 1e-05 1000 1.67698709183017 true uniform 1e-05;1000 +s_pAKT_ID9_HS746T_HM_5EGF s_pAKT_ID9_HS746T_HM_5EGF 1e-05 1000 2.77049977664041 true uniform 1e-05;1000 +s_pEGFR_ID10_HS746T_FM_EGF s_pEGFR_ID10_HS746T_FM_EGF 1e-05 1000 0.032354218187186 true uniform 1e-05;1000 +s_pEGFR_ID10_HS746T_FM_EGF_CET s_pEGFR_ID10_HS746T_FM_EGF_CET 1e-05 1000 0.022400982145811 true uniform 1e-05;1000 +s_pEGFR_ID12_MKN1_FM_HM s_pEGFR_ID12_MKN1_FM_HM 1e-05 1000 0.003947098871427 true uniform 1e-05;1000 +s_pEGFR_ID2_HS746T_HM s_pEGFR_ID2_HS746T_HM 1e-05 1000 0.049746460699075 true uniform 1e-05;1000 +s_pEGFR_ID2_MKN1_HM s_pEGFR_ID2_MKN1_HM 1e-05 1000 0.003753202514031 true uniform 1e-05;1000 +s_pEGFR_ID3_HS746T_FM s_pEGFR_ID3_HS746T_FM 1e-05 1000 0.023767228793376 true uniform 1e-05;1000 +s_pEGFR_ID3_MKN1_FM s_pEGFR_ID3_MKN1_FM 1e-05 1000 0.001662876885688 true uniform 1e-05;1000 +s_pEGFR_ID4_HS746T_HM_3min s_pEGFR_ID4_HS746T_HM_3min 1e-05 1000 0.029958617149803 true uniform 1e-05;1000 +s_pEGFR_ID4_MKN1_HM_3min s_pEGFR_ID4_MKN1_HM_3min 1e-05 1000 0.003148581459564 true uniform 1e-05;1000 +s_pEGFR_ID5_MKN1_FM_15min s_pEGFR_ID5_MKN1_FM_15min 1e-05 1000 0.004074681421567 true uniform 1e-05;1000 +s_pEGFR_ID5_MKN1_FM_1min s_pEGFR_ID5_MKN1_FM_1min 1e-05 1000 0.003385763936991 true uniform 1e-05;1000 +s_pEGFR_ID5_MKN1_FM_240min s_pEGFR_ID5_MKN1_FM_240min 1e-05 1000 0.009235226021509 true uniform 1e-05;1000 +s_pEGFR_ID5_MKN1_FM_3min s_pEGFR_ID5_MKN1_FM_3min 1e-05 1000 0.002985941781994 true uniform 1e-05;1000 +s_pEGFR_ID6_MKN1_HM_15min s_pEGFR_ID6_MKN1_HM_15min 1e-05 1000 0.004380222537516 true uniform 1e-05;1000 +s_pEGFR_ID6_MKN1_HM_1min s_pEGFR_ID6_MKN1_HM_1min 1e-05 1000 0.003271445404582 true uniform 1e-05;1000 +s_pEGFR_ID6_MKN1_HM_240min s_pEGFR_ID6_MKN1_HM_240min 1e-05 1000 0.028853840570141 true uniform 1e-05;1000 +s_pEGFR_ID6_MKN1_HM_3min s_pEGFR_ID6_MKN1_HM_3min 1e-05 1000 0.00301144882025 true uniform 1e-05;1000 +s_pEGFR_ID7_HS746T_FM_15min s_pEGFR_ID7_HS746T_FM_15min 1e-05 1000 0.032417660209381 true uniform 1e-05;1000 +s_pEGFR_ID7_HS746T_FM_1min s_pEGFR_ID7_HS746T_FM_1min 1e-05 1000 0.029022905035408 true uniform 1e-05;1000 +s_pEGFR_ID7_HS746T_FM_240min s_pEGFR_ID7_HS746T_FM_240min 1e-05 1000 0.034954599841572 true uniform 1e-05;1000 +s_pEGFR_ID7_HS746T_FM_3min s_pEGFR_ID7_HS746T_FM_3min 1e-05 1000 0.022998305694949 true uniform 1e-05;1000 +s_pEGFR_ID8_HS746T_HM_15min s_pEGFR_ID8_HS746T_HM_15min 1e-05 1000 0.03051527362925 true uniform 1e-05;1000 +s_pEGFR_ID8_HS746T_HM_1min s_pEGFR_ID8_HS746T_HM_1min 1e-05 1000 0.035259968991062 true uniform 1e-05;1000 +s_pEGFR_ID8_HS746T_HM_240min s_pEGFR_ID8_HS746T_HM_240min 1e-05 1000 0.045161490979622 true uniform 1e-05;1000 +s_pEGFR_ID8_HS746T_HM_3min s_pEGFR_ID8_HS746T_HM_3min 1e-05 1000 0.027187352281375 true uniform 1e-05;1000 +s_pEGFR_ID9_HS746T_FM s_pEGFR_ID9_HS746T_FM 1e-05 1000 0.02814165776208 true uniform 1e-05;1000 +s_pEGFR_ID9_HS746T_HM_30EGF s_pEGFR_ID9_HS746T_HM_30EGF 1e-05 1000 0.035877783271325 true uniform 1e-05;1000 +s_pEGFR_ID9_HS746T_HM_5EGF s_pEGFR_ID9_HS746T_HM_5EGF 1e-05 1000 0.045326092436772 true uniform 1e-05;1000 +s_pEGFR_ID9b_MKN1_HM_1EGF s_pEGFR_ID9b_MKN1_HM_1EGF 1e-05 1000 0.007407309900686 true uniform 1e-05;1000 +s_pEGFR_ID9b_MKN1_HM_5EGF s_pEGFR_ID9b_MKN1_HM_5EGF 1e-05 1000 0.005963149846749 true uniform 1e-05;1000 +s_pMAPK_ID10_HS746T_FM_EGF s_pMAPK_ID10_HS746T_FM_EGF 1e-05 1000 2.75179760626861 true uniform 1e-05;1000 +s_pMAPK_ID10_HS746T_FM_EGF_CET s_pMAPK_ID10_HS746T_FM_EGF_CET 1e-05 1000 2.09484640018571 true uniform 1e-05;1000 +s_pMAPK_ID12_MKN1_FM_HM s_pMAPK_ID12_MKN1_FM_HM 1e-05 1000 1.0356443522385 true uniform 1e-05;1000 +s_pMAPK_ID2_HS746T_HM s_pMAPK_ID2_HS746T_HM 1e-05 1000 2.26750712900066 true uniform 1e-05;1000 +s_pMAPK_ID2_MKN1_HM s_pMAPK_ID2_MKN1_HM 1e-05 1000 3.48658194152331 true uniform 1e-05;1000 +s_pMAPK_ID5_MKN1_FM_15min s_pMAPK_ID5_MKN1_FM_15min 1e-05 1000 1.75751916529346 true uniform 1e-05;1000 +s_pMAPK_ID5_MKN1_FM_1min s_pMAPK_ID5_MKN1_FM_1min 1e-05 1000 2.78052675601419 true uniform 1e-05;1000 +s_pMAPK_ID5_MKN1_FM_240min s_pMAPK_ID5_MKN1_FM_240min 1e-05 1000 1.78273745248395 true uniform 1e-05;1000 +s_pMAPK_ID5_MKN1_FM_3min s_pMAPK_ID5_MKN1_FM_3min 1e-05 1000 1.95249025711294 true uniform 1e-05;1000 +s_pMAPK_ID7_HS746T_FM_15min s_pMAPK_ID7_HS746T_FM_15min 1e-05 1000 3.48167902438847 true uniform 1e-05;1000 +s_pMAPK_ID7_HS746T_FM_1min s_pMAPK_ID7_HS746T_FM_1min 1e-05 1000 2.75650033636566 true uniform 1e-05;1000 +s_pMAPK_ID7_HS746T_FM_240min s_pMAPK_ID7_HS746T_FM_240min 1e-05 1000 2.8055366247965 true uniform 1e-05;1000 +s_pMAPK_ID7_HS746T_FM_3min s_pMAPK_ID7_HS746T_FM_3min 1e-05 1000 2.84771878844903 true uniform 1e-05;1000 +s_pMAPK_ID8_HS746T_HM_15min s_pMAPK_ID8_HS746T_HM_15min 1e-05 1000 3.02010438754109 true uniform 1e-05;1000 +s_pMAPK_ID8_HS746T_HM_1min s_pMAPK_ID8_HS746T_HM_1min 1e-05 1000 3.42012433266936 true uniform 1e-05;1000 +s_pMAPK_ID8_HS746T_HM_240min 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/dev/null +++ b/v2/SalazarCavazos_MBoC2020/experimentalCondition_SalazarCavazos_MBoC2020.tsv @@ -0,0 +1,5 @@ +conditionId targetId targetValue +dose1 EGFconc 5e-10 +dose2 EGFconc 5e-09 +dose3 EGFconc 5e-08 +EGF25nM EGFconc 2.5e-08 diff --git a/v2/SalazarCavazos_MBoC2020/experiments.tsv b/v2/SalazarCavazos_MBoC2020/experiments.tsv new file mode 100644 index 0000000..b21a810 --- /dev/null +++ b/v2/SalazarCavazos_MBoC2020/experiments.tsv @@ -0,0 +1,5 @@ +experimentId conditionId time +experiment____EGF25nM EGF25nM 0 +experiment____dose1 dose1 0 +experiment____dose2 dose2 0 +experiment____dose3 dose3 0 diff --git a/v2/SalazarCavazos_MBoC2020/measurementData_SalazarCavazos_MBoC2020.tsv b/v2/SalazarCavazos_MBoC2020/measurementData_SalazarCavazos_MBoC2020.tsv new file mode 100644 index 0000000..475bd72 --- /dev/null +++ b/v2/SalazarCavazos_MBoC2020/measurementData_SalazarCavazos_MBoC2020.tsv @@ -0,0 +1,19 @@ +experimentId observableId measurement time observableParameters noiseParameters 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noiseParameter1_observable_pY1068_percent +observable_pY1173_percent pY1173_percent (100*pY1173)/EGFRtot noiseParameter1_observable_pY1173_percent noiseParameter1_observable_pY1173_percent +observable_unphosR_per unphosR_per (100*unphosR)/EGFRtot noiseParameter1_observable_unphosR_per noiseParameter1_observable_unphosR_per +observable_phosR_per phosR_per (100*(EGFRtot-unphosR))/EGFRtot noiseParameter1_observable_phosR_per noiseParameter1_observable_phosR_per diff --git a/v2/SalazarCavazos_MBoC2020/parameters_SalazarCavazos_MBoC2020.tsv b/v2/SalazarCavazos_MBoC2020/parameters_SalazarCavazos_MBoC2020.tsv new file mode 100644 index 0000000..90f01d3 --- /dev/null +++ b/v2/SalazarCavazos_MBoC2020/parameters_SalazarCavazos_MBoC2020.tsv @@ -0,0 +1,7 @@ +parameterId lowerBound upperBound nominalValue estimate priorParameters +GRB2_total__FREE 10000.0 1000000.0 169853.19422230462 true +SHC1_total__FREE 10000.0 1000000.0 649425.6012099041 true +kdephosY1068__FREE 0.1 100.0 1.6588142136877735 true +kdephosYN__FREE 0.001 100.0 0.01718186979848268 true +ratio_kpkd_Y1068__FREE 0.01 100.0 0.15754585734593093 true +ratio_kpkd_YN__FREE 0.01 100.0 0.44476356871177164 true diff --git a/v2/Schwen_PONE2014/Schwen_PONE2014.yaml b/v2/Schwen_PONE2014/Schwen_PONE2014.yaml new file mode 100644 index 0000000..175e1e6 --- /dev/null +++ b/v2/Schwen_PONE2014/Schwen_PONE2014.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Schwen_PONE2014.tsv +model_files: + model_Schwen_PONE2014: + location: model_Schwen_PONE2014.xml + language: sbml +measurement_files: +- measurementData_Schwen_PONE2014.tsv +condition_files: +- experimentalCondition_Schwen_PONE2014.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Schwen_PONE2014.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Schwen_PONE2014/experimentalCondition_Schwen_PONE2014.tsv b/v2/Schwen_PONE2014/experimentalCondition_Schwen_PONE2014.tsv new file mode 100644 index 0000000..ab2d6d6 --- 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IR_obs_std model1_data6_IR2 +experiment____model1_data6 observable_IR2 47.837557803124 30.0 offset;scale IR_obs_std model1_data6_IR2 +experiment____model1_data7 observable_IR1 6.19759225171243 1.0 offset;scale IR_obs_std model1_data7_IR1 +experiment____model1_data7 observable_IR1 7.05776185201418 2.0 offset;scale IR_obs_std model1_data7_IR1 +experiment____model1_data7 observable_IR1 8.55389667532674 5.0 offset;scale IR_obs_std model1_data7_IR1 +experiment____model1_data7 observable_IR1 8.82925378076677 15.0 offset;scale IR_obs_std model1_data7_IR1 +experiment____model1_data7 observable_IR1 9.54412239183822 30.0 offset;scale IR_obs_std model1_data7_IR1 +experiment____model1_data7 observable_IR2 61.2759425051777 1.0 offset;scale IR_obs_std model1_data7_IR2 +experiment____model1_data7 observable_IR2 75.8474527353433 2.0 offset;scale IR_obs_std model1_data7_IR2 +experiment____model1_data7 observable_IR2 107.576150636188 5.0 offset;scale IR_obs_std model1_data7_IR2 +experiment____model1_data7 observable_IR2 118.060875641396 15.0 offset;scale IR_obs_std model1_data7_IR2 +experiment____model1_data7 observable_IR2 136.186481613691 30.0 offset;scale IR_obs_std model1_data7_IR2 +experiment____model1_data8 observable_Insulin 0.026231 15.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data8_Insulin +experiment____model1_data8 observable_Insulin 0.032385 15.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data8_Insulin +experiment____model1_data9 observable_Insulin 0.490769 0.25 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 0.479231 0.25 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 0.569615 0.5 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 0.534999999999999 0.5 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 0.731154 1.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 0.729230999999999 1.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 0.623462 2.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 0.590769 2.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 0.963845999999999 3.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 0.965768999999999 3.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 1.096538 4.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 0.994615 4.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 1.165769 5.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 1.104231 5.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 1.067692 7.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 1.044615 7.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 0.615769 10.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 0.588846000000001 10.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 0.944614999999999 15.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 0.919614999999999 15.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 1.175385 20.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 1.104231 20.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 1.213846 25.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 1.138846 25.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 1.296538 30.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 1.265769 30.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 1.361923 40.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 1.273462 40.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 0.486923 50.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 0.467692 50.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 0.390769 60.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin +experiment____model1_data9 observable_Insulin 0.371537999999999 60.0 offset_nExpID1;scaleElisa_nExpID1;fragments;km_nExpID1 std model1_data9_Insulin diff --git a/v2/Schwen_PONE2014/model_Schwen_PONE2014.xml b/v2/Schwen_PONE2014/model_Schwen_PONE2014.xml new file mode 100644 index 0000000..1760145 --- /dev/null +++ b/v2/Schwen_PONE2014/model_Schwen_PONE2014.xml @@ -0,0 +1,391 @@ + + + + + + 
