From 1ba8261572e3484b10478b875ef7ea2fcc8a8618 Mon Sep 17 00:00:00 2001 From: mariesieger Date: Fri, 15 Nov 2024 13:07:15 +0100 Subject: [PATCH 1/3] Add Mishra_model --- .../Mishra_MetabEng2023.yaml | 12 + .../Mishra_MetabEng2023/README-petab-files.md | 1 + .../experimentalConditions.tsv | 29 + .../Mishra_MetabEng2023/lipid_model.xml | 2882 +++++++++++++++++ .../Mishra_MetabEng2023/measurements.tsv | 543 ++++ .../Mishra_MetabEng2023/observables.tsv | 22 + .../Mishra_MetabEng2023/parameters.tsv | 319 ++ README.md | 1 + 8 files changed, 3809 insertions(+) create mode 100644 Benchmark-Models/Mishra_MetabEng2023/Mishra_MetabEng2023.yaml create mode 100644 Benchmark-Models/Mishra_MetabEng2023/README-petab-files.md create mode 100644 Benchmark-Models/Mishra_MetabEng2023/experimentalConditions.tsv create mode 100644 Benchmark-Models/Mishra_MetabEng2023/lipid_model.xml create mode 100644 Benchmark-Models/Mishra_MetabEng2023/measurements.tsv create mode 100644 Benchmark-Models/Mishra_MetabEng2023/observables.tsv create mode 100644 Benchmark-Models/Mishra_MetabEng2023/parameters.tsv diff --git a/Benchmark-Models/Mishra_MetabEng2023/Mishra_MetabEng2023.yaml b/Benchmark-Models/Mishra_MetabEng2023/Mishra_MetabEng2023.yaml new file mode 100644 index 0000000..f7d30b8 --- /dev/null +++ b/Benchmark-Models/Mishra_MetabEng2023/Mishra_MetabEng2023.yaml @@ -0,0 +1,12 @@ +format_version: 1 +parameter_file: parameters.tsv +problems: + - condition_files: + - experimentalConditions.tsv + measurement_files: + - measurements.tsv + observable_files: + - observables.tsv + sbml_files: + - lipid_model.xml + diff --git a/Benchmark-Models/Mishra_MetabEng2023/README-petab-files.md b/Benchmark-Models/Mishra_MetabEng2023/README-petab-files.md new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/Benchmark-Models/Mishra_MetabEng2023/README-petab-files.md @@ -0,0 +1 @@ + diff --git a/Benchmark-Models/Mishra_MetabEng2023/experimentalConditions.tsv b/Benchmark-Models/Mishra_MetabEng2023/experimentalConditions.tsv new file mode 100644 index 0000000..bcd9509 --- /dev/null +++ b/Benchmark-Models/Mishra_MetabEng2023/experimentalConditions.tsv @@ -0,0 +1,29 @@ +conditionId conditionName Vf_ALE1_a Vf_ALE1_b Vf_ALE1_c Vf_ALE1_d Vf_ALE1_e Vb_ALE1_a Vb_ALE1_b Vb_ALE1_c Vb_ALE1_d Vb_ALE1_e Vf_INO1 Vb_INO1 Vf_PSD1 Vb_PSD1 Vf_SCT1 Vb_SCT1 Ks_SCT1_Glyc3P Ks_SCT1_FCoA Kp_SCT1_LPA Ka_SCT1_PS Vf_DPL1 Vb_DPL1 Vf_ELO123 Vb_ELO123 Vf_YDC1 Vb_YDC1 Ks_YDC1_Cer Kp_YDC1_DHS_PHS Kp_YDC1_FA Vf_CHO2 Vb_CHO2 Vf_SUR1 Vb_SUR1 Vf_POX1 Vb_POX1 Vf_FAA1_FAA4 Vb_FAA1_FAA4 Vf_ACC1 Vb_ACC1 Vf_FAS1_FAS2 Vb_FAS1_FAS2 Vf_MmFAR Vb_MmFAR init_FOH +id_by4741 BY4741 Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_reg Vb_POX1_reg Vf_FAA1_FAA4_reg Vb_FAA1_FAA4_reg Vf_ACC1_reg Vb_ACC1_reg Vf_FAS1_FAS2_reg Vb_FAS1_FAS2_reg Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_by4741_ale1 BY4741 with ALE1 deletion Vf_ALE1_a_ko Vf_ALE1_b_ko Vf_ALE1_c_ko Vf_ALE1_d_ko Vf_ALE1_e_ko Vb_ALE1_a_ko Vb_ALE1_b_ko Vb_ALE1_c_ko Vb_ALE1_d_ko Vb_ALE1_e_ko Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_reg Vb_POX1_reg Vf_FAA1_FAA4_reg Vb_FAA1_FAA4_reg Vf_ACC1_reg Vb_ACC1_reg Vf_FAS1_FAS2_reg Vb_FAS1_FAS2_reg Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_by4741_ino1 BY4741 with INO1 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_ko Vb_INO1_ko Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_reg Vb_POX1_reg Vf_FAA1_FAA4_reg Vb_FAA1_FAA4_reg Vf_ACC1_reg Vb_ACC1_reg Vf_FAS1_FAS2_reg Vb_FAS1_FAS2_reg Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_by4741_psd1 BY4741 with PSD1 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_ko Vb_PSD1_ko Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_reg Vb_POX1_reg Vf_FAA1_FAA4_reg Vb_FAA1_FAA4_reg Vf_ACC1_reg Vb_ACC1_reg Vf_FAS1_FAS2_reg Vb_FAS1_FAS2_reg Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_by4741_sct1 BY4741 with SCT1 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_SCT1_ko Vb_SCT1_ko Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_reg Vb_POX1_reg Vf_FAA1_FAA4_reg Vb_FAA1_FAA4_reg Vf_ACC1_reg Vb_ACC1_reg Vf_FAS1_FAS2_reg Vb_FAS1_FAS2_reg Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_by4741_dpl1 BY4741 with DPL1 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_ko Vb_DPL1_ko Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_reg Vb_POX1_reg Vf_FAA1_FAA4_reg Vb_FAA1_FAA4_reg Vf_ACC1_reg Vb_ACC1_reg Vf_FAS1_FAS2_reg Vb_FAS1_FAS2_reg Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_by4741_elo3 BY4741 with ELO3 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_ko Vb_ELO123_ko Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_reg