{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Reimport MFA data after calculation in INCA" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "This is an example notebook for the reimport module that is a part of the INCA processing tools of BFAIR. The calculated fluxes/fragments/etc. (other output of INCA), can be reimported and worked on here in Python." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", "import numpy as np\n", "import time\n", "import ast\n", "import sys\n", "import escher\n", "from BFAIR.INCA import INCA_reimport" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "filename = 'data/MFA_modelInputsData/TestFile.mat'\n", "simulation_info = pd.read_csv('data/MFA_modelInputsData/Re-import/experimentalMS_data_I.csv')\n", "simulation_id = 'WTEColi_113C80_U13C20_01'" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Stepwise import" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "reimport_data = INCA_reimport()" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "# Succession of functions\n", "info = reimport_data.extract_file_info(filename)\n", "parallel, non_stationary = reimport_data.det_simulation_type(simulation_info)\n", "m, f = reimport_data.data_extraction(filename)\n", "model_info = reimport_data.extract_model_info(m)\n", "simulationParameters = reimport_data.extract_sim_params(simulation_id, info, m, filename)\n", "fittedData = reimport_data.extract_base_stats(f, simulation_id, info)\n", "f_mnt_info = reimport_data.get_fit_info(f)\n", "fittedMeasuredFluxes, fittedMeasuredFragments = reimport_data.sort_fit_info(f_mnt_info, simulation_info, fittedData)\n", "f_mnt_res_info = reimport_data.get_residuals_info(f, simulation_info)\n", "fittedMeasuredFluxResiduals, fittedMeasuredFragmentResiduals = reimport_data.sort_residual_info(f_mnt_res_info, simulation_info, fittedData)\n", "f_par_info = reimport_data.get_fitted_parameters(f, simulation_info)\n", "fittedFluxes, fittedFragments = reimport_data.sort_parameter_info(f_par_info, simulation_info, fittedData)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Alternative shortcut" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "There is also a summary function that performes all the custom re-import functions subsequently" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [], "source": [ "reimport_data_directly = INCA_reimport()" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [], "source": [ "fittedData2, fittedFluxes2, fittedFragments2, fittedMeasuredFluxes2, fittedMeasuredFragments2, fittedMeasuredFluxResiduals2, fittedMeasuredFragmentResiduals2, simulationParameters2 = reimport_data_directly.reimport(filename, simulation_info, simulation_id)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Output" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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fitted_echi2fitted_alffitted_chi2fitted_dofsimulation_idsimulation_dateAndTimeused_comment_
066.5006890.0530848.84549791WTEColi_113C80_U13C20_012021-02-10 16:29:22TrueNone
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" ], "text/plain": [ " fitted_echi2 fitted_alf fitted_chi2 fitted_dof \\\n", "0 66.500689 0.05 30848.845497 91 \n", "\n", " simulation_id simulation_dateAndTime used_ comment_ \n", "0 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 True None " ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "fittedData" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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simulation_idsimulation_dateAndTimerxn_idfluxflux_stdevflux_lbflux_ubflux_unitsfit_alffit_chi2sfit_corfit_covfreeused_comment_
0WTEColi_113C80_U13C20_012021-02-10 16:29:2226dap_DASH_MSYN2.295040e-010.0026080.2243920.234616mmol*gDCW-1*hr-10.05NoneNoneNoneFalseTrueNone
1WTEColi_113C80_U13C20_012021-02-10 16:29:22ACONTa_ACONTb2.074886e+0016996.8649761.1859841000.000000mmol*gDCW-1*hr-10.05NoneNoneNoneFalseTrueNone
2WTEColi_113C80_U13C20_012021-02-10 16:29:22ACONTa_ACONTb_reverse8.690514e-0715432.5920320.00000028.927600mmol*gDCW-1*hr-10.05NoneNoneNoneTrueTrueNone
3WTEColi_113C80_U13C20_012021-02-10 16:29:22AKGDH1.423617e-017673.6155920.0000001.919800mmol*gDCW-1*hr-10.05NoneNoneNoneFalseTrueNone
4WTEColi_113C80_U13C20_012021-02-10 16:29:22ALATA_L3.435520e-010.0039040.3359000.351204mmol*gDCW-1*hr-10.05NoneNoneNoneFalseTrueNone
................................................