PEtab implementation of the model from Schwen et al. (2015), PLoS One, 10, e0133653
+ + + + + + + + + + Schwen + Lars Ole + + + + + + 2019-11-29T09:41:48Z + + + 2019-11-29T09:41:48Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ini_R1 + + + + + init_Ins + + + + + + + ini_R1 + ini_R2fold + + + + + + + + + + + + + + + + + + ExtracellularMedium + Ins + Rec1 + ka1 + + + + + + + + + + + + + + + + + ExtracellularMedium + Ins + Rec2 + ka1 + ka2fold + + + + + + + + + + + + + + + + ExtracellularMedium + Ins + kon_unspec + + + + + + + + + + + + + + + + ExtracellularMedium + BoundUnspec + koff_unspec + + + + + + + + + + + + + + + + + ExtracellularMedium + IR1 + kd1 + + + + + + + + + + + + + + + + + ExtracellularMedium + IR2 + kd1 + kd2fold + + + + + + + + + + + + + + + + ExtracellularMedium + IR1 + kin + + + + + + + + + + + + + + + + ExtracellularMedium + IR2 + kin2 + + + + + + + + + + + + + + + + ExtracellularMedium + IR1in + kout + + + + + + + + + + + + + + + + ExtracellularMedium + IR2in + kout2 + + + + + + + + + + + + + + + + + ExtracellularMedium + IR1in + kout_frag + + + + + + + + + + + + + + + + + ExtracellularMedium + IR2in + kout_frag + + + + + + + + + + + + + + + + + + ExtracellularMedium + + + + + Ins + Rec1 + ka1 + + + + IR1 + kd1 + + + + + + + + + + + + + + + + + + + + ExtracellularMedium + + + + + Ins + Rec2 + ka1 + ka2fold + + + + IR2 + kd1 + kd2fold + + + + + + + + + diff --git a/v2/Schwen_PONE2014/observables_Schwen_PONE2014.tsv b/v2/Schwen_PONE2014/observables_Schwen_PONE2014.tsv new file mode 100644 index 0000000..eabbb6d --- /dev/null +++ b/v2/Schwen_PONE2014/observables_Schwen_PONE2014.tsv @@ -0,0 +1,5 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +observable_IR1 observableParameter2_observable_IR1 * (IR1 + IR1in + observableParameter1_observable_IR1) noiseParameter1_observable_IR1 observableParameter1_observable_IR1;observableParameter2_observable_IR1 noiseParameter1_observable_IR1 +observable_IR2 observableParameter2_observable_IR2 * (IR2 + IR2in + observableParameter1_observable_IR2) noiseParameter1_observable_IR2 observableParameter1_observable_IR2;observableParameter2_observable_IR2 noiseParameter1_observable_IR2 +observable_IRsum observableParameter2_observable_IRsum * (0.605 * IR1 + 0.395 * IR2 + 0.605 * IR1in + 0.395 * IR2in + observableParameter1_observable_IRsum) noiseParameter1_observable_IRsum observableParameter1_observable_IRsum;observableParameter2_observable_IRsum noiseParameter1_observable_IRsum +observable_Insulin observableParameter1_observable_Insulin + observableParameter2_observable_Insulin * (Ins + InsulinFragments * observableParameter3_observable_Insulin) / ((Ins + InsulinFragments * observableParameter3_observable_Insulin) / observableParameter4_observable_Insulin + 1) noiseParameter1_observable_Insulin observableParameter1_observable_Insulin;observableParameter2_observable_Insulin;observableParameter3_observable_Insulin;observableParameter4_observable_Insulin noiseParameter1_observable_Insulin diff --git a/v2/Schwen_PONE2014/parameters_Schwen_PONE2014.tsv b/v2/Schwen_PONE2014/parameters_Schwen_PONE2014.tsv new file mode 100644 index 0000000..a600404 --- /dev/null +++ b/v2/Schwen_PONE2014/parameters_Schwen_PONE2014.tsv @@ -0,0 +1,31 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorDistribution priorParameters +IR_obs_std IR_{obs,std} 1e-05 0.056234132519035 0.04718566713256 true uniform 1e-05;0.056234132519035 +fragments fragments 0.0 1.0 0.999999072086866 true uniform 0.0;1.0 +ini_R1 ini_{R1} 1e-05 1000.0 58.8503656504712 true log10-normal 1.809765366817905;3 +ini_R2fold ini_{R2fold} 1e-05 1000.0 15.6091614910056 true log10-normal 1.196922192866968;3 +ka1 ka1 1e-05 1000.0 0.003799559577141 true log10-normal -4.006774320046476;3 +ka2fold ka2fold 1e-05 1000.0 4.90235664339923 true log10-normal -0.018613892336092;3 +kd1 kd1 1e-05 1000.0 9.1452569352756 true log10-normal -0.917792647716124;3 +kd2fold kd2fold 1e-05 1000.0 6.94256361634239 true log10-normal -0.105608820817629;3 +kin kin 1e-05 1000.0 0.371867742056691 true uniform 1e-05;1000.0 +kin2 kin2 1e-05 1000.0 0.538281644062314 true uniform 1e-05;1000.0 +km_nExpID1 km_{nExpID1} 1000.0 100000000.0 99999998.6188564 true uniform 1000.0;100000000.0 +km_nExpID2 km_{nExpID2} 1000.0 100000000.0 99999999.9262277 true uniform 1000.0;100000000.0 +km_nExpID3 km_{nExpID3} 1000.0 100000000.0 99999999.4830626 true uniform 1000.0;100000000.0 +km_nExpID4 km_{nExpID4} 1000.0 100000000.0 99999999.7688987 true uniform 1000.0;100000000.0 +koff_unspec koff_{unspec} 1e-05 1000.0 10.0574365310404 true uniform 1e-05;1000.0 +kon_unspec kon_{unspec} 1e-05 1000.0 20.2497851212426 true uniform 1e-05;1000.0 +kout kout 1e-05 1000.0 0.045075006384889 true uniform 1e-05;1000.0 +kout2 kout2 1e-05 1000.0 0.035429930979713 true uniform 1e-05;1000.0 +kout_frag kout_{frag} 1e-05 1000.0 0.011016106452567 true uniform 1e-05;1000.0 +offset offset 1e-05 1000.0 14.6162752309182 true uniform 1e-05;1000.0 +offset_nExpID1 offset_{nExpID1} 1e-05 100000.0 0.025125178785146 true uniform 1e-05;100000.0 +offset_nExpID2 offset_{nExpID2} 1e-05 100000.0 0.021744798213588 true uniform 1e-05;100000.0 +offset_nExpID3 offset_{nExpID3} 1e-05 100000.0 0.007316811299973 true uniform 1e-05;100000.0 +offset_nExpID4 offset_{nExpID4} 1e-05 100000.0 1.56710171943085 true uniform 1e-05;100000.0 +scale scale 1e-05 1000.0 0.131806990818741 true uniform 1e-05;1000.0 +scaleElisa_nExpID1 scaleElisa_{nExpID1} 0.1 1.0 0.538009450729947 true uniform 0.1;1.0 +scaleElisa_nExpID2 scaleElisa_{nExpID2} 0.1 1.0 0.569911881220408 true uniform 0.1;1.0 +scaleElisa_nExpID3 scaleElisa_{nExpID3} 0.1 1.0 0.100000000170598 true uniform 0.1;1.0 +scaleElisa_nExpID4 scaleElisa_{nExpID4} 0.1 1.0 0.999999999951202 true uniform 0.1;1.0 +std std 1e-05 1000.0 0.24832414992796 true uniform 1e-05;1000.0 diff --git a/v2/Smith_BMCSystBiol2013/Smith_BMCSystBiol2013.yaml b/v2/Smith_BMCSystBiol2013/Smith_BMCSystBiol2013.yaml new file mode 100644 index 0000000..799cd05 --- /dev/null +++ b/v2/Smith_BMCSystBiol2013/Smith_BMCSystBiol2013.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Smith_BMCSystBiol2013.tsv +model_files: + model_Smith_BMCSystBiol2013: + location: model_Smith_BMCSystBiol2013.xml + language: sbml +measurement_files: +- measurementData_Smith_BMCSystBiol2013.tsv +condition_files: +- experimentalCondition_Smith_BMCSystBiol2013.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Smith_BMCSystBiol2013.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Smith_BMCSystBiol2013/experimentalCondition_Smith_BMCSystBiol2013.tsv b/v2/Smith_BMCSystBiol2013/experimentalCondition_Smith_BMCSystBiol2013.tsv new file mode 100644 index 0000000..cda0b54 --- /dev/null +++ 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+ + 0 + + + + + + + + + + time + 2880 + + + + + + + 499999 + + + + + + + + + + time + 2895 + + + + + + + 0 + + + + + + + diff --git a/v2/Smith_BMCSystBiol2013/observables_Smith_BMCSystBiol2013.tsv b/v2/Smith_BMCSystBiol2013/observables_Smith_BMCSystBiol2013.tsv new file mode 100644 index 0000000..9dc6a27 --- /dev/null +++ b/v2/Smith_BMCSystBiol2013/observables_Smith_BMCSystBiol2013.tsv @@ -0,0 +1,10 @@ +observableId observableFormula noiseFormula observablePlaceholders noisePlaceholders +PI3K_activity__2B sc_PI3K * IRS1_TyrP_PI3K 1.0 +Glucose_uptake__2B sc_GLUT_2B * cellsurface_GLUT4 1.0 +Cell_Bound_Ins__2B sc_BINS * InR_bound 1.0 +IRSYp__2C sc_PIRS * IRS1_TyrP 1.0 +PTP_activ__2D sc_PTP * (PTP1B / PTP1B_plus_PTP1B_ox) 1.0 +Glucose_uptake__120__3B sc_GLUT_3B_120 * cellsurface_GLUT4 1.0 +Glucose_uptake__240__3B sc_GLUT_3B_240 * cellsurface_GLUT4 1.0 +MnSOD_fold_induction__3C sc_SOD2 * cytoplasm_SOD2 1.0 +FOXO4__3C sc_FOXO1 * Foxo1_all 1.0 diff --git a/v2/Smith_BMCSystBiol2013/parameters_Smith_BMCSystBiol2013.tsv b/v2/Smith_BMCSystBiol2013/parameters_Smith_BMCSystBiol2013.tsv new file mode 100644 index 0000000..24ae1cc --- /dev/null +++ b/v2/Smith_BMCSystBiol2013/parameters_Smith_BMCSystBiol2013.tsv @@ -0,0 +1,80 @@ +parameterId lowerBound upperBound nominalValue estimate priorParameters +k1 2.0000000000000002e-07 0.002 2e-05 true +kminus1 120.72 1207200.0 12072.0 true +k2 1.2000000000000002e-07 0.0012000000000000001 1.2e-05 false +kminus2 900.0 9000000.0 90000.0 false +k3 25.0 250000.0 2500.0 false +kminus3 2e-08 0.00019999999999999998 2e-06 false +k4prime 2.1e-05 0.21 0.0021 false +kminus4prime 2.1000000000000002e-06 0.021 0.00021 false +k6 4.6099999999999996e-08 0.000461 4.61e-06 false +cellsurf_vol 0.01 100.0 1.0 false +cyto_vol 0.01 100.0 1.0 false +vextracellular 8.3e-14 8.3e-10 8.3e-12 false +vcellsurface 6.4e-16 6.4e-12 6.4e-14 false +vcytoplasm 1.65e-13 1.65e-09 1.65e-11 false +k9_basal 0.0013145000000000001 13.145000000000001 0.13145 false +k9 5.4999999999999995e-05 0.5499999999999999 0.0055 false +kminus9_basal 0.027000000000000003 270.0 2.7 false +kminus9 1.4e-05 0.13999999999999999 0.0014 false +k11 2.5e-07 0.0025 2.5e-05 false +kminus11 1.1878e-08 0.00011878000000000001 1.1878e-06 false +k12 3.5e-07 0.0034999999999999996 3.5e-05 false +kminus12 1.2500000000000001e-08 0.000125 1.25e-06 false +kr16a 3.3300000000000003e-06 0.0333 0.000333 false +kminusr16a 1e-08 9.999999999999999e-05 1e-06 false +k13_basal 0.00015 1.5 0.015 false +k13 7.5e-08 0.00075 7.5e-06 false +kminus13 0.00167 16.7 0.167 false +k14 1.1088 11088.0 110.88 false +kminus14 1.155e-05 0.1155 0.001155 false +sc_pip 10.0 100000.0 1000.0 false +pip3_basal 2.0 20000.0 200.0 false +k30f 0.0008 8.0 0.08 true +k30r 5e-05 0.5 0.005 true +k31f 2.7e-06 0.027 0.00027 false +k31r 2e-05 0.2 0.002 false +k34f 2.0000000000000002e-07 0.002 2e-05 false +k34r1 1e-05 0.1 0.001 false +k34r2 0.0025 25.0 0.25 false +k34r3 1e-05 0.1 0.001 false +k35f 4.5 45000.0 450.0 true +k35r 0.0012 12.0 0.12 false +k36f 1.8 18000.0 180.0 false +ros_perm 7400000.0 74000000000.0 740000000.0 false +k38r 0.02 200.0 2.0 false +k38f 0.0005 5.0 0.05 false +sc_ros 10.0 100000.0 1000.0 false +k7 0.057999999999999996 580.0 5.8 true +kminus7a 8.75e-07 0.008749999999999999 8.75e-05 true +kminus7b 2.8e-08 0.00028 2.8e-06 true +k8 2.6e-08 0.00026000000000000003 2.6e-06 true +kminus8 0.0155 155.0 1.55 true +IRp 900.0 9000000.0 90000.0 false +k2psp 2.2e-06 0.022000000000000002 0.00022 false +kcat82 0.03 300.0 3.0 false +Km82 1.0 10000.0 100.0 false +k_irs1_basal_degr 1e-05 0.1 0.001 false +k_irs1_polyserp_degr 0.0001 1.0 0.01 false +kcat51 0.0087 87.0 0.87 false +kcat52 0.0695 695.0 6.95 false +Km51 1.0 10000.0 100.0 false +Km52 1.0 10000.0 100.0 false +k42f 5e-07 0.005 5e-05 true +k42r 5e-09 4.9999999999999996e-05 5e-07 true +k43f 5e-07 0.005 5e-05 true +k43r 5e-09 4.9999999999999996e-05 5e-07 true +alpha_ox 0.05 500.0 5.0 false +k32f 5.999999999999999e-06 0.06 0.0006 true +k32r 4e-06 0.04 0.0004 true +by_jnk_phos_factor 0.02 200.0 2.0 false +by_ikk_phos_factor 0.03 300.0 3.0 false +sc_PI3K 0.0001 10000.0 1.6607492397638188 true +sc_GLUT_2B 0.0001 10000.0 0.005003654843537889 true +sc_BINS 0.0001 10000.0 0.001627712376345442 true +sc_PIRS 0.0001 10000.0 0.005656559423442325 true +sc_PTP 0.0001 10000.0 0.16 true +sc_GLUT_3B_120 0.0001 10000.0 0.024266666670408527 true +sc_GLUT_3B_240 0.0001 10000.0 0.026693333333333426 true +sc_SOD2 0.0001 10000.0 0.00019404164387341782 true +sc_FOXO1 0.0001 10000.0 0.0020877636326153692 true diff --git a/v2/Sneyd_PNAS2002/Sneyd_PNAS2002.yaml b/v2/Sneyd_PNAS2002/Sneyd_PNAS2002.yaml new file mode 100644 index 0000000..1e49ff4 --- /dev/null +++ b/v2/Sneyd_PNAS2002/Sneyd_PNAS2002.