Vb_POX1_reg Vf_FAA1_FAA4_reg Vb_FAA1_FAA4_reg Vf_ACC1_reg Vb_ACC1_reg Vf_FAS1_FAS2_reg Vb_FAS1_FAS2_reg Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_by4741_ydc1 BY4741 with YDC1 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YDC1_ko Vb_YDC1_ko Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_reg Vb_POX1_reg Vf_FAA1_FAA4_reg Vb_FAA1_FAA4_reg Vf_ACC1_reg Vb_ACC1_reg Vf_FAS1_FAS2_reg Vb_FAS1_FAS2_reg Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_scfa4 scFA4 Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_ko Vb_POX1_ko Vf_FAA1_FAA4_ko Vb_FAA1_FAA4_ko Vf_ACC1_reg Vb_ACC1_reg Vf_FAS1_FAS2_reg Vb_FAS1_FAS2_reg Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_scfa4_ale1 scFA4 with ALE1 deletion Vf_ALE1_a_ko Vf_ALE1_b_ko Vf_ALE1_c_ko Vf_ALE1_d_ko Vf_ALE1_e_ko Vb_ALE1_a_ko Vb_ALE1_b_ko Vb_ALE1_c_ko Vb_ALE1_d_ko Vb_ALE1_e_ko Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_ko Vb_POX1_ko Vf_FAA1_FAA4_ko Vb_FAA1_FAA4_ko Vf_ACC1_reg Vb_ACC1_reg Vf_FAS1_FAS2_reg Vb_FAS1_FAS2_reg Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_scfa4_cho2 scFA4 with CHO2 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_ko Vb_CHO2_ko Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_ko Vb_POX1_ko Vf_FAA1_FAA4_ko Vb_FAA1_FAA4_ko Vf_ACC1_reg Vb_ACC1_reg Vf_FAS1_FAS2_reg Vb_FAS1_FAS2_reg Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_scfa4_ino1 scFA4 with INO1 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_ko Vb_INO1_ko Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_ko Vb_POX1_ko Vf_FAA1_FAA4_ko Vb_FAA1_FAA4_ko Vf_ACC1_reg Vb_ACC1_reg Vf_FAS1_FAS2_reg Vb_FAS1_FAS2_reg Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_scfa4_sct1 scFA4 with SCT1 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_SCT1_ko Vb_SCT1_ko Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_ko Vb_POX1_ko Vf_FAA1_FAA4_ko Vb_FAA1_FAA4_ko Vf_ACC1_reg Vb_ACC1_reg Vf_FAS1_FAS2_reg Vb_FAS1_FAS2_reg Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_scfa4_dpl1 scFA4 with DPL1 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_ko Vb_DPL1_ko Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_ko Vb_POX1_ko Vf_FAA1_FAA4_ko Vb_FAA1_FAA4_ko Vf_ACC1_reg Vb_ACC1_reg Vf_FAS1_FAS2_reg Vb_FAS1_FAS2_reg Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_scfa4_elo3 scFA4 with ELO3 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_ko Vb_ELO123_ko Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_ko Vb_POX1_ko Vf_FAA1_FAA4_ko Vb_FAA1_FAA4_ko Vf_ACC1_reg Vb_ACC1_reg Vf_FAS1_FAS2_reg Vb_FAS1_FAS2_reg Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_scfa4_sur1 scFA4 with SUR1 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_ko Vb_SUR1_ko Vf_POX1_ko Vb_POX1_ko Vf_FAA1_FAA4_ko Vb_FAA1_FAA4_ko Vf_ACC1_reg Vb_ACC1_reg Vf_FAS1_FAS2_reg Vb_FAS1_FAS2_reg Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_scfa4_ydc1 scFA4 with YDC1 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YDC1_ko Vb_YDC1_ko Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_ko Vb_POX1_ko Vf_FAA1_FAA4_ko Vb_FAA1_FAA4_ko Vf_ACC1_reg Vb_ACC1_reg Vf_FAS1_FAS2_reg Vb_FAS1_FAS2_reg Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_scfa5 scFA5 Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_reg Vb_POX1_reg Vf_FAA1_FAA4_reg Vb_FAA1_FAA4_reg Vf_ACC1_up Vb_ACC1_up Vf_FAS1_FAS2_up Vb_FAS1_FAS2_up Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_scfa5_dpl1 scFA5 with DPL1 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_ko Vb_DPL1_ko Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_reg Vb_POX1_reg Vf_FAA1_FAA4_reg Vb_FAA1_FAA4_reg Vf_ACC1_up Vb_ACC1_up Vf_FAS1_FAS2_up Vb_FAS1_FAS2_up Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_scfa5_elo3 scFA5 with ELO3 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_ko Vb_ELO123_ko Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_reg Vb_POX1_reg Vf_FAA1_FAA4_reg Vb_FAA1_FAA4_reg Vf_ACC1_up Vb_ACC1_up Vf_FAS1_FAS2_up Vb_FAS1_FAS2_up Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_scfa5_sur1 scFA5 with SUR1 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_ko Vb_SUR1_ko Vf_POX1_reg Vb_POX1_reg Vf_FAA1_FAA4_reg Vb_FAA1_FAA4_reg Vf_ACC1_up Vb_ACC1_up Vf_FAS1_FAS2_up Vb_FAS1_FAS2_up Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_scfa5_ydc1 scFA5 with YDC1 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YDC1_ko Vb_YDC1_ko Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_reg Vb_POX1_reg Vf_FAA1_FAA4_reg Vb_FAA1_FAA4_reg Vf_ACC1_up Vb_ACC1_up Vf_FAS1_FAS2_up Vb_FAS1_FAS2_up Vf_MmFAR_ko Vb_MmFAR_ko init_FOH_ko +id_scfa7 scFA7 Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_reg