92WTEColi_113C80_U13C20_012021-02-10 16:29:22TPI2.175603e+0025620.6563410.0000001000.000000mmol*gDCW-1*hr-10.05NoneNoneNoneFalseTrueNone
93WTEColi_113C80_U13C20_012021-02-10 16:29:22TPI_reverse8.689299e-0724739.5936490.0000001000.000000mmol*gDCW-1*hr-10.05NoneNoneNoneTrueTrueNone
94WTEColi_113C80_U13C20_012021-02-10 16:29:22TrpSYN3.801600e-020.0004320.0371690.038863mmol*gDCW-1*hr-10.05NoneNoneNoneFalseTrueNone
95WTEColi_113C80_U13C20_012021-02-10 16:29:22TyrSYN9.222400e-020.0010480.0901700.094278mmol*gDCW-1*hr-10.05NoneNoneNoneFalseTrueNone
96WTEColi_113C80_U13C20_012021-02-10 16:29:22ValSYN2.830080e-010.0032160.2767050.289311mmol*gDCW-1*hr-10.05NoneNoneNoneFalseTrueNone
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" ], "text/plain": [ " simulation_id simulation_dateAndTime rxn_id \\\n", "0 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 26dap_DASH_MSYN \n", "1 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 ACONTa_ACONTb \n", "2 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 ACONTa_ACONTb_reverse \n", "3 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 AKGDH \n", "4 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 ALATA_L \n", ".. ... ... ... \n", "92 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 TPI \n", "93 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 TPI_reverse \n", "94 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 TrpSYN \n", "95 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 TyrSYN \n", "96 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 ValSYN \n", "\n", " flux flux_stdev flux_lb flux_ub flux_units \\\n", "0 2.295040e-01 0.002608 0.224392 0.234616 mmol*gDCW-1*hr-1 \n", "1 2.074886e+00 16996.864976 1.185984 1000.000000 mmol*gDCW-1*hr-1 \n", "2 8.690514e-07 15432.592032 0.000000 28.927600 mmol*gDCW-1*hr-1 \n", "3 1.423617e-01 7673.615592 0.000000 1.919800 mmol*gDCW-1*hr-1 \n", "4 3.435520e-01 0.003904 0.335900 0.351204 mmol*gDCW-1*hr-1 \n", ".. ... ... ... ... ... \n", "92 2.175603e+00 25620.656341 0.000000 1000.000000 mmol*gDCW-1*hr-1 \n", "93 8.689299e-07 24739.593649 0.000000 1000.000000 mmol*gDCW-1*hr-1 \n", "94 3.801600e-02 0.000432 0.037169 0.038863 mmol*gDCW-1*hr-1 \n", "95 9.222400e-02 0.001048 0.090170 0.094278 mmol*gDCW-1*hr-1 \n", "96 2.830080e-01 0.003216 0.276705 0.289311 mmol*gDCW-1*hr-1 \n", "\n", " fit_alf fit_chi2s fit_cor fit_cov free used_ comment_ \n", "0 0.05 None None None False True None \n", "1 0.05 None None None False True None \n", "2 0.05 None None None True True None \n", "3 0.05 None None None False True None \n", "4 0.05 None None None False True None \n", ".. ... ... ... ... ... ... ... \n", "92 0.05 None None None False True None \n", "93 0.05 None None None True True None \n", "94 0.05 None None None False True None \n", "95 0.05 None None None False True None \n", "96 0.05 None None None False True None \n", "\n", "[97 rows x 15 columns]" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "fittedFluxes" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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simulation_idsimulation_dateAndTimeexperiment_idsample_name_abbreviationtime_pointfragment_idfragment_massfit_valfit_stdevfit_unitsfit_alffit_corfit_covfreeused_comment_
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98WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc06pgc_c_C6H12O10P_MRM275.1275440.1394910.029912norm0.05NoneNoneTrueTrueNone
99WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0akg_c_C4H5O3_MRM101.0808800.0145670.001620norm0.05NoneNoneTrueTrueNone
100WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0akg_c_C5H5O5_MRM145.0904307.0031590.342067norm0.05NoneNoneTrueTrueNone
101WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0asp_DASH_L_c_C3H6NO2_MRM88.0853790.3805670.012953norm0.05NoneNoneTrueTrueNone
102WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0asp_DASH_L_c_C4H6NO4_MRM132.0949290.3520420.016582norm0.05NoneNoneTrueTrueNone
103WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0dhap_c_C3H6O6P_MRM169.0500580.3215540.033352norm0.05NoneNoneTrueTrueNone
104WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0fdp_c_C6H13O12P2_MRM339.1080570.0449150.004312norm0.05NoneNoneTrueTrueNone
105WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0g6p_c_C6H12O9P_MRM259.1281390.1096700.025212norm0.05NoneNoneTrueTrueNone
106WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0glc_DASH_D_c_C2H3O2_MRM59.0441130.6488140.016425norm0.05NoneNoneTrueTrueNone
107WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0glc_DASH_D_c_C6H11O6_MRM179.1482210.0077280.001388norm0.05NoneNoneTrueTrueNone
108WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0glu_DASH_L_c_C5H6NO3_MRM128.1062640.1431750.005395norm0.05NoneNoneTrueTrueNone
109WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0glu_DASH_L_c_C5H8NO4_MRM146.1215510.1431750.005395norm0.05NoneNoneTrueTrueNone
110WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0icit_c_C5H3O3_MRM111.0757380.5567310.078481norm0.05NoneNoneTrueTrueNone
111WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0icit_c_C6H7O7_MRM191.1158620.6596280.078770norm0.05NoneNoneTrueTrueNone
112WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0mal_DASH_L_c_C4H3O4_MRM115.0644030.3761960.010982norm0.05NoneNoneTrueTrueNone
113WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0mal_DASH_L_c_C4H5O5_MRM133.0796900.3761960.010982norm0.05NoneNoneTrueTrueNone
114WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0met_DASH_L_c_C5H10NO2S_MRM148.2034230.1900920.026700norm0.05NoneNoneTrueTrueNone
115WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0met_DASH_L_c_CH3S_MRM47.0993630.4848760.030054norm0.05NoneNoneTrueTrueNone
116WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0pep_c_C3H4O6P_MRM167.0341760.4688390.021512norm0.05NoneNoneTrueTrueNone
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120WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0pyr_c_C3H3O3_MRM87.0542580.4428240.009992norm0.05NoneNoneTrueTrueNone
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122WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0succ_c_C4H3O3_MRM99.0649980.2366330.014982norm0.05NoneNoneTrueTrueNone
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124WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0thr_DASH_L_c_C2H4NO2_MRM74.0587570.5181720.078920norm0.05NoneNoneTrueTrueNone
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" ], "text/plain": [ " simulation_id simulation_dateAndTime \\\n", "97 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "98 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "99 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "100 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "101 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "102 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "103 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "104 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "105 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "106 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "107 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "108 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "109 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "110 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "111 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "112 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "113 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "114 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "115 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "116 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "117 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "118 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "119 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "120 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "121 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "122 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "123 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "124 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "125 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 \n", "\n", " experiment_id sample_name_abbreviation time_point \\\n", "97 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "98 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "99 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "100 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "101 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "102 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "103 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "104 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "105 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "106 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "107 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "108 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "109 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "110 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "111 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "112 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "113 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "114 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "115 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "116 