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Sneyd_PNAS2002.tsv +model_files: + model_Sneyd_PNAS2002: + location: model_Sneyd_PNAS2002.xml + language: sbml +measurement_files: +- measurementData_Sneyd_PNAS2002.tsv +condition_files: +- experimentalCondition_Sneyd_PNAS2002.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Sneyd_PNAS2002.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Sneyd_PNAS2002/experimentalCondition_Sneyd_PNAS2002.tsv b/v2/Sneyd_PNAS2002/experimentalCondition_Sneyd_PNAS2002.tsv new file mode 100644 index 0000000..9380437 --- /dev/null +++ b/v2/Sneyd_PNAS2002/experimentalCondition_Sneyd_PNAS2002.tsv @@ -0,0 +1,19 @@ +conditionId targetId targetValue +Ca_dose_response__1 IP3 10.0 +Ca_dose_response__2 IP3 10.0 +Ca_dose_response__3 IP3 10.0 +Ca_dose_response__4 IP3 10.0 +Ca_dose_response__5 IP3 10.0 +Ca_dose_response__6 IP3 10.0 +IP3_dose_response__1 IP3 3.0 +IP3_dose_response__2 IP3 5.0 +IP3_dose_response__3 IP3 10.0 +Ca_dose_response__1 Ca 0.1 +Ca_dose_response__2 Ca 0.2 +Ca_dose_response__3 Ca 0.4 +Ca_dose_response__4 Ca 1.0 +Ca_dose_response__5 Ca 3.0 +Ca_dose_response__6 Ca 10.0 +IP3_dose_response__1 Ca 0.4 +IP3_dose_response__2 Ca 0.4 +IP3_dose_response__3 Ca 0.4 diff --git a/v2/Sneyd_PNAS2002/experiments.tsv b/v2/Sneyd_PNAS2002/experiments.tsv new file mode 100644 index 0000000..6540a44 --- /dev/null +++ b/v2/Sneyd_PNAS2002/experiments.tsv @@ -0,0 +1,10 @@ +experimentId conditionId time +experiment____Ca_dose_response__1 Ca_dose_response__1 0 +experiment____Ca_dose_response__2 Ca_dose_response__2 0 +experiment____Ca_dose_response__3 Ca_dose_response__3 0 +experiment____Ca_dose_response__4 Ca_dose_response__4 0 +experiment____Ca_dose_response__5 Ca_dose_response__5 0 +experiment____Ca_dose_response__6 Ca_dose_response__6 0 +experiment____IP3_dose_response__1 IP3_dose_response__1 0 +experiment____IP3_dose_response__2 IP3_dose_response__2 0 +experiment____IP3_dose_response__3 IP3_dose_response__3 0 diff --git a/v2/Sneyd_PNAS2002/measurementData_Sneyd_PNAS2002.tsv b/v2/Sneyd_PNAS2002/measurementData_Sneyd_PNAS2002.tsv new file mode 100644 index 0000000..cea43e0 --- /dev/null +++ b/v2/Sneyd_PNAS2002/measurementData_Sneyd_PNAS2002.tsv @@ -0,0 +1,136 @@ +experimentId observableId measurement time observableParameters noiseParameters experimentName replicateId useData +experiment____Ca_dose_response__1 open_probability -0.01 0.0 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__1 open_probability 0.113 0.07 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__1 open_probability 0.065 0.14 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__1 open_probability 0.037000000000000005 0.21 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__1 open_probability 0.022 0.28 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__1 open_probability 0.017 0.35 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__1 open_probability 0.008 0.42 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__1 open_probability 0.008 0.49 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__1 open_probability 0.011 0.56 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__1 open_probability 0.005 0.63 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__1 open_probability 0.01 0.7 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__1 open_probability 0.006 0.77 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__1 open_probability 0.009000000000000001 0.84 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__1 open_probability 0.006 0.91 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__1 open_probability 0.008 0.98 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__2 open_probability -0.018000000000000002 0.0 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__2 open_probability 0.174 0.07 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__2 open_probability 0.106 0.14 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__2 open_probability 0.065 0.21 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__2 open_probability 0.036000000000000004 0.28 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__2 open_probability 0.024 0.35 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__2 open_probability 0.015 0.42 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__2 open_probability 0.01 0.49 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__2 open_probability 0.006999999999999999 0.56 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__2 open_probability 0.005 0.63 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__2 open_probability 0.006 0.7 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__2 open_probability 0.008 0.77 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__2 open_probability 0.005 0.84 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__2 open_probability 0.017 0.91 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__2 open_probability 0.015 0.98 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__3 open_probability 0.008 0.0 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__3 open_probability 0.327 0.07 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__3 open_probability 0.297 0.14 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__3 open_probability 0.189 0.21 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__3 open_probability 0.121 0.28 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__3 open_probability 0.084 0.35 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__3 open_probability 0.057 0.42 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__3 open_probability 0.047 0.49 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__3 open_probability 0.04 0.56 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__3 open_probability 0.039 0.63 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__3 open_probability 0.036000000000000004 0.7 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__3 open_probability 0.03 0.77 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__3 open_probability 0.024 0.84 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__3 open_probability 0.024 0.91 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__3 open_probability 0.026 0.98 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__4 open_probability 0.012 0.0 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__4 open_probability 0.253 0.07 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__4 open_probability 0.214 0.14 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__4 open_probability 0.109 0.21 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__4 open_probability 0.047 0.28 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__4 open_probability 0.022 0.35 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__4 open_probability 0.016 0.42 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__4 open_probability 0.013 0.49 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__4 open_probability 0.012 0.56 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__4 open_probability 0.012 0.63 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__4 open_probability 0.012 0.7 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__4 open_probability 0.012 0.77 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__4 open_probability 0.012 0.84 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__4 open_probability 0.004 0.91 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__4 open_probability 0.005 0.98 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__5 open_probability 0.052000000000000005 0.0 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__5 open_probability 0.238 0.07 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__5 open_probability 0.17800000000000002 0.14 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__5 open_probability 0.095 0.21 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__5 open_probability 0.062 0.28 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__5 open_probability 0.035 0.35 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__5 open_probability 0.026 0.42 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__5 open_probability 0.019 0.49 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__5 open_probability 0.016 0.56 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__5 open_probability 0.018000000000000002 0.63 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__5 open_probability 0.008 0.7 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__5 open_probability 0.005 0.77 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__5 open_probability 0.01 0.84 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__5 open_probability 0.011 0.91 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__5 open_probability 0.006999999999999999 0.98 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__6 open_probability 0.014 0.0 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__6 open_probability 0.185 0.07 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__6 open_probability 0.17600000000000002 0.14 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__6 open_probability 0.141 0.21 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__6 open_probability 0.087 0.28 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__6 open_probability 0.049 0.35 sigma Ca^{2+} response 1 True +experiment____Ca_dose_response__6 open_probability 0.036000000000000004 0.42 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a/v2/Sneyd_PNAS2002/model_Sneyd_PNAS2002.xml b/v2/Sneyd_PNAS2002/model_Sneyd_PNAS2002.xml new file mode 100644 index 0000000..6e6c95b --- /dev/null +++ b/v2/Sneyd_PNAS2002/model_Sneyd_PNAS2002.xml @@ -0,0 +1,483 @@ + + + + + + 
PEtab implementation of the model from Sneyd et al. (2002), PNAS February 19, 2002 99 (4) 2398-2403