Vb_POX1_reg Vf_FAA1_FAA4_reg Vb_FAA1_FAA4_reg Vf_ACC1_up Vb_ACC1_up Vf_FAS1_FAS2_up Vb_FAS1_FAS2_up Vf_MmFAR_reg Vb_MmFAR_reg init_FOH_reg +id_scfa7_ale1 scFA7 with ALE1 deletion Vf_ALE1_a_ko Vf_ALE1_b_ko Vf_ALE1_c_ko Vf_ALE1_d_ko Vf_ALE1_e_ko Vb_ALE1_a_ko Vb_ALE1_b_ko Vb_ALE1_c_ko Vb_ALE1_d_ko Vb_ALE1_e_ko Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_reg Vb_POX1_reg Vf_FAA1_FAA4_reg Vb_FAA1_FAA4_reg Vf_ACC1_up Vb_ACC1_up Vf_FAS1_FAS2_up Vb_FAS1_FAS2_up Vf_MmFAR_reg Vb_MmFAR_reg init_FOH_reg +id_scfa7_cho2 scFA7 with CHO2 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_ko Vb_CHO2_ko Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_reg Vb_POX1_reg Vf_FAA1_FAA4_reg Vb_FAA1_FAA4_reg Vf_ACC1_up Vb_ACC1_up Vf_FAS1_FAS2_up Vb_FAS1_FAS2_up Vf_MmFAR_reg Vb_MmFAR_reg init_FOH_reg +id_scfa7_ino1 scFA7 with INO1 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_ko Vb_INO1_ko Vf_PSD1_reg Vb_PSD1_reg Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_reg Vb_POX1_reg Vf_FAA1_FAA4_reg Vb_FAA1_FAA4_reg Vf_ACC1_up Vb_ACC1_up Vf_FAS1_FAS2_up Vb_FAS1_FAS2_up Vf_MmFAR_reg Vb_MmFAR_reg init_FOH_reg +id_scfa7_psd1 scFA7 with PSD1 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_ko Vb_PSD1_ko Vf_GPT2 Vb_GPT2 Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_reg Vb_POX1_reg Vf_FAA1_FAA4_reg Vb_FAA1_FAA4_reg Vf_ACC1_up Vb_ACC1_up Vf_FAS1_FAS2_up Vb_FAS1_FAS2_up Vf_MmFAR_reg Vb_MmFAR_reg init_FOH_reg +id_scfa7_sct1 scFA7 with SCT1 deletion Vf_ALE1_a_reg Vf_ALE1_b_reg Vf_ALE1_c_reg Vf_ALE1_d_reg Vf_ALE1_e_reg Vb_ALE1_a_reg Vb_ALE1_b_reg Vb_ALE1_c_reg Vb_ALE1_d_reg Vb_ALE1_e_reg Vf_INO1_reg Vb_INO1_reg Vf_PSD1_reg Vb_PSD1_reg Vf_SCT1_ko Vb_SCT1_ko Ks_GPT2_Glyc3P Ks_GPT2_FCoA Kp_GPT2_LPA Ka_GPT2_PS Vf_DPL1_reg Vb_DPL1_reg Vf_ELO123_reg Vb_ELO123_reg Vf_YPC1 Vb_YPC1 Ks_YPC1_Cer Kp_YPC1_DHS_PHS Kp_YPC1_FA Vf_CHO2_reg Vb_CHO2_reg Vf_SUR1_reg Vb_SUR1_reg Vf_POX1_reg Vb_POX1_reg Vf_FAA1_FAA4_reg Vb_FAA1_FAA4_reg Vf_ACC1_up Vb_ACC1_up Vf_FAS1_FAS2_up Vb_FAS1_FAS2_up Vf_MmFAR_reg Vb_MmFAR_reg init_FOH_reg \ No newline at end of file diff --git a/Benchmark-Models/Mishra_MetabEng2023/lipid_model.xml b/Benchmark-Models/Mishra_MetabEng2023/lipid_model.xml new file mode 100644 index 0000000..7657938 --- /dev/null +++ b/Benchmark-Models/Mishra_MetabEng2023/lipid_model.xml @@ -0,0 +1,2882 @@ + + + + + + + + + + + + + + + + + + + + Vf_max + + + S1 + + + Km_s1 + + + Vb_max + + + P1 + + + Km_p1 + + + + + + + + Vf_max + + + S1 + Km_s1 + + + + + Vb_max + + + P1 + Km_p1 + + + + + + + + 1 + + + S1 + Km_s1 + + 1 + + + P1 + Km_p1 + + + 1 + + + + + + + + + + Vf_max + + + S1 + + + Km_s1 + + + S2 + + + Km_s2 + + + Vb_max + + + P1 + + + Km_p1 + + + + + + + + Vf_max + + + S1 + Km_s1 + + + + S2 + Km_s2 + + + + + Vb_max + + + P1 + Km_p1 + + + + + + + + + + + + 1 + + + S1 + Km_s1 + + + + + 1 + + + S2 + Km_s2 + + + + 1 + + + P1 + Km_p1 + + + 1 + + + + + + + + + + Vf_max + + + S1 + + + Km_s1 + + + Vb_max + + + P1 + + + Km_p1 + + + P2 + + + Km_p2 + + + + + + + + Vf_max + + + S1 + Km_s1 + + + + + Vb_max + + + P1 + Km_p1 + + + + P2 + Km_p2 + + + + + + + + 1 + + + S1 + Km_s1 + + + + + + 1 + + + P1 + Km_p1 + + + + + 1 + + + P2 + Km_p2 + + + + + 1 + + + + + + + + + + Vf_max + + + S1 + + + Km_s1 + + + S2 + + + Km_s2 + + + Vb_max + + + P1 + + + Km_p1 + + + P2 + + + Km_p2 + + + + + + + + Vf_max + + + S1 + Km_s1 + + + + S2 + Km_s2 + + + + + Vb_max + + + P1 + Km_p1 + + + + P2 + Km_p2 + + + + + + + + + + + + 1 + + + S1 + Km_s1 + + + + + 1 + + + S2 + Km_s2 + + + + + + + + 1 + + + P1 + Km_p1 + + + + + 1 + + + P2 + Km_p2 + + + + + 1 + + + + + + + + + + Vf_max + + + S1 + + + Km_s1 + + + Vb_max + + + P1 + + + Km_p1 + + + P2 + + + Km_p2 + + + P3 + + + Km_p3 + + + + + + + + Vf_max + + + S1 + Km_s1 + + + + + Vb_max + + + P1 + Km_p1 + + + + P2 + Km_p2 + + + + + + P3 + Km_p3 + + 2 + + + + + + + + 1 + + + S1 + Km_s1 + + + + + + 1 + + + P1 + Km_p1 + + + + + 1 + + + P2 + Km_p2 + + + + + 1 + + + P3 + Km_p3 + + + + + + P3 + Km_p3 + + 2 + + + + + 1 + + + + + + + + + + Vf_max + + + S1 + + + Km_s1 + + + S2 + + + Km_s2 + + + Vb_max + + + P1 + + + Km_p1 + + + + + + + + Vf_max + + + S1 + Km_s1 + + + + + + S2 + Km_s2 + + 7 + + + + + Vb_max + + + P1 + Km_p1 + + + + + + + + + + + + 1 + + + S1 + Km_s1 + + + + + + + 1 + + + S2 + Km_s2 + + + 7 + + + 1 + + + P1 + Km_p1 + + + 1 + + + + + + + + + + Vf_max + + + S1 + + + Km_s1 + + + Vb_max + + + P1 + + + Km_p1 + + + + + + + + Vf_max + + + + + S1 + Km_s1 + + 18 + + + + + Vb_max + + + P1 + Km_p1 + + + + + + + + 1 + + + + + S1 + Km_s1 + + 18 + + 1 + + + P1 + Km_p1 + + + 1 + + + + + + + + + + Vf_max + + + S1 + + + Km_s1 + + 