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "117 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "118 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "119 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "120 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "121 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "122 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "123 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "124 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "125 WTEColi_113C80_U13C20_01 OxicWtGlc 0 \n", "\n", " fragment_id fragment_mass fit_val fit_stdev fit_units \\\n", "97 3pg_c_C3H6O7P_MRM 185.049463 0.464103 0.017405 norm \n", "98 6pgc_c_C6H12O10P_MRM 275.127544 0.139491 0.029912 norm \n", "99 akg_c_C4H5O3_MRM 101.080880 0.014567 0.001620 norm \n", "100 akg_c_C5H5O5_MRM 145.090430 7.003159 0.342067 norm \n", "101 asp_DASH_L_c_C3H6NO2_MRM 88.085379 0.380567 0.012953 norm \n", "102 asp_DASH_L_c_C4H6NO4_MRM 132.094929 0.352042 0.016582 norm \n", "103 dhap_c_C3H6O6P_MRM 169.050058 0.321554 0.033352 norm \n", "104 fdp_c_C6H13O12P2_MRM 339.108057 0.044915 0.004312 norm \n", "105 g6p_c_C6H12O9P_MRM 259.128139 0.109670 0.025212 norm \n", "106 glc_DASH_D_c_C2H3O2_MRM 59.044113 0.648814 0.016425 norm \n", "107 glc_DASH_D_c_C6H11O6_MRM 179.148221 0.007728 0.001388 norm \n", "108 glu_DASH_L_c_C5H6NO3_MRM 128.106264 0.143175 0.005395 norm \n", "109 glu_DASH_L_c_C5H8NO4_MRM 146.121551 0.143175 0.005395 norm \n", "110 icit_c_C5H3O3_MRM 111.075738 0.556731 0.078481 norm \n", "111 icit_c_C6H7O7_MRM 191.115862 0.659628 0.078770 norm \n", "112 mal_DASH_L_c_C4H3O4_MRM 115.064403 0.376196 0.010982 norm \n", "113 mal_DASH_L_c_C4H5O5_MRM 133.079690 0.376196 0.010982 norm \n", "114 met_DASH_L_c_C5H10NO2S_MRM 148.203423 0.190092 0.026700 norm \n", "115 met_DASH_L_c_CH3S_MRM 47.099363 0.484876 0.030054 norm \n", "116 pep_c_C3H4O6P_MRM 167.034176 0.468839 0.021512 norm \n", "117 phe_DASH_L_c_C9H10NO2_MRM 164.181583 2.970986 0.417026 norm \n", "118 phe_DASH_L_c_C9H7O2_MRM 147.151057 2.970986 0.417026 norm \n", "119 prpp_c_C5H12O14P3_MRM 389.061948 0.283507 0.015233 norm \n", "120 pyr_c_C3H3O3_MRM 87.054258 0.442824 0.009992 norm \n", "121 s7p_c_C7H14O10P_MRM 289.154166 0.297171 0.028618 norm \n", "122 succ_c_C4H3O3_MRM 99.064998 0.236633 0.014982 norm \n", "123 succ_c_C4H5O4_MRM 117.080285 0.236633 0.014982 norm \n", "124 thr_DASH_L_c_C2H4NO2_MRM 74.058757 0.518172 0.078920 norm \n", "125 thr_DASH_L_c_C4H8NO3_MRM 118.111406 0.278460 0.058629 norm \n", "\n", " fit_alf fit_cor fit_cov free used_ comment_ \n", "97 0.05 None None True True None \n", "98 0.05 None None True True None \n", "99 0.05 None None True True None \n", "100 0.05 None None True True None \n", "101 0.05 None None True True None \n", "102 0.05 None None True True None \n", "103 0.05 None None True True None \n", "104 0.05 None None True True None \n", "105 0.05 None None True True None \n", "106 0.05 None None True True None \n", "107 0.05 None None True True None \n", "108 0.05 None None True True None \n", "109 0.05 None None True True None \n", "110 0.05 None None True True None \n", "111 0.05 None None True True None \n", "112 0.05 None None True True None \n", "113 0.05 None None True True None \n", "114 0.05 None None True True None \n", "115 0.05 None None True True None \n", "116 0.05 None None True True None \n", "117 0.05 None None True True None \n", "118 0.05 None None True True None \n", 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simulation_idsimulation_dateAndTimeexperiment_idsample_name_abbreviationrxn_idfitted_sresused_comment_
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simulation_idsimulation_dateAndTimeexperiment_idsample_name_abbreviationfragment_idfitted_sresused_comment_
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7WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlcasp_DASH_L_c_C3H6NO2_MRM1073.129640TrueNone
8WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlcasp_DASH_L_c_C4H6NO4_MRM913.677204TrueNone
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14WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlcglu_DASH_L_c_C5H6NO3_MRM1912.009969TrueNone
15WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlcglu_DASH_L_c_C5H8NO4_MRM1912.009969TrueNone
16WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlcicit_c_C5H3O3_MRM363.128831TrueNone
17WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlcicit_c_C6H7O7_MRM379.700785TrueNone
18WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlcmal_DASH_L_c_C4H3O4_MRM3211.350094TrueNone
19WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlcmal_DASH_L_c_C4H5O5_MRM3211.350094TrueNone
20WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlcmet_DASH_L_c_C5H10NO2S_MRM1493.029733TrueNone
21WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlcmet_DASH_L_c_CH3S_MRM306.906314TrueNone
22WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlcpep_c_C3H4O6P_MRM588.864673TrueNone
23WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlcphe_DASH_L_c_C9H10NO2_MRM152.138718TrueNone
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25WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlcprpp_c_C5H12O14P3_MRM222.820659TrueNone
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" ], "text/plain": [ " simulation_id simulation_dateAndTime experiment_id \\\n", "3 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "4 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "5 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "6 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "7 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "8 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "9 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "10 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "11 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "12 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "13 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "14 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "15 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "16 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "17 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "18 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "19 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "20 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "21 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "22 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "23 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "24 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "25 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "26 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "27 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "28 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "29 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "30 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "31 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "\n", " sample_name_abbreviation fragment_id fitted_sres used_ \\\n", "3 OxicWtGlc 3pg_c_C3H6O7P_MRM 1587.763805 True \n", "4 OxicWtGlc 6pgc_c_C6H12O10P_MRM 1563.596778 True \n", "5 OxicWtGlc akg_c_C4H5O3_MRM 1216.643767 True \n", "6 OxicWtGlc akg_c_C5H5O5_MRM 807.498659 True \n", "7 OxicWtGlc asp_DASH_L_c_C3H6NO2_MRM 1073.129640 True \n", "8 OxicWtGlc asp_DASH_L_c_C4H6NO4_MRM 913.677204 True \n", "9 OxicWtGlc dhap_c_C3H6O6P_MRM 458.596502 True \n", "10 OxicWtGlc fdp_c_C6H13O12P2_MRM 1405.172021 True \n", "11 OxicWtGlc g6p_c_C6H12O9P_MRM 946.401789 True \n", "12 OxicWtGlc glc_DASH_D_c_C2H3O2_MRM 423.003283 True \n", "13 OxicWtGlc glc_DASH_D_c_C6H11O6_MRM 2212.963611 True \n", "14 OxicWtGlc glu_DASH_L_c_C5H6NO3_MRM 1912.009969 True \n", "15 OxicWtGlc glu_DASH_L_c_C5H8NO4_MRM 1912.009969 True \n", "16 OxicWtGlc icit_c_C5H3O3_MRM 363.128831 True \n", "17 OxicWtGlc icit_c_C6H7O7_MRM 379.700785 True \n", "18 OxicWtGlc mal_DASH_L_c_C4H3O4_MRM 3211.350094 True \n", "19 OxicWtGlc mal_DASH_L_c_C4H5O5_MRM 3211.350094 True \n", "20 OxicWtGlc met_DASH_L_c_C5H10NO2S_MRM 1493.029733 True \n", "21 OxicWtGlc met_DASH_L_c_CH3S_MRM 306.906314 True \n", "22 OxicWtGlc pep_c_C3H4O6P_MRM 588.864673 True \n", "23 OxicWtGlc phe_DASH_L_c_C9H10NO2_MRM 152.138718 True \n", "24 OxicWtGlc phe_DASH_L_c_C9H7O2_MRM 152.138718 True \n", "25 OxicWtGlc prpp_c_C5H12O14P3_MRM 222.820659 True \n", "26 OxicWtGlc pyr_c_C3H3O3_MRM 542.990231 True \n", "27 OxicWtGlc s7p_c_C7H14O10P_MRM 524.879652 True \n", "28 OxicWtGlc succ_c_C4H3O3_MRM 1535.567686 True \n", "29 OxicWtGlc succ_c_C4H5O4_MRM 1535.567686 True \n", "30 OxicWtGlc thr_DASH_L_c_C2H4NO2_MRM 86.390543 True \n", "31 OxicWtGlc thr_DASH_L_c_C4H8NO3_MRM 109.554083 True \n", "\n", " comment_ \n", "3 None \n", "4 None \n", "5 None \n", "6 None \n", "7 None \n", "8 None \n", "9 None \n", "10 None \n", "11 None \n", "12 None \n", "13 None \n", "14 None \n", "15 None \n", "16 None \n", "17 None \n", "18 None \n", "19 None \n", "20 None \n", "21 None \n", "22 None \n", "23 None \n", "24 None \n", "25 None \n", "26 None \n", "27 None \n", "28 None \n", "29 None \n", "30 None \n", "31 None " ] }, "execution_count": 11, "metadata": {}, "output_type": "execute_result" } ], "source": [ "fittedMeasuredFragments" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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simulation_idsimulation_dateAndTimeexperiment_idsample_name_abbreviationtime_pointrxn_idres_datares_fitres_peakres_stdevres_valres_msensres_esensused_comment_