+ + + + + + + + + + Sneyd + James + + + + + + 2019-11-29T09:41:48Z + + + 2019-11-29T09:41:48Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k_1 + k1 + + + + l_2 + l2 + + + + + + + + + + + k_2 + k2 + + + + l_4 + l4 + + + + + + + + + + + k_4 + k4 + + + + l_6 + l6 + + + + + + + + + + + + + + + + + + + + + + k_2 + + + l_4 + Ca + + + + + 1 + + + Ca + L5 + + + + IPR_O + + + + + + + + + + + + + + + + + + + + + + k2 + L3 + + + + l4 + Ca + + + + + L3 + + + Ca + + + 1 + + + L3 + L1 + + + + + + IP3 + IPR_R + + + + + + + + + + + + + + + + + + + + + + + + k1 + L1 + + l2 + + Ca + + + + L1 + + + Ca + + + 1 + + + L1 + L3 + + + + + + IPR_R + + + + + + + + + + + + + + + + + + k_1 + l_2 + + IPR_I1 + + + + + + + + + + + + + + + + + + + + + + + + k4 + L5 + + l6 + + Ca + + + + L5 + Ca + + + IPR_O + + + + + + + + + + + + + + + + + + + + L1 + + + k_4 + l_6 + + + + + L1 + Ca + + + IPR_A + + + + + + + + + + + + + + + + + + + + + + + + k1 + L1 + + l2 + + Ca + + + + L1 + Ca + + + IPR_A + + + + + + + + + + + + + + + + + + k_1 + l_2 + + IPR_I2 + + + + + + + + + + + + + + + + + + + + k3 + L5 + + + + L5 + Ca + + + IPR_O + + + + + + + + + + + + + + + + k_3 + IPR_S + + + + + + + diff --git a/v2/Sneyd_PNAS2002/observables_Sneyd_PNAS2002.tsv b/v2/Sneyd_PNAS2002/observables_Sneyd_PNAS2002.tsv new file mode 100644 index 0000000..b627c72 --- /dev/null +++ b/v2/Sneyd_PNAS2002/observables_Sneyd_PNAS2002.tsv @@ -0,0 +1,2 @@ +observableId observableFormula observableName noiseDistribution noiseFormula observablePlaceholders noisePlaceholders +open_probability (0.9 * IPR_A + 0.1 * IPR_O)^4 noiseParameter1_open_probability noiseParameter1_open_probability diff --git a/v2/Sneyd_PNAS2002/parameters_Sneyd_PNAS2002.tsv b/v2/Sneyd_PNAS2002/parameters_Sneyd_PNAS2002.tsv new file mode 100644 index 0000000..d4b7d98 --- /dev/null +++ b/v2/Sneyd_PNAS2002/parameters_Sneyd_PNAS2002.tsv @@ -0,0 +1,16 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorParameters +k1 k1 0.001 100000 3.72721095730996 true +k2 k2 0.001 100000 99999.9999999908 true +k3 k3 0.001 100000 15.7453406923706 true +k4 k4 0.001 100000 99938.2576283144 true +k_1 k_{1} 0.001 100000 0.923924728172173 true +k_2 k_{2} 0.001 100000 0.001002494725324 true +k_3 k_{3} 0.001 100000 1.91463005974811 true +k_4 k_{4} 0.001 100000 3079.20732487903 true +l2 l2 0.001 100000 0.940077018858089 true +l4 l4 0.001 100000 2.85837713545253 true +l6 l6 0.001 100000 99999.9999999908 true +l_2 l_{2} 0.001 100000 0.347664459128102 true +l_4 l_{4} 0.001 100000 0.01388020361713 true +l_6 l_{6} 0.001 100000 0.001 true +sigma \sigma 1e-05 1000 0.022665679544462 true diff --git a/v2/Weber_BMC2015/Weber_BMC2015.yaml b/v2/Weber_BMC2015/Weber_BMC2015.yaml new file mode 100644 index 0000000..4bb317c --- /dev/null +++ b/v2/Weber_BMC2015/Weber_BMC2015.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Weber_BMC2015.tsv +model_files: + model_Weber_BMC2015: + location: model_Weber_BMC2015.xml + language: sbml +measurement_files: +- measurementData_Weber_BMC2015.tsv +condition_files: +- experimentalCondition_Weber_BMC2015.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Weber_BMC2015.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Weber_BMC2015/experimentalCondition_Weber_BMC2015.tsv b/v2/Weber_BMC2015/experimentalCondition_Weber_BMC2015.tsv new file mode 100644 index 0000000..30bcafe --- /dev/null +++ b/v2/Weber_BMC2015/experimentalCondition_Weber_BMC2015.tsv @@ -0,0 +1,19 @@ +conditionId targetId targetValue +model1_data1 Ect_Expr_CERT_flag 0 +model1_data2 Ect_Expr_CERT_flag 0 +model1_data3 Ect_Expr_CERT_flag 1 +model1_data1 Ect_Expr_PI4K3beta_flag 0 +model1_data2 Ect_Expr_PI4K3beta_flag 1 +model1_data3 Ect_Expr_PI4K3beta_flag 0 +model1_data1 PdBu_dose 0 +model1_data2 PdBu_dose 1 +model1_data3 PdBu_dose 0 +model1_data1 PdBu_time 0 +model1_data2 PdBu_time 24 +model1_data3 PdBu_time 0 +model1_data1 kb_NB142_70_dose 0 +model1_data2 kb_NB142_70_dose 0 +model1_data3 kb_NB142_70_dose 10 +model1_data1 kb_NB142_70_time 0 +model1_data2 kb_NB142_70_time 0 +model1_data3 kb_NB142_70_time 24 diff --git a/v2/Weber_BMC2015/experiments.tsv b/v2/Weber_BMC2015/experiments.tsv new file mode 100644 index 0000000..117ed6f --- /dev/null +++ b/v2/Weber_BMC2015/experiments.tsv @@ -0,0 +1,5 @@ +experimentId conditionId time +experiment__model1_data1___model1_data2 model1_data1 -inf +experiment__model1_data1___model1_data2 model1_data2 0.0 +experiment__model1_data1___model1_data3 model1_data1 -inf +experiment__model1_data1___model1_data3 model1_data3 0.0 diff --git a/v2/Weber_BMC2015/measurementData_Weber_BMC2015.tsv b/v2/Weber_BMC2015/measurementData_Weber_BMC2015.tsv new file mode 100644 index 0000000..770afc5 --- /dev/null +++ b/v2/Weber_BMC2015/measurementData_Weber_BMC2015.tsv @@ -0,0 +1,136 @@ +experimentId observableId measurement 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std_yPI4K3Bt +experiment__model1_data1___model1_data3 yPI4K3Bt 1910527.83511041 0.0 std_yPI4K3Bt +experiment__model1_data1___model1_data3 yPI4K3Bt 1910527.83511041 0.0 std_yPI4K3Bt +experiment__model1_data1___model1_data3 yCERTt 465126404.56577 24.0 std_yCERTt +experiment__model1_data1___model1_data3 yCERTt 465126404.56577 24.0 std_yCERTt +experiment__model1_data1___model1_data3 yCERTt 465126404.56577 24.0 std_yCERTt diff --git a/v2/Weber_BMC2015/model_Weber_BMC2015.xml b/v2/Weber_BMC2015/model_Weber_BMC2015.xml new file mode 100644 index 0000000..58baddd --- /dev/null +++ b/v2/Weber_BMC2015/model_Weber_BMC2015.xml @@ -0,0 +1,623 @@ + + + + + + 
PEtab implementation of the model from Weber et al. (2015), BMC Syst. Biol., 9, 9
+ + + + + + + + + + Weber + Patrick + + + + + + 2019-11-29T09:41:48Z + + + 2019-11-29T09:41:48Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + + + + + + + 0 + + + time + 0 + + + + Ect_Expr_PI4K3beta_flag + + + + + + + + + 0 + + + time + 0 + + + + Ect_Expr_CERT_flag + + + + + + + + + 0 + + + + + time + PdBu_time + + 0 + + + + PdBu_dose + + + + + + + + + kb_NB142_70_dose + + + 0 + + + + + time + kb_NB142_70_time + + 0 + + + + 1 + + + + + + + + + + + + + + + + + + + + + + + cyt + + + + + CERTERa + PI4K3Ba + PKD + p11 + p31 + + + + + + PI4K3Ba + m31 + + + + m11 + + + + + CERTERa + PI4K3Ba + p31 + + + + PI4K3Ba + m31 + + + + + + + + + + + + + + + + + + + + + cyt + PKD + p12 + + + + + pu5 + u5 + + 1 + + + + + + + + + + + + + + + + + cyt + PKDDAGa + p13 + + + + + pu6 + u6 + + 1 + + + + + + + + + + + + + + cyt + s12 + + + + + + + + + + + + + cyt + pu2 + u2 + + + + + + + + + + + + + cyt + PKD + 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0000000..3674c8d --- /dev/null +++ b/v2/Weber_BMC2015/observables_Weber_BMC2015.tsv @@ -0,0 +1,9 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +yCERTpRN24 CERT * observableParameter1_yCERTpRN24 / (CERT + CERTERa + CERTTGNa) noiseParameter1_yCERTpRN24 observableParameter1_yCERTpRN24 noiseParameter1_yCERTpRN24 +yCERTt CERT + CERTERa + CERTTGNa noiseParameter1_yCERTt noiseParameter1_yCERTt +yPI4K3BpRN24 PI4K3Ba * observableParameter1_yPI4K3BpRN24 / (PI4K3B + PI4K3Ba) noiseParameter1_yPI4K3BpRN24 observableParameter1_yPI4K3BpRN24 noiseParameter1_yPI4K3BpRN24 +yPI4K3Bt PI4K3B + PI4K3Ba noiseParameter1_yPI4K3Bt noiseParameter1_yPI4K3Bt +yPKDpN0 PKDDAGa * observableParameter1_yPKDpN0 noiseParameter1_yPKDpN0 observableParameter1_yPKDpN0 noiseParameter1_yPKDpN0 +yPKDpN24 PKDDAGa * observableParameter1_yPKDpN24 noiseParameter1_yPKDpN24 observableParameter1_yPKDpN24 noiseParameter1_yPKDpN24 +yPKDpN25 PKDDAGa * observableParameter1_yPKDpN25 noiseParameter1_yPKDpN25 observableParameter1_yPKDpN25 noiseParameter1_yPKDpN25 +yPKDt PKD + PKDDAGa noiseParameter1_yPKDt noiseParameter1_yPKDt diff --git a/v2/Weber_BMC2015/parameters_Weber_BMC2015.tsv b/v2/Weber_BMC2015/parameters_Weber_BMC2015.tsv new file mode 100644 index 0000000..bec5441 --- /dev/null +++ b/v2/Weber_BMC2015/parameters_Weber_BMC2015.tsv @@ -0,0 +1,41 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorParameters +a11 a11 0.0001 100 0.182532326367113 true +a12 a12 0.0001 100 26.6713328753608 true +a21 a21 0.0001 100 1.87704479834148 true +a22 a22 0.0001 100 0.0001 true +a31 a31 0.0001 100 0.135335059339132 true +a32 a32 0.0001 100 0.0001 true +a33 a33 0.0001 100 0.0001 true +m11 m11 100.0 10000000000 10000000000.0 true +m22 m22 100.0 10000000000 2153.51392335252 true +m31 m31 100.0 10000000000 9970035709.05734 true +m33 m33 100.0 10000000000 41871228.8317411 true +p11 p11 1e-05 100000 4.24383990916234 true +p12 p12 1e-05 100000 0.005935939292274 true +p13 p13 1e-05 100000 0.002460257477278 true +p21 p21 1e-05 100000 5.6290367522644 true +p22 p22 1e-05 100000 21.7856860653472 true +p31 p31 1e-05 100000 2537.97413617078 true +p32 p32 1e-05 100000 16.7677390849425 true +p33 p33 1e-05 100000 21658.8400024158 true +pu2 pu2 1e-05 1000 1.0 false +pu3 pu3 0.1 100000000 100000000.0 true +pu4 pu4 0.1 100000000 33133606.9433133 true +pu5 pu5 0.1 100000000 33.6959765525242 true +pu6 pu6 0.1 100000000 113.366007469962 true +s12 s12 100.0 10000000 88461.2150536401 true +s21 s21 100.0 10000000 2961147.46928213 true +s31 s31 100.0 10000000 4327961.43037034 true +scale_yCERTpRN24 scale_{yCERTpRN24} 1e-05 1000 121.028409854968 true +scale_yPI4K3BpRN24 scale_{yPI4K3BpRN24} 1e-05 1000 3.39366857781642 true +scale_yPKDpN0 scale_{yPKDpN0} 1e-05 1000 0.007176447966379 true +scale_yPKDpN24 scale_{yPKDpN24} 1e-05 1000 0.003370141139919 true +scale_yPKDpN25 scale_{yPKDpN25} 1e-05 1000 0.000237349365354 true +std_yPKDt std_{yPKDt} 0.01 10000000000 1910527.835 false +std_yPI4K3Bt std_{yPI4K3Bt} 0.01 10000000000 887676.131 false +std_yCERTt std_{yCERTt} 0.01 10000000000 244727220.419 false +std_yPKDpN0 std_{yPKDpN0} 0.01 100 0.974100018572643 true +std_yPKDpN24 std_{yPKDpN24} 0.01 100 1.08030443428794 true +std_yPKDpN25 std_{yPKDpN25} 0.01 100 0.117466359121065 true +std_yPI4K3BpRN24 std_{yPI4K3BpRN24} 0.01 100 0.414223339385595 true +std_yCERTpRN24 std_{yCERTpRN24} 0.01 100 0.066162154188523 true diff --git a/v2/Zhao_QuantBiol2020/Zhao_QuantBiol2020.yaml b/v2/Zhao_QuantBiol2020/Zhao_QuantBiol2020.yaml new file mode 100644 index 0000000..68dd868 --- /dev/null +++ b/v2/Zhao_QuantBiol2020/Zhao_QuantBiol2020.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Zhao_QuantBiol2020.tsv +model_files: + model_Zhao_QuantBiol2020: + location: model_Zhao_QuantBiol2020.xml + language: sbml +measurement_files: +- measurementData_training_Zhao_QuantBiol2020.tsv +condition_files: +- experimentalCondition_Zhao_QuantBiol2020.tsv +experiment_files: +- experiments.tsv +observable_files: +- observable_Zhao_QuantBiol2020.