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+obsId_DAG id_scfa7_ale1 0.006144270334172106 20.0 1 0.0001840730381258058 +obsId_EE id_scfa7_ale1 0.002979587865302934 20.0 1 0.00022224665213833037 +obsId_Ergosterol id_scfa7_ale1 0.0016465529307316655 20.0 1 0.00011732684533810371 +obsId_IPC id_scfa7_ale1 0.0012916874063166372 20.0 1 2.8048344076078115e-05 +obsId_LPC id_scfa7_ale1 0.00039842552874149497 20.0 1 1.143313744736931e-05 +obsId_LPE id_scfa7_ale1 0.000488745710489573 20.0 1 3.576842683582592e-05 +obsId_LPI id_scfa7_ale1 0.0021547399238713385 20.0 1 0.0001676256985354191 +obsId_LPS id_scfa7_ale1 0.0011680567032574284 20.0 1 0.00013783042666826037 +obsId_MIP2C id_scfa7_ale1 0.001358181773590914 20.0 1 0.00021382579626480743 +obsId_MIPC id_scfa7_ale1 0.00016436726663556452 20.0 1 1.7298299062388138e-05 +obsId_PA id_scfa7_ale1 0.0007879897571331367 20.0 1 3.653752792411804e-05 +obsId_PC id_scfa7_ale1 0.012257453654191628 20.0 1 0.0006299006377654678 +obsId_PE id_scfa7_ale1 0.0007914947925849043 20.0 1 2.9764584609973737e-05 +obsId_PG id_scfa7_ale1 0.0002442079322412978 20.0 1 2.0478460316095604e-05 +obsId_PI id_scfa7_ale1 0.007674178855348828 20.0 1 0.0003138199890139102 +obsId_PS id_scfa7_ale1 0.0036651876970886037 20.0 1 0.0005732067830717856 +obsId_TAG id_scfa7_ale1 0.025426717115639385 20.0 1 0.0006681139055724666 +obsId_FA id_scfa7_ale1 0.1298909020705804 20.0 1 0.004852988417434296 +obsId_FOH id_scfa7_ale1 0.00876456403374134 20.0 1 0.0002439368645791971 +obsId_Cer id_scfa7_cho2 0.000555971216351679 20.0 1 4.6170686854147804e-05 +obsId_DAG id_scfa7_cho2 0.011621199232002956 20.0 1 0.0009110759826021003 +obsId_EE id_scfa7_cho2 0.003826495102256987 20.0 1 0.00042726493755112057 +obsId_Ergosterol id_scfa7_cho2 0.003076043673702061 20.0 1 0.0005534243027520531 +obsId_IPC id_scfa7_cho2 0.001879078537781116 20.0 1 0.00016780924762240356 +obsId_LPC id_scfa7_cho2 0.0001960221948348263 20.0 1 1.1979798953420268e-05 +obsId_LPE id_scfa7_cho2 0.0008600482328245153 20.0 1 0.00010059508355131552 +obsId_LPI id_scfa7_cho2 0.0024161680051585028 20.0 1 0.0003884347256874545 +obsId_LPS id_scfa7_cho2 0.000462866017755672 20.0 1 1.5168457430545073e-05 +obsId_MIP2C id_scfa7_cho2 0.0037429818071628295 20.0 1 1.9335291986087456e-05 +obsId_MIPC id_scfa7_cho2 0.0002486425051255109 20.0 1 2.5281738002930188e-05 +obsId_PA id_scfa7_cho2 0.0024214130194929 20.0 1 0.00013775521656252807 +obsId_PC id_scfa7_cho2 0.0034937227879179764 20.0 1 8.715742858283297e-05 +obsId_PE id_scfa7_cho2 0.008699695744341285 20.0 1 0.0007854698931345716 +obsId_PG id_scfa7_cho2 0.00015864736958373 20.0 1 1.6635760111022324e-05 +obsId_PI id_scfa7_cho2 0.012736326609121716 20.0 1 0.0007151693745502571 +obsId_PS id_scfa7_cho2 0.0014883486605014264 20.0 1 0.0001757164958024874 +obsId_TAG id_scfa7_cho2 0.057065548553245644 20.0 1 0.0007805040918364217 +obsId_FA id_scfa7_cho2 0.1433202376824776 20.0 1 0.01003381504827619 +obsId_FOH id_scfa7_cho2 0.00711635345037529 20.0 1 0.0006257768207576552 +obsId_Cer id_scfa7_ino1 0.0013138037317566489 20.0 1 6.131507510758402e-05 +obsId_DAG id_scfa7_ino1 0.011557414912776303 20.0 1 0.0005531713662957897 +obsId_EE id_scfa7_ino1 0.0036564110607888918 20.0 1 0.00018469516472734168 +obsId_Ergosterol id_scfa7_ino1 0.002002976609302819 20.0 1 5.5798763622197684e-05 +obsId_IPC id_scfa7_ino1 0.0012128642273560863 20.0 1 0.00015072677527529118 +obsId_LPA id_scfa7_ino1 0.00038168738364202637 20.0 1 2.443508605345411e-05 +obsId_LPC id_scfa7_ino1 0.0007497640124312324 20.0 1 5.199350845575364e-05 +obsId_LPE id_scfa7_ino1 0.00044019594134931165 20.0 1 1.7881789696680766e-05 +obsId_LPI id_scfa7_ino1 0.0005420027071316287 20.0 1 6.639363330371143e-05 +obsId_LPS id_scfa7_ino1 0.0008592058189873891 20.0 1 0.00013102337266247306 +obsId_MIP2C id_scfa7_ino1 0.001645723910380813 20.0 1 2.182324964914704e-05 +obsId_MIPC id_scfa7_ino1 0.0009553818715053016 20.0 1 2.5131561360847743e-05 +obsId_PA id_scfa7_ino1 0.0044361296140864 20.0 1 8.174628899532652e-05 +obsId_PC id_scfa7_ino1 0.014926105509873557 20.0 1 0.00036058155903221343 +obsId_PE id_scfa7_ino1 0.0022062971605333105 20.0 1 0.00012951837518138405 +obsId_PG id_scfa7_ino1 0.0003505147576951324 20.0 1 2.0196766828516715e-05 +obsId_PI id_scfa7_ino1 0.0006465095359706497 20.0 1 2.1546543892036088e-05 +obsId_PS id_scfa7_ino1 0.00332387973398079 20.0 1 0.00024153697207168504 +obsId_TAG id_scfa7_ino1 0.030622480465393707 20.0 1 0.0002947626758206762 +obsId_FA id_scfa7_ino1 0.1291305623597369 20.0 1 0.002070795802124011 +obsId_FOH id_scfa7_ino1 0.009686776997601917 20.0 1 0.00025423579955615637 +obsId_Cer id_scfa7_psd1 0.000500006346224167 