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1WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0EX_ac_LPAREN_e_RPAREN_2.1302.130None0.5009.405809e-12NoneNoneTrueNone
2WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0EX_glc_LPAREN_e_RPAREN_7.4007.400None0.200-8.073542e-12NoneNoneTrueNone
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" ], "text/plain": [ " simulation_id simulation_dateAndTime experiment_id \\\n", "0 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "1 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "2 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "\n", " sample_name_abbreviation time_point rxn_id res_data \\\n", "0 OxicWtGlc 0 Ec_Biomass_INCA 0.704 \n", "1 OxicWtGlc 0 EX_ac_LPAREN_e_RPAREN_ 2.130 \n", "2 OxicWtGlc 0 EX_glc_LPAREN_e_RPAREN_ 7.400 \n", "\n", " res_fit res_peak res_stdev res_val res_msens res_esens used_ \\\n", "0 0.704 None 0.008 2.511880e-12 None None True \n", "1 2.130 None 0.500 9.405809e-12 None None True \n", "2 7.400 None 0.200 -8.073542e-12 None None True \n", "\n", " comment_ \n", "0 None \n", "1 None \n", "2 None " ] }, "execution_count": 12, "metadata": {}, "output_type": "execute_result" } ], "source": [ "fittedMeasuredFluxResiduals" ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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15WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0glu_DASH_L_c_C5H8NO4_MRM146.1215510.1344160.135597M+00.0051100.231207NoneNoneTrueNone
16WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0icit_c_C5H3O3_MRM111.0757380.2718970.527267M+00.0765343.336682NoneNoneTrueNone
17WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0icit_c_C6H7O7_MRM191.1158620.2554390.617962M+00.0783644.626148NoneNoneTrueNone
18WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0mal_DASH_L_c_C4H3O4_MRM115.0644030.3246390.360182M+00.0105403.372176NoneNoneTrueNone
19WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0mal_DASH_L_c_C4H5O5_MRM133.0796900.3246390.360182M+00.0105403.372176NoneNoneTrueNone
20WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0met_DASH_L_c_C5H10NO2S_MRM148.2034230.1160970.180032M+00.0254442.512787NoneNoneTrueNone
21WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0met_DASH_L_c_CH3S_MRM47.0993630.4739370.479632M+00.0297310.191543NoneNoneTrueNone
22WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0pep_c_C3H4O6P_MRM167.0341760.4393650.453790M+00.0208350.692360NoneNoneTrueNone
23WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0phe_DASH_L_c_C9H10NO2_MRM164.1815830.2502540.265110M+10.0372670.398648NoneNoneTrueNone
24WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0phe_DASH_L_c_C9H7O2_MRM147.1510570.2502540.265110M+10.0372670.398648NoneNoneTrueNone
25WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0prpp_c_C5H12O14P3_MRM389.0619480.2666590.268503M+00.0144290.127800NoneNoneTrueNone
26WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0pyr_c_C3H3O3_MRM87.0542580.4249060.428610M+00.0096730.382893NoneNoneTrueNone
27WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0s7p_c_C7H14O10P_MRM289.1541660.2101870.275388M+00.0267672.435895NoneNoneTrueNone
28WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0succ_c_C4H3O3_MRM99.0649980.2178450.226561M+00.0143530.607219NoneNoneTrueNone
29WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0succ_c_C4H5O4_MRM117.0802850.2178450.226561M+00.0143530.607219NoneNoneTrueNone
30WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0thr_DASH_L_c_C2H4NO2_MRM74.0587570.5018320.507023M+00.0772350.067213NoneNoneTrueNone
31WTEColi_113C80_U13C20_012021-02-10 16:29:22WTEColi_113C80_U13C20_01OxicWtGlc0thr_DASH_L_c_C4H8NO3_MRM118.1114060.2621390.266607M+00.0561470.079581NoneNoneTrueNone
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" ], "text/plain": [ " simulation_id simulation_dateAndTime experiment_id \\\n", "3 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "4 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "5 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "6 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "7 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "8 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "9 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "10 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "11 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "12 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "13 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "14 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "15 