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Zhao_QuantBiol2020/experimentalCondition_Zhao_QuantBiol2020.tsv b/v2/Zhao_QuantBiol2020/experimentalCondition_Zhao_QuantBiol2020.tsv new file mode 100644 index 0000000..d0697a1 --- /dev/null +++ b/v2/Zhao_QuantBiol2020/experimentalCondition_Zhao_QuantBiol2020.tsv @@ -0,0 +1,43 @@ +conditionId targetId targetValue +model1_Wuhan_Stage_I Trigger_Stage_I 1 +model1_Wuhan_Stage_II Trigger_Stage_I 0 +model1_Wuhan_Stage_III Trigger_Stage_I 0 +model1_Hubei_Stage_I Trigger_Stage_I 1 +model1_Hubei_Stage_II Trigger_Stage_I 0 +model1_China_Stage_I Trigger_Stage_I 1 +model1_China_Stage_II Trigger_Stage_I 0 +model1_Wuhan_Stage_I Trigger_Stage_II 0 +model1_Wuhan_Stage_II Trigger_Stage_II 1 +model1_Wuhan_Stage_III Trigger_Stage_II 0 +model1_Hubei_Stage_I Trigger_Stage_II 0 +model1_Hubei_Stage_II Trigger_Stage_II 1 +model1_China_Stage_I Trigger_Stage_II 0 +model1_China_Stage_II Trigger_Stage_II 1 +model1_Wuhan_Stage_I Trigger_Stage_III 0 +model1_Wuhan_Stage_II Trigger_Stage_III 0 +model1_Wuhan_Stage_III Trigger_Stage_III 1 +model1_Hubei_Stage_I Trigger_Stage_III 0 +model1_Hubei_Stage_II Trigger_Stage_III 0 +model1_China_Stage_I Trigger_Stage_III 0 +model1_China_Stage_II Trigger_Stage_III 0 +model1_Wuhan_Stage_I Trigger_Wuhan 1 +model1_Wuhan_Stage_II Trigger_Wuhan 1 +model1_Wuhan_Stage_III Trigger_Wuhan 1 +model1_Hubei_Stage_I Trigger_Wuhan 0 +model1_Hubei_Stage_II Trigger_Wuhan 0 +model1_China_Stage_I Trigger_Wuhan 0 +model1_China_Stage_II Trigger_Wuhan 0 +model1_Wuhan_Stage_I Trigger_Hubei 0 +model1_Wuhan_Stage_II Trigger_Hubei 0 +model1_Wuhan_Stage_III Trigger_Hubei 0 +model1_Hubei_Stage_I Trigger_Hubei 1 +model1_Hubei_Stage_II Trigger_Hubei 1 +model1_China_Stage_I Trigger_Hubei 0 +model1_China_Stage_II Trigger_Hubei 0 +model1_Wuhan_Stage_I Trigger_China 0 +model1_Wuhan_Stage_II Trigger_China 0 +model1_Wuhan_Stage_III Trigger_China 0 +model1_Hubei_Stage_I Trigger_China 0 +model1_Hubei_Stage_II Trigger_China 0 +model1_China_Stage_I Trigger_China 1 +model1_China_Stage_II Trigger_China 1 diff --git a/v2/Zhao_QuantBiol2020/experiments.tsv b/v2/Zhao_QuantBiol2020/experiments.tsv new file mode 100644 index 0000000..f067c1b --- /dev/null +++ b/v2/Zhao_QuantBiol2020/experiments.tsv @@ -0,0 +1,8 @@ +experimentId conditionId time +experiment____model1_China_Stage_I model1_China_Stage_I 0 +experiment____model1_China_Stage_II model1_China_Stage_II 0 +experiment____model1_Hubei_Stage_I model1_Hubei_Stage_I 0 +experiment____model1_Hubei_Stage_II model1_Hubei_Stage_II 0 +experiment____model1_Wuhan_Stage_I model1_Wuhan_Stage_I 0 +experiment____model1_Wuhan_Stage_II model1_Wuhan_Stage_II 0 +experiment____model1_Wuhan_Stage_III model1_Wuhan_Stage_III 0 diff --git a/v2/Zhao_QuantBiol2020/measurementData_training_Zhao_QuantBiol2020.tsv b/v2/Zhao_QuantBiol2020/measurementData_training_Zhao_QuantBiol2020.tsv new file mode 100644 index 0000000..2948a92 --- /dev/null +++ b/v2/Zhao_QuantBiol2020/measurementData_training_Zhao_QuantBiol2020.tsv @@ -0,0 +1,83 @@ +experimentId observableId measurement time observableParameters noiseParameters datasetId +experiment____model1_Wuhan_Stage_I observable_confirmed_infected 258 15 sd_confirmed_infected_Wuhan_Stage_I model1_data_observable_confirmed_infected_Wuhan_Stage_I +experiment____model1_Wuhan_Stage_I observable_confirmed_infected 363 16 sd_confirmed_infected_Wuhan_Stage_I model1_data_observable_confirmed_infected_Wuhan_Stage_I +experiment____model1_Wuhan_Stage_I observable_confirmed_infected 425 17 sd_confirmed_infected_Wuhan_Stage_I model1_data_observable_confirmed_infected_Wuhan_Stage_I +experiment____model1_Wuhan_Stage_I observable_confirmed_infected 495 18 sd_confirmed_infected_Wuhan_Stage_I model1_data_observable_confirmed_infected_Wuhan_Stage_I +experiment____model1_Wuhan_Stage_I observable_confirmed_infected 572 19 sd_confirmed_infected_Wuhan_Stage_I model1_data_observable_confirmed_infected_Wuhan_Stage_I +experiment____model1_Wuhan_Stage_I observable_confirmed_infected 618 20 sd_confirmed_infected_Wuhan_Stage_I model1_data_observable_confirmed_infected_Wuhan_Stage_I +experiment____model1_Wuhan_Stage_I observable_confirmed_infected 698 21 sd_confirmed_infected_Wuhan_Stage_I model1_data_observable_confirmed_infected_Wuhan_Stage_I +experiment____model1_Wuhan_Stage_I observable_confirmed_infected 1590 22 sd_confirmed_infected_Wuhan_Stage_I model1_data_observable_confirmed_infected_Wuhan_Stage_I +experiment____model1_Wuhan_Stage_I observable_confirmed_infected 1905 23 sd_confirmed_infected_Wuhan_Stage_I model1_data_observable_confirmed_infected_Wuhan_Stage_I +experiment____model1_Wuhan_Stage_I observable_confirmed_infected 2261 24 sd_confirmed_infected_Wuhan_Stage_I model1_data_observable_confirmed_infected_Wuhan_Stage_I +experiment____model1_Wuhan_Stage_II observable_confirmed_infected 1905 0 sd_confirmed_infected_Wuhan_Stage_II model1_data_observable_confirmed_infected_Wuhan_Stage_II +experiment____model1_Wuhan_Stage_II observable_confirmed_infected 2261 1 sd_confirmed_infected_Wuhan_Stage_II model1_data_observable_confirmed_infected_Wuhan_Stage_II +experiment____model1_Wuhan_Stage_II observable_confirmed_infected 2639 2 sd_confirmed_infected_Wuhan_Stage_II model1_data_observable_confirmed_infected_Wuhan_Stage_II +experiment____model1_Wuhan_Stage_II observable_confirmed_infected 3215 3 sd_confirmed_infected_Wuhan_Stage_II model1_data_observable_confirmed_infected_Wuhan_Stage_II +experiment____model1_Wuhan_Stage_II observable_confirmed_infected 4109 4 sd_confirmed_infected_Wuhan_Stage_II model1_data_observable_confirmed_infected_Wuhan_Stage_II +experiment____model1_Wuhan_Stage_II observable_confirmed_infected 5142 5 sd_confirmed_infected_Wuhan_Stage_II model1_data_observable_confirmed_infected_Wuhan_Stage_II +experiment____model1_Wuhan_Stage_II observable_confirmed_infected 6384 6 sd_confirmed_infected_Wuhan_Stage_II model1_data_observable_confirmed_infected_Wuhan_Stage_II +experiment____model1_Wuhan_Stage_II observable_confirmed_infected 8351 7 sd_confirmed_infected_Wuhan_Stage_II model1_data_observable_confirmed_infected_Wuhan_Stage_II +experiment____model1_Wuhan_Stage_II observable_confirmed_infected 10117 8 sd_confirmed_infected_Wuhan_Stage_II model1_data_observable_confirmed_infected_Wuhan_Stage_II +experiment____model1_Wuhan_Stage_II observable_confirmed_infected 11618 9 sd_confirmed_infected_Wuhan_Stage_II model1_data_observable_confirmed_infected_Wuhan_Stage_II +experiment____model1_Wuhan_Stage_II observable_confirmed_infected 13603 10 sd_confirmed_infected_Wuhan_Stage_II model1_data_observable_confirmed_infected_Wuhan_Stage_II +experiment____model1_Wuhan_Stage_II observable_confirmed_infected 14982 11 sd_confirmed_infected_Wuhan_Stage_II model1_data_observable_confirmed_infected_Wuhan_Stage_II +experiment____model1_Wuhan_Stage_II observable_confirmed_infected 16902 12 sd_confirmed_infected_Wuhan_Stage_II model1_data_observable_confirmed_infected_Wuhan_Stage_II +experiment____model1_Wuhan_Stage_II observable_confirmed_infected 18454 13 sd_confirmed_infected_Wuhan_Stage_II model1_data_observable_confirmed_infected_Wuhan_Stage_II +experiment____model1_Wuhan_Stage_II observable_confirmed_infected 19558 14 sd_confirmed_infected_Wuhan_Stage_II model1_data_observable_confirmed_infected_Wuhan_Stage_II +experiment____model1_Wuhan_Stage_III observable_confirmed_infected 35991 0 sd_confirmed_infected_Wuhan_Stage_III model1_data_observable_confirmed_infected_Wuhan_Stage_III +experiment____model1_Wuhan_Stage_III observable_confirmed_infected 37914 1 sd_confirmed_infected_Wuhan_Stage_III model1_data_observable_confirmed_infected_Wuhan_Stage_III +experiment____model1_Wuhan_Stage_III observable_confirmed_infected 39462 2 sd_confirmed_infected_Wuhan_Stage_III model1_data_observable_confirmed_infected_Wuhan_Stage_III +experiment____model1_Wuhan_Stage_III observable_confirmed_infected 41152 3 sd_confirmed_infected_Wuhan_Stage_III model1_data_observable_confirmed_infected_Wuhan_Stage_III +experiment____model1_Wuhan_Stage_III observable_confirmed_infected 42752 4 sd_confirmed_infected_Wuhan_Stage_III model1_data_observable_confirmed_infected_Wuhan_Stage_III +experiment____model1_Wuhan_Stage_III observable_confirmed_infected 44412 5 sd_confirmed_infected_Wuhan_Stage_III model1_data_observable_confirmed_infected_Wuhan_Stage_III +experiment____model1_Wuhan_Stage_III observable_confirmed_infected 45027 6 sd_confirmed_infected_Wuhan_Stage_III model1_data_observable_confirmed_infected_Wuhan_Stage_III +experiment____model1_Hubei_Stage_I observable_confirmed_infected 12 15 sd_confirmed_infected_Hubei_Stage_I model1_data_observable_confirmed_infected_Hubei_Stage_I +experiment____model1_Hubei_Stage_I observable_confirmed_infected 12 16 sd_confirmed_infected_Hubei_Stage_I model1_data_observable_confirmed_infected_Hubei_Stage_I +experiment____model1_Hubei_Stage_I observable_confirmed_infected 19 17 sd_confirmed_infected_Hubei_Stage_I model1_data_observable_confirmed_infected_Hubei_Stage_I +experiment____model1_Hubei_Stage_I observable_confirmed_infected 54 18 sd_confirmed_infected_Hubei_Stage_I model1_data_observable_confirmed_infected_Hubei_Stage_I +experiment____model1_Hubei_Stage_I observable_confirmed_infected 157 19 sd_confirmed_infected_Hubei_Stage_I model1_data_observable_confirmed_infected_Hubei_Stage_I +experiment____model1_Hubei_Stage_I observable_confirmed_infected 434 20 sd_confirmed_infected_Hubei_Stage_I model1_data_observable_confirmed_infected_Hubei_Stage_I +experiment____model1_Hubei_Stage_I observable_confirmed_infected 725 21 sd_confirmed_infected_Hubei_Stage_I model1_data_observable_confirmed_infected_Hubei_Stage_I +experiment____model1_Hubei_Stage_I observable_confirmed_infected 1124 22 sd_confirmed_infected_Hubei_Stage_I model1_data_observable_confirmed_infected_Hubei_Stage_I +experiment____model1_Hubei_Stage_I observable_confirmed_infected 1649 23 sd_confirmed_infected_Hubei_Stage_I model1_data_observable_confirmed_infected_Hubei_Stage_I +experiment____model1_Hubei_Stage_I observable_confirmed_infected 2325 24 sd_confirmed_infected_Hubei_Stage_I model1_data_observable_confirmed_infected_Hubei_Stage_I +experiment____model1_Hubei_Stage_II observable_confirmed_infected 1649 0 sd_confirmed_infected_Hubei_Stage_II model1_data_observable_confirmed_infected_Hubei_Stage_II +experiment____model1_Hubei_Stage_II observable_confirmed_infected 2325 1 sd_confirmed_infected_Hubei_Stage_II model1_data_observable_confirmed_infected_Hubei_Stage_II +experiment____model1_Hubei_Stage_II observable_confirmed_infected 3167 2 sd_confirmed_infected_Hubei_Stage_II model1_data_observable_confirmed_infected_Hubei_Stage_II +experiment____model1_Hubei_Stage_II observable_confirmed_infected 3938 3 sd_confirmed_infected_Hubei_Stage_II model1_data_observable_confirmed_infected_Hubei_Stage_II +experiment____model1_Hubei_Stage_II observable_confirmed_infected 4965 4 sd_confirmed_infected_Hubei_Stage_II model1_data_observable_confirmed_infected_Hubei_Stage_II +experiment____model1_Hubei_Stage_II observable_confirmed_infected 6035 5 sd_confirmed_infected_Hubei_Stage_II model1_data_observable_confirmed_infected_Hubei_Stage_II +experiment____model1_Hubei_Stage_II observable_confirmed_infected 7138 6 sd_confirmed_infected_Hubei_Stage_II model1_data_observable_confirmed_infected_Hubei_Stage_II +experiment____model1_Hubei_Stage_II observable_confirmed_infected 8327 7 sd_confirmed_infected_Hubei_Stage_II model1_data_observable_confirmed_infected_Hubei_Stage_II +experiment____model1_Hubei_Stage_II observable_confirmed_infected 9548 8 sd_confirmed_infected_Hubei_Stage_II model1_data_observable_confirmed_infected_Hubei_Stage_II +experiment____model1_Hubei_Stage_II observable_confirmed_infected 10494 9 sd_confirmed_infected_Hubei_Stage_II model1_data_observable_confirmed_infected_Hubei_Stage_II +experiment____model1_Hubei_Stage_II observable_confirmed_infected 11350 10 sd_confirmed_infected_Hubei_Stage_II model1_data_observable_confirmed_infected_Hubei_Stage_II +experiment____model1_Hubei_Stage_II observable_confirmed_infected 12118 11 sd_confirmed_infected_Hubei_Stage_II model1_data_observable_confirmed_infected_Hubei_Stage_II +experiment____model1_Hubei_Stage_II observable_confirmed_infected 12729 12 sd_confirmed_infected_Hubei_Stage_II model1_data_observable_confirmed_infected_Hubei_Stage_II +experiment____model1_Hubei_Stage_II observable_confirmed_infected 12824 13 sd_confirmed_infected_Hubei_Stage_II model1_data_observable_confirmed_infected_Hubei_Stage_II +experiment____model1_Hubei_Stage_II observable_confirmed_infected 13808 14 sd_confirmed_infected_Hubei_Stage_II