20.0 1 2.6823664927821598e-05 +obsId_DAG id_scfa7_psd1 0.006230184921227851 20.0 1 0.00010960626134099169 +obsId_EE id_scfa7_psd1 0.003700004685571264 20.0 1 0.00029002840067705117 +obsId_Ergosterol id_scfa7_psd1 0.0026287613442023826 20.0 1 0.00023684998579294212 +obsId_IPC id_scfa7_psd1 0.0008899241710125145 20.0 1 5.1118895154150356e-05 +obsId_LPC id_scfa7_psd1 0.0004972570834540128 20.0 1 1.3276737894025895e-05 +obsId_LPE id_scfa7_psd1 0.0004731056197679751 20.0 1 2.4436855166907375e-05 +obsId_LPI id_scfa7_psd1 0.0014475271238797152 20.0 1 0.00023710873410571307 +obsId_LPS id_scfa7_psd1 0.0012322338459351218 20.0 1 5.9855653339795596e-05 +obsId_MIP2C id_scfa7_psd1 0.0024610243988806763 20.0 1 3.132374631803452e-05 +obsId_MIPC id_scfa7_psd1 0.00010456492769462584 20.0 1 1.0320285906225108e-05 +obsId_PA id_scfa7_psd1 0.0012772059999226503 20.0 1 0.0001369633507131329 +obsId_PC id_scfa7_psd1 0.014929937283569214 20.0 1 0.00020714667829351582 +obsId_PE id_scfa7_psd1 0.0010029268715969146 20.0 1 0.00018255158715651894 +obsId_PG id_scfa7_psd1 0.00030820709296316046 20.0 1 4.3480393632881983e-05 +obsId_PI id_scfa7_psd1 0.009403554924703787 20.0 1 8.090739999341879e-05 +obsId_PS id_scfa7_psd1 0.006876986503359449 20.0 1 0.0010070261199538427 +obsId_TAG id_scfa7_psd1 0.026365382950433645 20.0 1 0.0005591855609004214 +obsId_FA id_scfa7_psd1 0.195263234784166 20.0 1 0.03339719185953266 +obsId_FOH id_scfa7_psd1 0.011444857355323069 20.0 1 0.0003009446765197289 +obsId_Cer id_scfa7_sct1 0.0004121423993747579 20.0 1 1.3965787078711701e-05 +obsId_DAG id_scfa7_sct1 0.0067448330801692805 20.0 1 0.00035940450313883595 +obsId_EE id_scfa7_sct1 0.0030097294366103846 20.0 1 0.00023215971530424865 +obsId_Ergosterol id_scfa7_sct1 0.0014632833486673766 20.0 1 0.0001563458946761576 +obsId_IPC id_scfa7_sct1 0.0006832665161241565 20.0 1 3.707755605607734e-05 +obsId_LPC id_scfa7_sct1 0.0007094250758034504 20.0 1 0.00013783104906801516 +obsId_LPI id_scfa7_sct1 0.0016399345984118234 20.0 1 0.00022224382434103045 +obsId_LPS id_scfa7_sct1 0.0010455260470901568 20.0 1 2.94960262572373e-05 +obsId_MIP2C id_scfa7_sct1 0.00045067167236597245 20.0 1 2.8505323602637988e-05 +obsId_MIPC id_scfa7_sct1 0.00016257305641172992 20.0 1 1.6667398235814335e-05 +obsId_PA id_scfa7_sct1 0.0011125601462586327 20.0 1 0.00020972003429209853 +obsId_PC id_scfa7_sct1 0.011535944732656423 20.0 1 0.00025786947051436226 +obsId_PE id_scfa7_sct1 0.0025323017566097083 20.0 1 0.0002740313089369614 +obsId_PG id_scfa7_sct1 0.000447426096238488 20.0 1 2.6676023584630278e-05 +obsId_PI id_scfa7_sct1 0.003372094722880177 20.0 1 0.0002288595734723655 +obsId_PS id_scfa7_sct1 0.003525625901017303 20.0 1 0.0004912257187550415 +obsId_TAG id_scfa7_sct1 0.02740814049615226 20.0 1 0.0006447203570171872 +obsId_FA id_scfa7_sct1 0.1328099871050088 20.0 1 0.0011321025764794211 +obsId_FOH id_scfa7_sct1 0.0114131734076962 20.0 1 0.00012610284560404412 diff --git a/Benchmark-Models/Mishra_MetabEng2023/observables.tsv b/Benchmark-Models/Mishra_MetabEng2023/observables.tsv new file mode 100644 index 0000000..94e65cf --- /dev/null +++ b/Benchmark-Models/Mishra_MetabEng2023/observables.tsv @@ -0,0 +1,22 @@ +observableId observableName observableFormula noiseFormula +obsId_Cer Cer observableParameter1_obsId_Cer * Cer noiseParameter1_obsId_Cer +obsId_DAG DAG observableParameter1_obsId_DAG * DAG noiseParameter1_obsId_DAG +obsId_EE EE observableParameter1_obsId_EE * EE noiseParameter1_obsId_EE +obsId_Ergosterol Ergosterol observableParameter1_obsId_Ergosterol * Ergst noiseParameter1_obsId_Ergosterol +obsId_IPC IPC observableParameter1_obsId_IPC * IPC noiseParameter1_obsId_IPC +obsId_LPA LPA observableParameter1_obsId_LPA * LPA noiseParameter1_obsId_LPA +obsId_LPC LPC observableParameter1_obsId_LPC * LPC noiseParameter1_obsId_LPC +obsId_LPE LPE observableParameter1_obsId_LPE * LPE noiseParameter1_obsId_LPE +obsId_LPI LPI observableParameter1_obsId_LPI * LPI noiseParameter1_obsId_LPI +obsId_LPS LPS observableParameter1_obsId_LPS * LPS noiseParameter1_obsId_LPS +obsId_MIP2C MIP2C observableParameter1_obsId_MIP2C * MIP2C noiseParameter1_obsId_MIP2C +obsId_MIPC MIPC observableParameter1_obsId_MIPC * MIPC noiseParameter1_obsId_MIPC +obsId_PA PA observableParameter1_obsId_PA * PA noiseParameter1_obsId_PA +obsId_PC PC observableParameter1_obsId_PC * PC noiseParameter1_obsId_PC +obsId_PE PE observableParameter1_obsId_PE * PE noiseParameter1_obsId_PE +obsId_PG PG observableParameter1_obsId_PG * PG noiseParameter1_obsId_PG +obsId_PI PI observableParameter1_obsId_PI * PmI noiseParameter1_obsId_PI +obsId_PS PS observableParameter1_obsId_PS * PS noiseParameter1_obsId_PS +obsId_TAG TAG observableParameter1_obsId_TAG * TAG noiseParameter1_obsId_TAG +obsId_FA FA observableParameter1_obsId_FA * FA noiseParameter1_obsId_FA +obsId_FOH FOH observableParameter1_obsId_FOH * FOH noiseParameter1_obsId_FOH \ No newline at end of file diff --git a/Benchmark-Models/Mishra_MetabEng2023/parameters.tsv b/Benchmark-Models/Mishra_MetabEng2023/parameters.tsv new file mode 100644 index 0000000..821d91e --- /dev/null +++ b/Benchmark-Models/Mishra_MetabEng2023/parameters.tsv @@ -0,0 +1,319 @@ +parameterId parameterScale lowerBound upperBound nominalValue estimate +init_ACoA log10 1.00E-02 1 1 1 +init_MCoA log10 1.00E-06 1.00E-04 1 1 +init_FCoA log10 1.00E-06 1.00E-04 1 1 +init_Glyc3P log10 1.00E-02 1 1 1 +init_LPA log10 1.00E-06 1.00E-04 1 1 +init_PA log10 1.00E-06 1.00E-04 1 1 +init_CDPDAG log10 1.00E-06 1.00E-04 1 1 +init_Glu6P log10 1.00E-02 1 1 1 +init_mIno log10 1.00E-06 1.00E-04 1 1 +init_PmI log10 1.00E-06 1.00E-04 1 1 +init_PmI4P log10 1.00E-06 1.00E-04 1 1 +init_LPI log10 1.00E-06 1.00E-04 1 1 +init_PG log10 1.00E-06 1.00E-04 1 1 +init_CL log10 1.00E-06 1.00E-04 1 1 +init_PS log10 1.00E-06 1.00E-04 1 1 +init_LPS log10 1.00E-06 1.00E-04 1 1 +init_PE log10 1.00E-06 1.00E-04 1 1 +init_LPE log10 1.00E-06 1.00E-04 1 1 +init_PME log10 1.00E-06 1.00E-04 1 1 +init_CDPEthn log10 1.00E-06 1.00E-04 1 1 +init_PC log10 1.00E-06 1.00E-04 1 1 +init_LPC log10 1.00E-06 1.00E-04 1 1 +init_CDPChol log10 1.00E-06 1.00E-04 1 1 +init_DAG log10 1.00E-06 1.00E-04 1 1 +init_TAG log10 1.00E-06 1.00E-04 1 1 +init_Ergst log10 1.00E-06 1.00E-04 1 1 +init_EE log10 1.00E-06 1.00E-04 1 1 +init_DHS_PHS log10 1.00E-06 1.00E-04 1 1 +init_C26CoA log10 1.00E-06 1.00E-04 1 1 +init_Cer log10 1.00E-06 1.00E-04 1 1 +init_IPC log10 1.00E-06 1.00E-04 1 1 +init_MIPC log10 1.00E-06 1.00E-04 1 1 +init_MIP2C log10 1.00E-06 1.00E-04 1 1 +init_FA log10 1.00E-06 1.00E-04 1 1 +init_FOH_reg log10 1.00E-06 1.00E-04 1 1 +Vf_ACC1_reg log10 1.00E-05 1000 1 1 +Vb_ACC1_reg log10 1.00E-05 1 1 1 +Ks_ACC1_ACoA log10 1.00E-05 1 1 1 +Kp_ACC1_MCoA log10 1.00E-05 1 1 1 +Ki_ACC1_FCoA log10 1.00E-05 1 1 1 +Ki_ACC1_C26CoA log10 1.00E-05 1 1 1 +Ka_ACC1_PA log10 1.00E-05 1 1 1 +Vf_FAS1_FAS2_reg log10 1.00E-05 1000 1 1 +Vb_FAS1_FAS2_reg log10 1.00E-05 1 1 1 +Ks_FAS1_FAS2_ACoA log10 1.00E-05 1 1 1 +Ks_FAS1_FAS2_MCoA log10 1.00E-05 1 1 1 +Kp_FAS1_FAS2_FCoA log10 1.00E-05 1 1 1 +Ka_FAS1_FAS2_PA log10 1.00E-05 1 1 1 +Vf_GPT2 log10 1.00E-05 1000 1 1 +Vb_GPT2 log10 1.00E-05 1 1 1 +Ks_GPT2_Glyc3P log10 1.00E-05 1 1 1 +Ks_GPT2_FCoA log10 1.00E-05 1 1 1 +Kp_GPT2_LPA log10 1.00E-05 1 1 1 +Ka_GPT2_PS log10 1.00E-05 1 1 1 +Vf_SLC1 log10 1.00E-05 1000 1 1 +Vb_SLC1 log10 1.00E-05 1 1 1 +Ks_SLC1_LPA log10 1.00E-05 1 1 1 +Ks_SLC1_FCoA log10 1.00E-05 1 1 1 +Kp_SLC1_PA log10 1.00E-05 1 1 1 +Vf_ALE1_a_reg log10 1.00E-05 1000 1 1 +Vb_ALE1_a_reg log10 1.00E-05 1 1 1 +Ks_ALE1_a_LPA log10 1.00E-05 1 1 1 +Ks_ALE1_a_FCoA log10 1.00E-05 1 1 1 +Kp_ALE1_a_PA log10 1.00E-05 1 1 1 +Vf_ALE1_b_reg log10 1.00E-05 1000 1 1 +Vb_ALE1_b_reg log10 1.00E-05 1 1 1 +Ks_ALE1_b_LPE log10 1.00E-05 1 1 1 +Ks_ALE1_b_FCoA log10 1.00E-05 1 1 1 +Kp_ALE1_b_PE log10 1.00E-05 1 1 1 +Vf_ALE1_c_reg log10 1.00E-05 1000 1 1 +Vb_ALE1_c_reg log10 1.00E-05 1 1 1 +Ks_ALE1_c_LPS log10 1.00E-05 1 1 1 +Ks_ALE1_c_FCoA log10 1.00E-05 1 1 1 +Kp_ALE1_c_PS log10 1.00E-05 1 1 1 +Vf_ALE1_d_reg log10 1.00E-05 1000 1 1 +Vb_ALE1_d_reg log10 1.00E-05 1 1 1 +Ks_ALE1_d_LPI log10 1.00E-05 1 1 1 +Ks_ALE1_d_FCoA log10 1.00E-05 1 1 1 +Kp_ALE1_d_PmI log10 1.00E-05 1 1 1 +Vf_ALE1_e_reg log10 1.00E-05 1000 1 1 +Vb_ALE1_e_reg log10 1.00E-05 1 1 1 +Ks_ALE1_e_LPC log10 1.00E-05 1 1 1 +Ks_ALE1_e_FCoA log10 1.00E-05 1 1 1 +Kp_ALE1_e_PC log10 1.00E-05 1 1 1 +Vf_CDS1 log10 1.00E-05 1000 1 1 +Vb_CDS1 log10 1.00E-05 1 1 1 +Ks_CDS1_PA log10 1.00E-05 1 1 1 +Kp_CDS1_CDPDAG log10 1.00E-05 1 1 1 +Ka_CDS1_PA log10 1.00E-05 1 1 1 +Vf_INO1_reg log10 1.00E-05 1000 1 1 +Vb_INO1_reg log10 1.00E-05 1 1 1 +Ks_INO1_Glu6P log10 1.00E-05 1 1 1 +Kp_INO1_mIno log10 1.00E-05 1 1 1 +Ka_INO1_PA log10 1.00E-05 1 1 1 +Vf_INM1_PIS1 log10 1.00E-05 1000 1 1 +Vb_INM1_PIS1 log10 1.00E-05 1 1 1 +Ks_INM1_PIS1_CDPDAG log10 1.00E-05 1 1 1 +Ks_INM1_PIS1_mIno log10 1.00E-05 1 1 1 +Kp_INM1_PIS1_PmI log10 1.00E-05 1 1 1 +Ka_INM1_PIS1_PA log10 1.00E-05 1 1 1 +Vf_PIK1 log10 1.00E-05 1000 1 1 +Vb_PIK1 log10 1.00E-05 1 1 1 +Ks_PIK1_PmI log10 1.00E-05 1 1 1 +Kp_PIK1_PmI4P log10 1.00E-05 1 1 1 +Vf_PGS1_GEP4 log10 1.00E-05 1000 1 1 +Vb_PGS1_GEP4 log10 1.00E-05 1 1 1 +Ks_PGS1_GEP4_CDPDAG log10 1.00E-05 1 1 1 +Ks_PGS1_GEP4_Glyc3P log10 1.00E-05 1 1 1 +Kp_PGS1_GEP4_PG log10 1.00E-05 1 1 