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "16 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "17 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "18 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "19 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "20 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "21 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "22 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "23 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "24 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "25 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "26 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "27 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "28 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "29 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "30 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "31 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 \n", "\n", " sample_name_abbreviation time_point fragment_id \\\n", "3 OxicWtGlc 0 3pg_c_C3H6O7P_MRM \n", "4 OxicWtGlc 0 6pgc_c_C6H12O10P_MRM \n", "5 OxicWtGlc 0 akg_c_C4H5O3_MRM \n", "6 OxicWtGlc 0 akg_c_C5H5O5_MRM \n", "7 OxicWtGlc 0 asp_DASH_L_c_C3H6NO2_MRM \n", "8 OxicWtGlc 0 asp_DASH_L_c_C4H6NO4_MRM \n", "9 OxicWtGlc 0 dhap_c_C3H6O6P_MRM \n", "10 OxicWtGlc 0 fdp_c_C6H13O12P2_MRM \n", "11 OxicWtGlc 0 g6p_c_C6H12O9P_MRM \n", "12 OxicWtGlc 0 glc_DASH_D_c_C2H3O2_MRM \n", "13 OxicWtGlc 0 glc_DASH_D_c_C6H11O6_MRM \n", "14 OxicWtGlc 0 glu_DASH_L_c_C5H6NO3_MRM \n", "15 OxicWtGlc 0 glu_DASH_L_c_C5H8NO4_MRM \n", "16 OxicWtGlc 0 icit_c_C5H3O3_MRM \n", "17 OxicWtGlc 0 icit_c_C6H7O7_MRM \n", "18 OxicWtGlc 0 mal_DASH_L_c_C4H3O4_MRM \n", "19 OxicWtGlc 0 mal_DASH_L_c_C4H5O5_MRM \n", "20 OxicWtGlc 0 met_DASH_L_c_C5H10NO2S_MRM \n", "21 OxicWtGlc 0 met_DASH_L_c_CH3S_MRM \n", "22 OxicWtGlc 0 pep_c_C3H4O6P_MRM \n", "23 OxicWtGlc 0 phe_DASH_L_c_C9H10NO2_MRM \n", "24 OxicWtGlc 0 phe_DASH_L_c_C9H7O2_MRM \n", "25 OxicWtGlc 0 prpp_c_C5H12O14P3_MRM \n", "26 OxicWtGlc 0 pyr_c_C3H3O3_MRM \n", "27 OxicWtGlc 0 s7p_c_C7H14O10P_MRM \n", "28 OxicWtGlc 0 succ_c_C4H3O3_MRM \n", "29 OxicWtGlc 0 succ_c_C4H5O4_MRM \n", "30 OxicWtGlc 0 thr_DASH_L_c_C2H4NO2_MRM \n", "31 OxicWtGlc 0 thr_DASH_L_c_C4H8NO3_MRM \n", "\n", " fragment_mass res_data res_fit res_peak res_stdev res_val res_msens \\\n", "3 185.049463 0.434465 0.449206 M+0 0.016856 0.874535 None \n", "4 275.127544 0.095200 0.130680 M+0 0.028053 1.264734 None \n", "5 101.080880 0.013870 0.013947 M+0 0.001551 0.049918 None \n", "6 145.090430 0.353333 0.362609 M+1 0.017717 0.523606 None \n", "7 88.085379 0.362688 0.368352 M+0 0.012540 0.451634 None \n", "8 132.094929 0.326136 0.337056 M+0 0.015887 0.687353 None \n", "9 169.050058 0.285900 0.311233 M+0 0.032310 0.784057 None \n", "10 339.108057 0.041052 0.042078 M+0 0.004040 0.253959 None \n", "11 259.128139 0.062617 0.102742 M+0 0.023661 1.695852 None \n", "12 59.044113 0.624426 0.634855 M+0 0.016085 0.648315 None \n", "13 179.148221 0.006977 0.007240 M+0 0.001300 0.202349 None \n", "14 128.106264 0.134416 0.135597 M+0 0.005110 0.231207 None \n", "15 146.121551 0.134416 0.135597 M+0 0.005110 0.231207 None \n", "16 111.075738 0.271897 0.527267 M+0 0.076534 3.336682 None \n", "17 191.115862 0.255439 0.617962 M+0 0.078364 4.626148 None \n", "18 115.064403 0.324639 0.360182 M+0 0.010540 3.372176 None \n", "19 133.079690 0.324639 0.360182 M+0 0.010540 3.372176 None \n", "20 148.203423 0.116097 0.180032 M+0 0.025444 2.512787 None \n", "21 47.099363 0.473937 0.479632 M+0 0.029731 0.191543 None \n", "22 167.034176 0.439365 0.453790 M+0 0.020835 0.692360 None \n", "23 164.181583 0.250254 0.265110 M+1 0.037267 0.398648 None \n", "24 147.151057 0.250254 0.265110 M+1 0.037267 0.398648 None \n", "25 389.061948 0.266659 0.268503 M+0 0.014429 0.127800 None \n", "26 87.054258 0.424906 0.428610 M+0 0.009673 0.382893 None \n", "27 289.154166 0.210187 0.275388 M+0 0.026767 2.435895 None \n", "28 99.064998 0.217845 0.226561 M+0 0.014353 0.607219 None \n", "29 117.080285 0.217845 0.226561 M+0 0.014353 0.607219 None \n", "30 74.058757 0.501832 0.507023 M+0 0.077235 0.067213 None \n", "31 118.111406 0.262139 0.266607 M+0 0.056147 0.079581 None \n", "\n", " res_esens used_ comment_ \n", "3 None True None \n", "4 None True None \n", "5 None True None \n", "6 None True None \n", "7 None True None \n", "8 None True None \n", "9 None True None \n", "10 None True None \n", "11 None True None \n", "12 None True None \n", "13 None True None \n", "14 None True None \n", "15 None True None \n", "16 None True None \n", "17 None True None \n", "18 None True None \n", "19 None True None \n", "20 