model1_data_observable_confirmed_infected_Hubei_Stage_II +experiment____model1_China_Stage_I observable_confirmed_infected 21 30 sd_confirmed_infected_China_Stage_I model1_data_observable_confirmed_infected_China_Stage_I +experiment____model1_China_Stage_I observable_confirmed_infected 65 31 sd_confirmed_infected_China_Stage_I model1_data_observable_confirmed_infected_China_Stage_I +experiment____model1_China_Stage_I observable_confirmed_infected 127 32 sd_confirmed_infected_China_Stage_I model1_data_observable_confirmed_infected_China_Stage_I +experiment____model1_China_Stage_I observable_confirmed_infected 281 33 sd_confirmed_infected_China_Stage_I model1_data_observable_confirmed_infected_China_Stage_I +experiment____model1_China_Stage_I observable_confirmed_infected 558 34 sd_confirmed_infected_China_Stage_I model1_data_observable_confirmed_infected_China_Stage_I +experiment____model1_China_Stage_I observable_confirmed_infected 923 35 sd_confirmed_infected_China_Stage_I model1_data_observable_confirmed_infected_China_Stage_I +experiment____model1_China_Stage_I observable_confirmed_infected 1321 36 sd_confirmed_infected_China_Stage_I model1_data_observable_confirmed_infected_China_Stage_I +experiment____model1_China_Stage_I observable_confirmed_infected 1801 37 sd_confirmed_infected_China_Stage_I model1_data_observable_confirmed_infected_China_Stage_I +experiment____model1_China_Stage_I observable_confirmed_infected 2420 38 sd_confirmed_infected_China_Stage_I model1_data_observable_confirmed_infected_China_Stage_I +experiment____model1_China_Stage_I observable_confirmed_infected 3125 39 sd_confirmed_infected_China_Stage_I model1_data_observable_confirmed_infected_China_Stage_I +experiment____model1_China_Stage_II observable_confirmed_infected 3886 0 sd_confirmed_infected_China_Stage_II model1_data_observable_confirmed_infected_China_Stage_II +experiment____model1_China_Stage_II observable_confirmed_infected 4638 1 sd_confirmed_infected_China_Stage_II model1_data_observable_confirmed_infected_China_Stage_II +experiment____model1_China_Stage_II observable_confirmed_infected 5306 2 sd_confirmed_infected_China_Stage_II model1_data_observable_confirmed_infected_China_Stage_II +experiment____model1_China_Stage_II observable_confirmed_infected 6059 3 sd_confirmed_infected_China_Stage_II model1_data_observable_confirmed_infected_China_Stage_II +experiment____model1_China_Stage_II observable_confirmed_infected 6949 4 sd_confirmed_infected_China_Stage_II model1_data_observable_confirmed_infected_China_Stage_II +experiment____model1_China_Stage_II observable_confirmed_infected 7685 5 sd_confirmed_infected_China_Stage_II model1_data_observable_confirmed_infected_China_Stage_II +experiment____model1_China_Stage_II observable_confirmed_infected 8395 6 sd_confirmed_infected_China_Stage_II model1_data_observable_confirmed_infected_China_Stage_II +experiment____model1_China_Stage_II observable_confirmed_infected 9099 7 sd_confirmed_infected_China_Stage_II model1_data_observable_confirmed_infected_China_Stage_II +experiment____model1_China_Stage_II observable_confirmed_infected 9645 8 sd_confirmed_infected_China_Stage_II model1_data_observable_confirmed_infected_China_Stage_II +experiment____model1_China_Stage_II observable_confirmed_infected 10151 9 sd_confirmed_infected_China_Stage_II model1_data_observable_confirmed_infected_China_Stage_II +experiment____model1_China_Stage_II observable_confirmed_infected 10604 10 sd_confirmed_infected_China_Stage_II model1_data_observable_confirmed_infected_China_Stage_II +experiment____model1_China_Stage_II observable_confirmed_infected 10980 11 sd_confirmed_infected_China_Stage_II model1_data_observable_confirmed_infected_China_Stage_II +experiment____model1_China_Stage_II observable_confirmed_infected 11364 12 sd_confirmed_infected_China_Stage_II model1_data_observable_confirmed_infected_China_Stage_II +experiment____model1_China_Stage_II observable_confirmed_infected 11676 13 sd_confirmed_infected_China_Stage_II model1_data_observable_confirmed_infected_China_Stage_II +experiment____model1_China_Stage_II observable_confirmed_infected 11946 14 sd_confirmed_infected_China_Stage_II model1_data_observable_confirmed_infected_China_Stage_II diff --git a/v2/Zhao_QuantBiol2020/model_Zhao_QuantBiol2020.xml b/v2/Zhao_QuantBiol2020/model_Zhao_QuantBiol2020.xml new file mode 100644 index 0000000..d1b80e5 --- /dev/null +++ b/v2/Zhao_QuantBiol2020/model_Zhao_QuantBiol2020.xml @@ -0,0 +1,1585 @@ + + + + + + + 
Background - The coronavirus disease 2019 (COVID-19) is rapidly spreading in China and more than 30 countries over last two months. COVID-19 has multiple characteristics distinct from other infectious diseases, including high infectivity during incubation, time delay between real dynamics and daily observed number of confirmed cases, and the intervention effects of implemented quarantine and control measures. Methods - We develop a Susceptible, Un-quanrantined infected, Quarantined infected, Confirmed infected (SUQC) model to characterize the dynamics of COVID-19 and explicitly parameterize the intervention effects of control measures, which is more suitable for analysis than other existing epidemic models. Results - The SUQC model is applied to the daily released data of the confirmed infections to analyze the outbreak of COVID-19 in Wuhan, Hubei (excluding Wuhan), China (excluding Hubei) and four first-tier cities of China. We found that, before January 30, 2020, all these regions except Beijing had a reproductive number R > 1, and after January 30, all regions had a reproductive number R lesser than 1, indicating that the quarantine and control measures are effective in preventing the spread of COVID-19. The confirmation rate of Wuhan estimated by our model is 0.0643, substantially lower than that of Hubei excluding Wuhan (0.1914), and that of China excluding Hubei (0.2189), but it jumps to 0.3229 after February 12 when clinical evidence was adopted in new diagnosis guidelines. The number of unquarantined infected cases in Wuhan on February 12, 2020 is estimated to be 3,509 and declines to 334 on February 21, 2020. After fitting the model with data as of February 21, 2020, we predict that the end time of COVID-19 in Wuhan and Hubei is around late March, around mid March for China excluding Hubei, and before early March 2020 for the four tier-one cities. A total of 80,511 individuals are estimated to be infected in China, among which 49,510 are from Wuhan, 17,679 from Hubei (excluding Wuhan), and the rest 13,322 from other regions of China (excluding Hubei). Note that the estimates are from a deterministic ODE model and should be interpreted with some uncertainty. Conclusions - We suggest that rigorous quarantine and control measures should be kept before early March in Beijing, Shanghai, Guangzhou and Shenzhen, and before late March in Hubei. The model can also be useful to predict the trend of epidemic and provide quantitative guide for other countries at high risk of outbreak, such as South Korea, Japan, Italy and Iran.
+ + + + + + + + + + Ramachandran + Kausthubh + + kramachandran@ebi.ac.uk + + EMBL-EBI + + + + + + 2020-08-26T10:14:39Z + + + 2020-08-26T10:14:39Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2020-08-26T10:14:39Z + + + + + kramachandran@ebi.ac.uk + + + Ramachandran + Kausthubh + + + + + EMBL-EBI + + + + + + + + + + + + + + + + + + 2020-08-26T09:17:34Z + + + + + + + + + + alpha + + + S + + + U + + + N + + + + + + alpha + S + U + + N + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2020-08-26T10:14:57Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2020-08-26T10:15:02Z + + + + + + + + + + + + + 
Wuhan - initial values
+Stage I - 258
+Stage II - 15270
+Stage III - 4000
+
+Hubei - initial values
+Stage I - 270
+Stage II - 5700
+
+China - initial values
+Stage I - 291 (Set model initial time to -30. Keep it at 0 for everything else)
+Stage II - 2800
+ + + + + + + + + + + + + + + + + + + + + + + 2020-08-26T10:15:04Z + + + + + + + + + + + + + 
Wuhan - initial values
+Stage I - 0
+Stage II - 0
+Stage III - 5000
+
+Hubei - initial values
+Stage I - 0
+Stage II - 1500
+
+China - initial values
+Stage I - 0 (Set model initial time to -30 for Stage I alone. Keep it at 0 for everything else)
+Stage II - 2000
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + 2020-08-26T10:15:06Z + + + + + + + + + + + + + + 
Wuhan - initial values
+Stage I - 258
+Stage II - 2000
+Stage III - 36000
+
+Hubei - initial values
+Stage I - 0
+Stage II - 1600
+
+China - initial values
+Stage I - 0 (Set model initial time to -30. Keep it at 0 for everything else)
+Stage II - 4000
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2020-08-26T12:42:49Z + + + + + + + + + + + + + + + 2020-08-26T12:42:54Z + + + + + + + + + + + + Total_Pop + + + + + + + + + Trigger_Wuhan + + + + + Trigger_Stage_I + 258 + + + + Trigger_Stage_II + 15270 + + + + Trigger_Stage_III + 4000 + + + + + + Trigger_Hubei + + + + + Trigger_Stage_I + 270 + + + + Trigger_Stage_II + 5700 + + + + + + Trigger_China + + + + + Trigger_Stage_I + 291 + + + + Trigger_Stage_II + 2800 + + + + + + + + + + + + + Trigger_Wuhan + + + + + Trigger_Stage_I + 0 + + + + Trigger_Stage_II + 0 + + + + Trigger_Stage_III + 5000 + + + + + + Trigger_Hubei + + + + + Trigger_Stage_I + 0 + + + + Trigger_Stage_II + 1500 + + + + + + Trigger_China + + + + + Trigger_Stage_I + 0 + + + + Trigger_Stage_II + 2000 + + + + + + + + + + + + + Trigger_Wuhan + + + + + Trigger_Stage_I + 258 + + + + Trigger_Stage_II + 2000 + + + + Trigger_Stage_III + 36000 + + + + + + Trigger_Hubei + + + + + Trigger_Stage_I + 0 + + + + Trigger_Stage_II + 1600 + + + + + + Trigger_China + + + + + 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Trigger_Stage_II + gamma_2_Stage_II_Hubei + + + + + + Trigger_China + + + + + Trigger_Stage_I + gamma_2_Stage_I_China + + + + Trigger_Stage_II + gamma_2_Stage_II_China + + + + + + + + + + + gamma_2 + + + + + 1 + gamma_2 + + sigma + + + + + + + + + + + Trigger_Wuhan + + + + + Trigger_Stage_I + R_Stage_I_Wuhan + + + + Trigger_Stage_II + R_Stage_II_Wuhan + + + + Trigger_Stage_III + R_Stage_III_Wuhan + + + + + + Trigger_Hubei + + + + + Trigger_Stage_I + R_Stage_I_Hubei + + + + Trigger_Stage_II + R_Stage_II_Hubei + + + + + + Trigger_China + + + + + Trigger_Stage_I + R_Stage_I_China + + + + Trigger_Stage_II + R_Stage_II_China + + + + + + + + + + + R + gamma_1 + + + + + + + + + + + + + + + + + + + + + + + + + + + 2020-08-26T10:15:35Z + + + + + + + + + + + + + + + + + + + China + + Rate_Law_for_R1 + alpha + Susceptible + Unquarantined_Infected + Total_Pop + + + + + + + + + + + + + + + + + + + + + + + + + + + 2020-08-26T10:15:37Z + + + + + + + + + + + + + + + + + + + China + gamma_1 + Unquarantined_Infected + + + + + + + + + + + + + + + + + + + + + + + + + + 2020-08-26T10:15:38Z + + + + + + + + + + + + + + + + + + + China + beta + Quarantined_Infected + + + + + + + diff --git a/v2/Zhao_QuantBiol2020/observable_Zhao_QuantBiol2020.tsv b/v2/Zhao_QuantBiol2020/observable_Zhao_QuantBiol2020.tsv new file mode 100644 index 0000000..9fb8bdc --- /dev/null +++ b/v2/Zhao_QuantBiol2020/observable_Zhao_QuantBiol2020.tsv @@ -0,0 +1,6 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +observable_confirmed_infected confirmed_infected Confirmed_Infected