1 +Vf_CRD1 log10 1.00E-05 1000 1 1 +Vb_CRD1 log10 1.00E-05 1 1 1 +Ks_CRD1_CDPDAG 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1.00E-05 1 1 1 +Kp_TGL1_FA log10 1.00E-05 1 1 1 +Vf_ELO123_reg log10 1.00E-05 1000 1 1 +Vb_ELO123_reg log10 1.00E-05 1 1 1 +Ks_ELO123_FCoA log10 1.00E-05 1 1 1 +Ks_ELO123_MCoA log10 1.00E-05 1 1 1 +Kp_ELO123_C26CoA log10 1.00E-05 1 1 1 +Vf_LCB1 log10 1.00E-05 1000 1 1 +Vb_LCB1 log10 1.00E-05 1 1 1 +Ks_LCB1_FCoA log10 1.00E-05 1 1 1 +Kp_LCB1_DHS_PHS log10 1.00E-05 1 1 1 +Vf_DPL1_reg log10 1.00E-05 1000 1 1 +Vb_DPL1_reg log10 1.00E-05 1 1 1 +Ks_DPL1_DHS_PHS log10 1.00E-05 1 1 1 +Kp_DPL1_CDPEthn log10 1.00E-05 1 1 1 +Kp_DPL1_FA log10 1.00E-05 1 1 1 +Vf_LAC1 log10 1.00E-05 1000 1 1 +Vb_LAC1 log10 1.00E-05 1 1 1 +Ks_LAC1_DHS_PHS log10 1.00E-05 1 1 1 +Ks_LAC1_C26CoA log10 1.00E-05 1 1 1 +Kp_LAC1_Cer log10 1.00E-05 1 1 1 +Vf_YPC1 log10 1.00E-05 1000 1 1 +Vb_YPC1 log10 1.00E-05 1 1 1 +Ks_YPC1_Cer log10 1.00E-05 1 1 1 +Kp_YPC1_DHS_PHS log10 1.00E-05 1 1 1 +Kp_YPC1_FA log10 1.00E-05 1 1 1 +Vf_AUR1 log10 1.00E-05 1000 1 1 +Vb_AUR1 log10 1.00E-05 1 1 1 +Ks_AUR1_Cer log10 1.00E-05 1 1 1 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@@ -29,6 +29,7 @@ Contributions to the collection are very welcome. Please see [CONTRIBUTING.md](C | [Lang_PLOSComputBiol2024](Benchmark-Models/Lang_PLOSComputBiol2024/) | 1 | 294 | 0 | | 0 | 0 | 9600 | 16 | normal | laplace; uniform | 124 | [\[1\]](http://identifiers.org/doi/10.1371/journal.pcbi.1011151) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Lang_PLOSComputBiol2024/model_Lang_PLOSComputBiol2024.xml) | | [Laske_PLOSComputBiol2019](Benchmark-Models/Laske_PLOSComputBiol2019/) | 3 | 13 | 0 | | 0 | 0 | 42 | 13 | normal; log-normal | | 41 | [\[1\]](http://identifiers.org/biomodels.db/BIOMD0000000463) [\[2\]](http://identifiers.org/biomodels.db/MODEL1307270000) [\[3\]](http://identifiers.org/doi/10.1371/journal.pcbi.1006944) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Laske_PLOSComputBiol2019/model_Laske_PLOSComputBiol2019.xml) | | [Lucarelli_CellSystems2018](Benchmark-Models/Lucarelli_CellSystems2018/) | 16 | 84 | 0 | | 0 | 0 | 1755 | 65 | normal; log10-normal | | 33 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2017.11.010) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Lucarelli_CellSystems2018/model_Lucarelli_CellSystems2018.xml) | +| [Mishra_MetabEng2023](Benchmark-Models/Mishra_MetabEng2023/) | 28 | 281 | 0 | | 0 | 0 | 542 | 21 | normal | | 35 | [\[1\]](http://identifiers.org/doi/10.1016/j.ymben.2022.11.003) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Mishra_MetabEng2023/lipid_model.xml) | | [Okuonghae_ChaosSolitonsFractals2020](Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/) | 1 | 16 | 0 | | 0 | 0 | 92 | 2 | normal | | 9 | [\[1\]](http://identifiers.org/doi/10.1016/j.chaos.2020.110032) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml) | | [Oliveira_NatCommun2021](Benchmark-Models/Oliveira_NatCommun2021/) | 1 | 12 | 0 | ✓ | 0 | 0 | 120 | 2 | normal | | 9 | [\[1\]](http://identifiers.org/doi/10.1038/s41467-020-19798-3) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml) | | [Perelson_Science1996](Benchmark-Models/Perelson_Science1996/) | 1 | 3 | 0 | | 0 | 0 | 16 | 1 | log10-normal | | 4 | [\[1\]](http://identifiers.org/doi/10.1126/science.271.5255.1582) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Perelson_Science1996/model_Perelson_Science1996.xml) | From ffb7fa41903bca4780fcc39e7f97225da423e999 Mon Sep 17 00:00:00 2001 From: mariesieger Date: Fri, 15 Nov 2024 13:24:33 +0100 Subject: [PATCH 2/3] Add Mishra_model README.md --- .../Mishra_MetabEng2023/README-petab-files.md | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) diff --git a/Benchmark-Models/Mishra_MetabEng2023/README-petab-files.md b/Benchmark-Models/Mishra_MetabEng2023/README-petab-files.md index 8b13789..48b8b0f 100644 --- a/Benchmark-Models/Mishra_MetabEng2023/README-petab-files.md +++ b/Benchmark-Models/Mishra_MetabEng2023/README-petab-files.md @@ -1 +1,66 @@ +```python +import pandas as pd +import matplotlib.pyplot as plt +from matplotlib import cm + +def plot_measurements_vs_simulation(simulation_df, measurement_df, output_file=None): + """ + Generates a logarithmic scatter plot comparing measurements and simulations. + + Parameters: + simulation_df (pd.DataFrame): DataFrame containing simulation data. + measurement_df (pd.DataFrame): DataFrame containing measurement data. + output_file (str, optional): If provided, saves the plot to this file. Defaults to None. + + Returns: + None + """ + # Merge the dataframes on relevant columns + df_merged = pd.merge( + pd.DataFrame(simulation_df), + pd.DataFrame(measurement_df), + on=['observableId', 'simulationConditionId', 'time', 'datasetId'] + ) + + # Modify datasetID + df_merged['datasetId'] = df_merged['datasetId'].str.extract(r'^[^_]*_([^_]*)_')[0] + + # Map unique colors to each datasetId + unique_datasets = df_merged['datasetId'].unique() + colors = cm.get_cmap('tab10', len(unique_datasets)) # Using 'tab10' color map + + # Initialize the plot + plt.figure(figsize=(8, 8)) + plt.xscale('log') + plt.yscale('log') + + # Scatter plot with color mapping for each datasetId + for i, dataset in enumerate(unique_datasets): + subset = df_merged[df_merged['datasetId'] == dataset] + plt.scatter(subset['measurement'], subset['simulation'], color=colors(i), label=dataset) + + # Add bisectrix (y=x line) + x_min, x_max = df_merged['measurement'].min(), df_merged['measurement'].max() + plt.plot([x_min, x_max], [x_min, x_max], 'k--') + + # Labels, title, and legend + plt.xlabel("Measurement (log scale)") + plt.ylabel("Simulation (log scale)") + plt.title("Logarithmic Measurement vs Simulation by Dataset") + plt.legend(title="Dataset ID") + + # Show or save the plot + if output_file: + plt.savefig(output_file, dpi=300, bbox_inches='tight') + else: + plt.show() + +# Assuming `simulation_df` and `measurement_df` are predefined dataframes +plot_measurements_vs_simulation(simulation_df, measurement_df) + +# To save the plot instead of showing it +plot_measurements_vs_simulation(simulation_df, measurement_df, output_file="measurements_vs_simulation.png") + + +``` From 767581069f0da64cfeef325f6589876cb4cca6d3 Mon Sep 17 00:00:00 2001 From: mariesieger Date: Fri, 15 Nov 2024 15:35:36 +0100 Subject: [PATCH 3/3] Add Mishra_model README.md --- .../Mishra_MetabEng2023/README-petab-files.md | 40 +++++++++++++------ 1 file changed, 28 insertions(+), 12 deletions(-) diff --git a/Benchmark-Models/Mishra_MetabEng2023/README-petab-files.md b/Benchmark-Models/Mishra_MetabEng2023/README-petab-files.md index 48b8b0f..f365775 100644 --- a/Benchmark-Models/Mishra_MetabEng2023/README-petab-files.md +++ b/Benchmark-Models/Mishra_MetabEng2023/README-petab-files.md @@ -4,9 +4,15 @@ import pandas as pd import matplotlib.pyplot as plt from matplotlib import cm +from matplotlib import cm # Import cm for colormaps +import matplotlib.pyplot as plt +from sklearn.metrics import r2_score, mean_squared_error + + def plot_measurements_vs_simulation(simulation_df, measurement_df, output_file=None): """ - Generates a logarithmic scatter plot comparing measurements and simulations. + Generates a logarithmic scatter plot comparing measurements and simulations, + with R² and MSE displayed on the plot. Parameters: simulation_df (pd.DataFrame): DataFrame containing simulation data. @@ -28,33 +34,43 @@ def plot_measurements_vs_simulation(simulation_df, measurement_df, output_file=N # Map unique colors to each datasetId unique_datasets = df_merged['datasetId'].unique() - colors = cm.get_cmap('tab10', len(unique_datasets)) # Using 'tab10' color map - - # Initialize the plot + colors = colormaps['tab10'] # Use the updated colormap API + color_list = [colors(i) for i in range(len(unique_datasets))] + + # Plotting plt.figure(figsize=(8, 8)) plt.xscale('log') plt.yscale('log') - - # Scatter plot with color mapping for each datasetId + for i, dataset in enumerate(unique_datasets): subset = df_merged[df_merged['datasetId'] == dataset] - plt.scatter(subset['measurement'], subset['simulation'], color=colors(i), label=dataset) - - # Add bisectrix (y=x line) + plt.scatter(subset['measurement'], subset['simulation'], color=color_list[i], label=dataset) + + # Calculate R² and MSE + r2 = r2_score(df_merged['measurement'], df_merged['simulation']) + mse = mean_squared_error(df_merged['measurement'], df_merged['simulation']) + + # Add R² and MSE to the plot x_min, x_max = df_merged['measurement'].min(), df_merged['measurement'].max() plt.plot([x_min, x_max], [x_min, x_max], 'k--') - - # Labels, title, and legend + plt.text( + x_min * 1.2, x_max / 2, + f"$R^2$: {r2:.3f}\nMSE: {mse:.3e}", + fontsize=10, bbox=dict(facecolor='white', alpha=0.8, edgecolor='gray') + ) + + # Add labels and legend plt.xlabel("Measurement (log scale)") plt.ylabel("Simulation (log scale)") - plt.title("Logarithmic Measurement vs Simulation by Dataset") plt.legend(title="Dataset ID") + plt.show() # Show or save the plot if output_file: plt.savefig(output_file, dpi=300, bbox_inches='tight') else: plt.show() + # Assuming `simulation_df` and `measurement_df` are predefined dataframes plot_measurements_vs_simulation(simulation_df, measurement_df)