noiseParameter1_observable_confirmed_infected normal noiseParameter1_observable_confirmed_infected +observable_susceptible susceptible Susceptible noiseParameter1_observable_susceptible normal noiseParameter1_observable_susceptible +observable_unquarantined_infected unquarantined_infected Unquarantined_Infected noiseParameter1_observable_unquarantined_infected normal noiseParameter1_observable_unquarantined_infected +observable_quarantined_infected quarantined_infected Quarantined_Infected noiseParameter1_observable_quarantined_infected normal noiseParameter1_observable_quarantined_infected +observable_cumulative_infected cumulative_infected Cumulative_Infected noiseParameter1_observable_cumulative_infected normal noiseParameter1_observable_cumulative_infected diff --git a/v2/Zhao_QuantBiol2020/parameters_Zhao_QuantBiol2020.tsv b/v2/Zhao_QuantBiol2020/parameters_Zhao_QuantBiol2020.tsv new file mode 100644 index 0000000..2112176 --- /dev/null +++ b/v2/Zhao_QuantBiol2020/parameters_Zhao_QuantBiol2020.tsv @@ -0,0 +1,30 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorDistribution priorParameters +sigma sigma 1e-08 1 0.0 false uniform 1e-08;1 +R_Stage_I_Wuhan R_Stage_I_Wuhan 0.001 100 4.7092 true uniform 0.001;100 +gamma_1_Stage_I_Wuhan gamma_1_Stage_I_Wuhan 1e-08 1 0.063 true uniform 1e-08;1 +gamma_2_Stage_I_Wuhan gamma_2_Stage_I_Wuhan 1e-08 1 0.05 true uniform 1e-08;1 +R_Stage_II_Wuhan R_Stage_II_Wuhan 0.001 100 0.7575 true uniform 0.001;100 +gamma_1_Stage_II_Wuhan gamma_1_Stage_II_Wuhan 1e-08 1 0.3917 true uniform 1e-08;1 +gamma_2_Stage_II_Wuhan gamma_2_Stage_II_Wuhan 1e-08 1 0.0643 true uniform 1e-08;1 +R_Stage_III_Wuhan R_Stage_III_Wuhan 0.001 100 0.4797 true uniform 0.001;100 +gamma_1_Stage_III_Wuhan gamma_1_Stage_III_Wuhan 1e-08 1 0.6185 true uniform 1e-08;1 +gamma_2_Stage_III_Wuhan gamma_2_Stage_III_Wuhan 1e-08 1 0.322 true uniform 1e-08;1 +R_Stage_I_Hubei R_Stage_I_Hubei 0.001 100 5.934 true uniform 0.001;100 +gamma_1_Stage_I_Hubei gamma_1_Stage_I_Hubei 1e-08 1 0.05 true uniform 1e-08;1 +gamma_2_Stage_I_Hubei gamma_2_Stage_I_Hubei 1e-08 1 0.05 true uniform 1e-08;1 +R_Stage_II_Hubei R_Stage_II_Hubei 0.001 100 0.6079 true uniform 0.001;100 +gamma_1_Stage_II_Hubei gamma_1_Stage_II_Hubei 1e-08 1 0.488 true uniform 1e-08;1 +gamma_2_Stage_II_Hubei gamma_2_Stage_II_Hubei 1e-08 1 0.1914 true uniform 1e-08;1 +R_Stage_I_China R_Stage_I_China 0.001 100 1.5283 true uniform 0.001;100 +gamma_1_Stage_I_China gamma_1_Stage_I_China 1e-08 1 0.1941 true uniform 1e-08;1 +gamma_2_Stage_I_China gamma_2_Stage_I_China 1e-08 1 0.05 true uniform 1e-08;1 +R_Stage_II_China R_Stage_II_China 0.001 100 0.5753 true uniform 0.001;100 +gamma_1_Stage_II_China gamma_1_Stage_II_China 1e-08 1 0.5157 true uniform 1e-08;1 +gamma_2_Stage_II_China gamma_2_Stage_II_China 1e-08 1 0.2189 true uniform 1e-08;1 +sd_confirmed_infected_Wuhan_Stage_I sd_confirmed_infected_Wuhan_Stage_I 0.001 100000 1000.0 true uniform 0.001;100000 +sd_confirmed_infected_Wuhan_Stage_II sd_confirmed_infected_Wuhan_Stage_II 0.001 100000 1000.0 true uniform 0.001;100000 +sd_confirmed_infected_Wuhan_Stage_III sd_confirmed_infected_Wuhan_Stage_III 0.001 100000 1000.0 true uniform 0.001;100000 +sd_confirmed_infected_Hubei_Stage_I sd_confirmed_infected_Hubei_Stage_I 0.001 100000 1000.0 true uniform 0.001;100000 +sd_confirmed_infected_Hubei_Stage_II sd_confirmed_infected_Hubei_Stage_II 0.001 100000 1000.0 true uniform 0.001;100000 +sd_confirmed_infected_China_Stage_I sd_confirmed_infected_China_Stage_I 0.001 100000 1000.0 true uniform 0.001;100000 +sd_confirmed_infected_China_Stage_II sd_confirmed_infected_China_Stage_II 0.001 100000 1000.0 true uniform 0.001;100000 diff --git a/v2/Zheng_PNAS2012/Zheng_PNAS2012.yaml b/v2/Zheng_PNAS2012/Zheng_PNAS2012.yaml new file mode 100644 index 0000000..1870404 --- /dev/null +++ b/v2/Zheng_PNAS2012/Zheng_PNAS2012.yaml @@ -0,0 +1,17 @@ +format_version: 2.0.0 +parameter_files: +- parameters_Zheng_PNAS2012.tsv +model_files: + model_Zheng_PNAS2012: + location: model_Zheng_PNAS2012.xml + language: sbml +measurement_files: +- measurementData_Zheng_PNAS2012.tsv +condition_files: +- experimentalCondition_Zheng_PNAS2012.tsv +experiment_files: +- experiments.tsv +observable_files: +- observables_Zheng_PNAS2012.tsv +mapping_files: [] +extensions: {} diff --git a/v2/Zheng_PNAS2012/experimentalCondition_Zheng_PNAS2012.tsv b/v2/Zheng_PNAS2012/experimentalCondition_Zheng_PNAS2012.tsv new file mode 100644 index 0000000..864ed63 --- /dev/null +++ b/v2/Zheng_PNAS2012/experimentalCondition_Zheng_PNAS2012.tsv @@ -0,0 +1,3 @@ +conditionId targetId targetValue +preequilibration dilution 1 +simCondition dilution 0 diff --git a/v2/Zheng_PNAS2012/experiments.tsv b/v2/Zheng_PNAS2012/experiments.tsv new file mode 100644 index 0000000..d54350f --- /dev/null +++ b/v2/Zheng_PNAS2012/experiments.tsv @@ -0,0 +1,3 @@ +experimentId conditionId time +experiment__preequilibration___simCondition preequilibration -inf +experiment__preequilibration___simCondition simCondition 0.0 diff --git a/v2/Zheng_PNAS2012/measurementData_Zheng_PNAS2012.tsv b/v2/Zheng_PNAS2012/measurementData_Zheng_PNAS2012.tsv new file mode 100644 index 0000000..905a58e --- /dev/null +++ b/v2/Zheng_PNAS2012/measurementData_Zheng_PNAS2012.tsv @@ -0,0 +1,61 @@ +experimentId observableId measurement time observableParameters noiseParameters +experiment__preequilibration___simCondition observable_K27me0K36me0 0.0043100000000000005 0 sigma +experiment__preequilibration___simCondition observable_K27me0K36me0 0.00093 5 sigma +experiment__preequilibration___simCondition observable_K27me0K36me0 0.0005099999999999999 10 sigma +experiment__preequilibration___simCondition observable_K27me0K36me0 0.00054 25 sigma +experiment__preequilibration___simCondition observable_K27me0K36me1 0.007890000000000001 0 sigma +experiment__preequilibration___simCondition observable_K27me0K36me1 0.00499 5 sigma +experiment__preequilibration___simCondition observable_K27me0K36me1 0.0030800000000000003 10 sigma +experiment__preequilibration___simCondition observable_K27me0K36me1 0.00131 25 sigma +experiment__preequilibration___simCondition observable_K27me1K36me0 0.00216 0 sigma +experiment__preequilibration___simCondition observable_K27me1K36me0 0.00159 5 sigma +experiment__preequilibration___simCondition observable_K27me1K36me0 0.00123 10 sigma +experiment__preequilibration___simCondition observable_K27me1K36me0 0.00091 25 sigma +experiment__preequilibration___simCondition observable_K27me0K36me2 0.16777 0 sigma +experiment__preequilibration___simCondition observable_K27me0K36me2 0.14469 5 sigma +experiment__preequilibration___simCondition observable_K27me0K36me2 0.1214 10 sigma +experiment__preequilibration___simCondition observable_K27me0K36me2 0.05789 25 sigma +experiment__preequilibration___simCondition observable_K27me1K36me1 0.00908 0 sigma +experiment__preequilibration___simCondition observable_K27me1K36me1 0.007240000000000002 5 sigma +experiment__preequilibration___simCondition observable_K27me1K36me1 0.00619 10 sigma +experiment__preequilibration___simCondition observable_K27me1K36me1 0.00323 25 sigma +experiment__preequilibration___simCondition observable_K27me2K36me0 0.006229999999999999 0 sigma +experiment__preequilibration___simCondition observable_K27me2K36me0 0.006840000000000001 5 sigma +experiment__preequilibration___simCondition observable_K27me2K36me0 0.006229999999999999 10 sigma +experiment__preequilibration___simCondition observable_K27me2K36me0 0.00609 25 sigma +experiment__preequilibration___simCondition observable_K27me0K36me3 0.04922 0 sigma +experiment__preequilibration___simCondition observable_K27me0K36me3 0.05666 5 sigma +experiment__preequilibration___simCondition observable_K27me0K36me3 0.060289999999999996 10 sigma +experiment__preequilibration___simCondition observable_K27me0K36me3 0.05922 25 sigma +experiment__preequilibration___simCondition observable_K27me1K36me2 0.59615 0 sigma +experiment__preequilibration___simCondition observable_K27me1K36me2 0.60752 5 sigma +experiment__preequilibration___simCondition observable_K27me1K36me2 0.61758 10 sigma +experiment__preequilibration___simCondition observable_K27me1K36me2 0.6578 25 sigma +experiment__preequilibration___simCondition observable_K27me2K36me1 0.013619999999999998 0 sigma +experiment__preequilibration___simCondition observable_K27me2K36me1 0.013669999999999998 5 sigma +experiment__preequilibration___simCondition observable_K27me2K36me1 0.01347 10 sigma +experiment__preequilibration___simCondition observable_K27me2K36me1 0.0131 25 sigma +experiment__preequilibration___simCondition observable_K27me3K36me0 0.00285 0 sigma +experiment__preequilibration___simCondition observable_K27me3K36me0 0.00309 5 sigma +experiment__preequilibration___simCondition observable_K27me3K36me0 0.00365 10 sigma +experiment__preequilibration___simCondition observable_K27me3K36me0 0.00398 25 sigma +experiment__preequilibration___simCondition observable_K27me1K36me3 0.10672000000000001 0 sigma +experiment__preequilibration___simCondition observable_K27me1K36me3 0.11679 5 sigma +experiment__preequilibration___simCondition observable_K27me1K36me3 0.1198 10 sigma +experiment__preequilibration___simCondition observable_K27me1K36me3 0.14836 25 sigma +experiment__preequilibration___simCondition observable_K27me2K36me2 0.02539 0 sigma +experiment__preequilibration___simCondition observable_K27me2K36me2 0.027089999999999996 5 sigma +experiment__preequilibration___simCondition observable_K27me2K36me2 0.037160000000000006 10 sigma +experiment__preequilibration___simCondition observable_K27me2K36me2 0.03508 25 sigma +experiment__preequilibration___simCondition observable_K27me3K36me1 0.00223 0 sigma +experiment__preequilibration___simCondition observable_K27me3K36me1 0.00263 5 sigma +experiment__preequilibration___simCondition observable_K27me3K36me1 0.00255 10 sigma +experiment__preequilibration___simCondition observable_K27me3K36me1 0.00312 25 sigma +experiment__preequilibration___simCondition observable_K27me2K36me3 0.00527 0 sigma +experiment__preequilibration___simCondition observable_K27me2K36me3 0.00483 5 sigma +experiment__preequilibration___simCondition observable_K27me2K36me3 0.00575 10 sigma +experiment__preequilibration___simCondition observable_K27me2K36me3 0.00747 25 sigma +experiment__preequilibration___simCondition observable_K27me3K36me2 0.00112 0 sigma +experiment__preequilibration___simCondition observable_K27me3K36me2 0.00148 5 sigma +experiment__preequilibration___simCondition observable_K27me3K36me2 0.00112 10 sigma +experiment__preequilibration___simCondition observable_K27me3K36me2 0.00186 25 sigma diff --git a/v2/Zheng_PNAS2012/model_Zheng_PNAS2012.xml b/v2/Zheng_PNAS2012/model_Zheng_PNAS2012.xml new file mode 100644 index 0000000..a720229 --- /dev/null +++ b/v2/Zheng_PNAS2012/model_Zheng_PNAS2012.xml @@ -0,0 +1,2832 @@ + + + + + + 
PEtab implementation of the model from Zheng et al. (2012), Proc. Natl. Acad. Sci. USA, 109, 13549–13554
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inflow + + + + + + + + + + + + + + default + + Function_for_v_57 + K27me3K36me1 + default + inflow + + + + + + + + + + + + + + default + + Function_for_v_58 + K27me2K36me3 + default + inflow + + + + + + + + + + + + + + default + + Function_for_v_59 + K27me3K36me2 + default + inflow + + + + + + + + diff --git a/v2/Zheng_PNAS2012/observables_Zheng_PNAS2012.tsv b/v2/Zheng_PNAS2012/observables_Zheng_PNAS2012.tsv new file mode 100644 index 0000000..72529db --- /dev/null +++ b/v2/Zheng_PNAS2012/observables_Zheng_PNAS2012.tsv @@ -0,0 +1,16 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders +observable_K27me0K36me0 observable_K27me0K36me0 K27me0K36me0 / (K27me0K36me0 + K27me0K36me1 + K27me0K36me2 + K27me0K36me3 + K27me1K36me0 + K27me1K36me1 + K27me1K36me2 + K27me1K36me3 + K27me2K36me0 + K27me2K36me1 + K27me2K36me2 + K27me2K36me3 + K27me3K36me0 + K27me3K36me1 + K27me3K36me2) noiseParameter1_observable_K27me0K36me0 noiseParameter1_observable_K27me0K36me0 +observable_K27me0K36me1 observable_K27me0K36me1 K27me0K36me1 / (K27me0K36me0 + K27me0K36me1 + K27me0K36me2 + K27me0K36me3 + K27me1K36me0 + K27me1K36me1 + K27me1K36me2 + K27me1K36me3 + K27me2K36me0 + K27me2K36me1 + K27me2K36me2 + K27me2K36me3 + K27me3K36me0 + K27me3K36me1 + K27me3K36me2) noiseParameter1_observable_K27me0K36me1 noiseParameter1_observable_K27me0K36me1 +observable_K27me0K36me2 observable_K27me0K36me2 K27me0K36me2 / (K27me0K36me0 + K27me0K36me1 + K27me0K36me2 + K27me0K36me3 + K27me1K36me0 + K27me1K36me1 + K27me1K36me2 + K27me1K36me3 + K27me2K36me0 + K27me2K36me1 + K27me2K36me2 + K27me2K36me3 + K27me3K36me0 + K27me3K36me1 + K27me3K36me2) noiseParameter1_observable_K27me0K36me2 noiseParameter1_observable_K27me0K36me2 +observable_K27me0K36me3 observable_K27me0K36me3 K27me0K36me3 / (K27me0K36me0 + K27me0K36me1 + K27me0K36me2 + K27me0K36me3 + K27me1K36me0 + K27me1K36me1 + K27me1K36me2 + K27me1K36me3 + K27me2K36me0 + K27me2K36me1 + K27me2K36me2 + K27me2K36me3 + K27me3K36me0 + K27me3K36me1 + K27me3K36me2) noiseParameter1_observable_K27me0K36me3 noiseParameter1_observable_K27me0K36me3 +observable_K27me1K36me0 observable_K27me1K36me0 K27me1K36me0 / (K27me0K36me0 + K27me0K36me1 + K27me0K36me2 + K27me0K36me3 + K27me1K36me0 + K27me1K36me1 + K27me1K36me2 + K27me1K36me3 + K27me2K36me0 + K27me2K36me1 + K27me2K36me2 + K27me2K36me3 + K27me3K36me0 + K27me3K36me1 + K27me3K36me2) noiseParameter1_observable_K27me1K36me0 noiseParameter1_observable_K27me1K36me0 +observable_K27me1K36me1 observable_K27me1K36me1 K27me1K36me1 / (K27me0K36me0 + K27me0K36me1 + K27me0K36me2 + K27me0K36me3 + K27me1K36me0 + K27me1K36me1 + K27me1K36me2 + K27me1K36me3 + K27me2K36me0 + K27me2K36me1 + K27me2K36me2 + K27me2K36me3 + K27me3K36me0 + K27me3K36me1 + K27me3K36me2) noiseParameter1_observable_K27me1K36me1 noiseParameter1_observable_K27me1K36me1 +observable_K27me1K36me2 observable_K27me1K36me2 K27me1K36me2 / (K27me0K36me0 + K27me0K36me1 + K27me0K36me2 + K27me0K36me3 + K27me1K36me0 + K27me1K36me1 + K27me1K36me2 + K27me1K36me3 + K27me2K36me0 + K27me2K36me1 + K27me2K36me2 + K27me2K36me3 + K27me3K36me0 + K27me3K36me1 + K27me3K36me2) noiseParameter1_observable_K27me1K36me2 noiseParameter1_observable_K27me1K36me2 +observable_K27me1K36me3 observable_K27me1K36me3 K27me1K36me3 / (K27me0K36me0 + K27me0K36me1 + K27me0K36me2 + K27me0K36me3 + K27me1K36me0 + K27me1K36me1 + K27me1K36me2 + K27me1K36me3 + K27me2K36me0 + K27me2K36me1 + K27me2K36me2 + K27me2K36me3 + K27me3K36me0 + K27me3K36me1 + K27me3K36me2) noiseParameter1_observable_K27me1K36me3 noiseParameter1_observable_K27me1K36me3 +observable_K27me2K36me0 observable_K27me2K36me0 K27me2K36me0 / (K27me0K36me0 + K27me0K36me1 + K27me0K36me2 + K27me0K36me3 + K27me1K36me0 + K27me1K36me1 + K27me1K36me2 + K27me1K36me3 + K27me2K36me0 + K27me2K36me1 + K27me2K36me2 + K27me2K36me3 + K27me3K36me0 + K27me3K36me1 + K27me3K36me2) noiseParameter1_observable_K27me2K36me0 noiseParameter1_observable_K27me2K36me0 +observable_K27me2K36me1 observable_K27me2K36me1 K27me2K36me1 / (K27me0K36me0 + K27me0K36me1 + K27me0K36me2 + K27me0K36me3 + K27me1K36me0 + K27me1K36me1 + K27me1K36me2 + K27me1K36me3 + K27me2K36me0 + K27me2K36me1 + K27me2K36me2 + K27me2K36me3 + K27me3K36me0 + K27me3K36me1 + K27me3K36me2) noiseParameter1_observable_K27me2K36me1 noiseParameter1_observable_K27me2K36me1 +observable_K27me2K36me2 observable_K27me2K36me2 K27me2K36me2 / (K27me0K36me0 + K27me0K36me1 + K27me0K36me2 + K27me0K36me3 + K27me1K36me0 + K27me1K36me1 + K27me1K36me2 + K27me1K36me3 + K27me2K36me0 + K27me2K36me1 + K27me2K36me2 + K27me2K36me3 + K27me3K36me0 + K27me3K36me1 + K27me3K36me2) noiseParameter1_observable_K27me2K36me2 noiseParameter1_observable_K27me2K36me2 +observable_K27me2K36me3 observable_K27me2K36me3 K27me2K36me3 / (K27me0K36me0 + K27me0K36me1 + K27me0K36me2 + K27me0K36me3 + K27me1K36me0 + K27me1K36me1 + K27me1K36me2 + K27me1K36me3 + K27me2K36me0 + K27me2K36me1 + K27me2K36me2 + K27me2K36me3 + K27me3K36me0 + K27me3K36me1 + K27me3K36me2) noiseParameter1_observable_K27me2K36me3 noiseParameter1_observable_K27me2K36me3 +observable_K27me3K36me0 observable_K27me3K36me0 K27me3K36me0 / (K27me0K36me0 + K27me0K36me1 + K27me0K36me2 + K27me0K36me3 + K27me1K36me0 + K27me1K36me1 + K27me1K36me2 + K27me1K36me3 + K27me2K36me0 + K27me2K36me1 + K27me2K36me2 + K27me2K36me3 + K27me3K36me0 + K27me3K36me1 + K27me3K36me2) noiseParameter1_observable_K27me3K36me0 noiseParameter1_observable_K27me3K36me0 +observable_K27me3K36me1 observable_K27me3K36me1 K27me3K36me1 / (K27me0K36me0 + K27me0K36me1 + K27me0K36me2 + K27me0K36me3 + K27me1K36me0 + K27me1K36me1 + K27me1K36me2 + K27me1K36me3 + K27me2K36me0 + K27me2K36me1 + K27me2K36me2 + K27me2K36me3 + K27me3K36me0 + K27me3K36me1 + K27me3K36me2) noiseParameter1_observable_K27me3K36me1 noiseParameter1_observable_K27me3K36me1 +observable_K27me3K36me2 observable_K27me3K36me2 K27me3K36me2 / (K27me0K36me0 + K27me0K36me1 + K27me0K36me2 + K27me0K36me3 + K27me1K36me0 + K27me1K36me1 + K27me1K36me2 + K27me1K36me3 + K27me2K36me0 + K27me2K36me1 + K27me2K36me2 + K27me2K36me3 + K27me3K36me0 + K27me3K36me1 + K27me3K36me2) noiseParameter1_observable_K27me3K36me2 noiseParameter1_observable_K27me3K36me2 diff --git a/v2/Zheng_PNAS2012/parameters_Zheng_PNAS2012.tsv b/v2/Zheng_PNAS2012/parameters_Zheng_PNAS2012.tsv new file mode 100644 index 0000000..9a88efe --- /dev/null +++ b/v2/Zheng_PNAS2012/parameters_Zheng_PNAS2012.tsv @@ -0,0 +1,47 @@ +parameterId parameterName lowerBound upperBound nominalValue estimate priorParameters +inflowp {inflowp} 1e-05 1000 0.030481175027538 true +k00_01 k_{00->01} 1e-05 1000 997.285248531849 true +k00_10 k_{00->10} 1e-05 1000 0.234022855508701 true +k01_00 k_{01->00} 1e-05 1000 479.841669671183 true +k01_02 k_{01->02} 1e-05 1000 1.91338331591714 true +k01_11 k_{01->11} 1e-05 1000 2.65149503233364 true +k02_01 k_{02->01} 1e-05 1000 0.069963622479452 true +k02_03 k_{02->03} 1e-05 1000 1.00000043186406e-05 true +k02_12 k_{02->12} 1e-05 1000 1.00000120988758e-05 true +k03_02 k_{03->02} 1e-05 1000 1.00000000000005e-05 true +k03_13 k_{03->13} 1e-05 1000 988.122424319195 true +k10_00 k_{10->00} 1e-05 1000 1.00000000016979e-05 true +k10_11 k_{10->11} 1e-05 1000 1.00000002387735e-05 true +k10_20 k_{10->20} 1e-05 1000 0.269191681409128 true +k11_01 k_{11->01} 1e-05 1000 1.00000000001725e-05 true +k11_10 k_{11->10} 1e-05 1000 1.0002960370593e-05 true +k11_12 k_{11->12} 1e-05 1000 11.8517895122981 true +k11_21 k_{11->21} 1e-05 1000 1.00000003508203e-05 true +k12_02 k_{12->02} 1e-05 1000 1.00000000000196e-05 true +k12_11 k_{12->11} 1e-05 1000 0.1069993783787 true +k12_13 k_{12->13} 1e-05 1000 0.035629896010771 true +k12_22 k_{12->22} 1e-05 1000 0.010616590659942 true +k13_03 k_{13->03} 1e-05 1000 450.435886070063 true +k13_12 k_{13->12} 1e-05 1000 0.195255677936969 true +k13_23 k_{13->23} 1e-05 1000 1.00000000438336e-05 true +k20_10 k_{20->10} 1e-05 1000 1.00000000000005e-05 true +k20_21 k_{20->21} 1e-05 1000 1.00000043202964e-05 true +k20_30 k_{20->30} 1e-05 1000 0.150740144379533 true +k21_11 k_{21->11} 1e-05 1000 1.00035442572023e-05 true +k21_20 k_{21->20} 1e-05 1000 0.035397749723473 true +k21_22 k_{21->22} 1e-05 1000 999.279628838538 true +k21_31 k_{21->31} 1e-05 1000 1.00000000261933e-05 true +k22_12 k_{22->12} 1e-05 1000 0.053379637739473 true +k22_21 k_{22->21} 1e-05 1000 426.143170255777 true +k22_23 k_{22->23} 1e-05 1000 0.151741400816166 true +k22_32 k_{22->32} 1e-05 1000 1.00000000000005e-05 true +k23_13 k_{23->13} 1e-05 1000 0.791201186423607 true +k23_22 k_{23->22} 1e-05 1000 1.00000757856028e-05 true +k30_20 k_{30->20} 1e-05 1000 1.00000137963734e-05 true +k30_31 k_{30->31} 1e-05 1000 0.281302432113616 true +k31_21 k_{31->21} 1e-05 1000 1.00087528532117e-05 true +k31_30 k_{31->30} 1e-05 1000 1.00002400994625e-05 true +k31_32 k_{31->32} 1e-05 1000 0.353631402713609 true +k32_22 k_{32->22} 1e-05 1000 0.632981853600849 true +k32_31 k_{32->31} 1e-05 1000 1.00000000000005e-05 true +sigma {sigma} 1e-05 1000 0.002339466852399 true From 2142cbfd06542fa392b4ea66aa0d760e66ae248e Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Thu, 16 Oct 2025 21:32:56 +0200 Subject: [PATCH 4/4] .. --- v2/Brannmark_JBC2010/measurementData_Brannmark_JBC2010.tsv | 2 +- v2/Isensee_JCB2018/measurementData_Isensee_JCB2018.tsv | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/v2/Brannmark_JBC2010/measurementData_Brannmark_JBC2010.tsv b/v2/Brannmark_JBC2010/measurementData_Brannmark_JBC2010.tsv index 366dbe9..0b7f06c 100644 --- a/v2/Brannmark_JBC2010/measurementData_Brannmark_JBC2010.tsv +++ b/v2/Brannmark_JBC2010/measurementData_Brannmark_JBC2010.tsv @@ -1,4 +1,4 @@ -experimentId observableId measurement time observableParameters noiseParameters experiment_id_49153f7b-5405-4cd6-ac86-bac6addcccf0 independentVariableId +experimentId observableId measurement time observableParameters noiseParameters experiment_id_2ca5faf0-b135-4795-9e20-c3e3c30e6c07 independentVariableId experiment__Dose_0___Dose_0 IRS1_P_DosR 18.385 10.0 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 experiment__Dose_0___Dose_001 IRS1_P_DosR 29.115 10.0 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 experiment__Dose_0___Dose_01 IRS1_P_DosR 26.365 10.0 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 diff --git a/v2/Isensee_JCB2018/measurementData_Isensee_JCB2018.tsv b/v2/Isensee_JCB2018/measurementData_Isensee_JCB2018.tsv index d5e6087..b5430c5 100644 --- a/v2/Isensee_JCB2018/measurementData_Isensee_JCB2018.tsv +++ b/v2/Isensee_JCB2018/measurementData_Isensee_JCB2018.tsv @@ -1,4 +1,4 @@ -experimentId observableId measurement time observableParameters noiseParameters experiment_id_625de0df-fa85-4ac2-8a29-cb2cdb570d85 datasetId replicateId +experimentId observableId measurement time observableParameters noiseParameters experiment_id_447fe5a6-032b-4cf1-8516-3a0199ede029 datasetId replicateId experiment__model1_data49___model1_data1 pRII_Microscopy 972.085779630542 65 s_pRII_JI09_150302_Drg345_343_CycNuc s_pRII_JI09_150302_Drg345_343_CycNuc JI09_150302_Drg345_343_CycNuc JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_ctrl Drg345 experiment__model1_data49___model1_data1 pRII_Microscopy 1024.03993090021 65 s_pRII_JI09_150302_Drg345_343_CycNuc s_pRII_JI09_150302_Drg345_343_CycNuc JI09_150302_Drg345_343_CycNuc JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_ctrl Drg345 experiment__model1_data49___model1_data1 pRII_Microscopy 979.241778646168 65 s_pRII_JI09_150302_Drg345_343_CycNuc s_pRII_JI09_150302_Drg345_343_CycNuc JI09_150302_Drg345_343_CycNuc JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_ctrl Drg345