None True None \n", "21 None True None \n", "22 None True None \n", "23 None True None \n", "24 None True None \n", "25 None True None \n", "26 None True None \n", "27 None True None \n", "28 None True None \n", "29 None True None \n", "30 None True None \n", "31 None True None " ] }, "execution_count": 13, "metadata": {}, "output_type": "execute_result" } ], "source": [ "fittedMeasuredFragmentResiduals" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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cont_alphacont_reltolcont_stepsfit_nudgefit_reinitfit_reltolfit_startsfit_tauhpc_onint_maxstep...sim_senssim_sssim_tunithpc_mcrhpc_servesimulation_idsimulation_dateAndTimeoriginal_filenameused_comment_
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1 rows × 31 columns

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" ], "text/plain": [ " cont_alpha cont_reltol cont_steps fit_nudge fit_reinit fit_reltol \\\n", "0 0.05 1.0 5.0 1.0 True 0.01 \n", "\n", " fit_starts fit_tau hpc_on int_maxstep ... sim_sens sim_ss \\\n", "0 10.0 0.000001 False inf ... False True \n", "\n", " sim_tunit hpc_mcr hpc_serve simulation_id \\\n", "0 h 0.0 parfor WTEColi_113C80_U13C20_01 \n", "\n", " simulation_dateAndTime original_filename used_ \\\n", "0 2021-02-10 16:29:22 data/MFA_modelInputsData/TestFile.mat True \n", "\n", " comment_ \n", "0 None \n", "\n", "[1 rows x 31 columns]" ] }, "execution_count": 14, "metadata": {}, "output_type": "execute_result" } ], "source": [ "simulationParameters" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Visualization" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Fluxes can easily be visulaized using \"Escher\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "First we have to set up a dictionary containing our calculated flux values together with their corresponding reaction IDs" ] }, { "cell_type": "code", "execution_count": 15, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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simulation_idsimulation_dateAndTimerxn_idfluxflux_stdevflux_lbflux_ubflux_unitsfit_alffit_chi2sfit_corfit_covfreeused_comment_
0WTEColi_113C80_U13C20_012021-02-10 16:29:2226dap_DASH_MSYN2.295040e-010.0026080.2243920.234616mmol*gDCW-1*hr-10.05NoneNoneNoneFalseTrueNone
1WTEColi_113C80_U13C20_012021-02-10 16:29:22ACONTa_ACONTb2.074886e+0016996.8649761.1859841000.000000mmol*gDCW-1*hr-10.05NoneNoneNoneFalseTrueNone
2WTEColi_113C80_U13C20_012021-02-10 16:29:22ACONTa_ACONTb_reverse8.690514e-0715432.5920320.00000028.927600mmol*gDCW-1*hr-10.05NoneNoneNoneTrueTrueNone
3WTEColi_113C80_U13C20_012021-02-10 16:29:22AKGDH1.423617e-017673.6155920.0000001.919800mmol*gDCW-1*hr-10.05NoneNoneNoneFalseTrueNone
4WTEColi_113C80_U13C20_012021-02-10 16:29:22ALATA_L3.435520e-010.0039040.3359000.351204mmol*gDCW-1*hr-10.05NoneNoneNoneFalseTrueNone
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92WTEColi_113C80_U13C20_012021-02-10 16:29:22TPI2.175603e+0025620.6563410.0000001000.000000mmol*gDCW-1*hr-10.05NoneNoneNoneFalseTrueNone
93WTEColi_113C80_U13C20_012021-02-10 16:29:22TPI_reverse8.689299e-0724739.5936490.0000001000.000000mmol*gDCW-1*hr-10.05NoneNoneNoneTrueTrueNone
94WTEColi_113C80_U13C20_012021-02-10 16:29:22TrpSYN3.801600e-020.0004320.0371690.038863mmol*gDCW-1*hr-10.05NoneNoneNoneFalseTrueNone
95WTEColi_113C80_U13C20_012021-02-10 16:29:22TyrSYN9.222400e-020.0010480.0901700.094278mmol*gDCW-1*hr-10.05NoneNoneNoneFalseTrueNone
96WTEColi_113C80_U13C20_012021-02-10 16:29:22ValSYN2.830080e-010.0032160.2767050.289311mmol*gDCW-1*hr-10.05NoneNoneNoneFalseTrueNone
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97 rows × 15 columns

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" ], "text/plain": [ " simulation_id simulation_dateAndTime rxn_id \\\n", "0 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 26dap_DASH_MSYN \n", "1 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 ACONTa_ACONTb \n", "2 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 ACONTa_ACONTb_reverse \n", "3 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 AKGDH \n", "4 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 ALATA_L \n", ".. ... ... ... \n", "92 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 TPI \n", "93 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 TPI_reverse \n", "94 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 TrpSYN \n", "95 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 TyrSYN \n", "96 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 ValSYN \n", "\n", " flux flux_stdev flux_lb flux_ub flux_units \\\n", "0 2.295040e-01 0.002608 0.224392 0.234616 mmol*gDCW-1*hr-1 \n", "1 2.074886e+00 16996.864976 1.185984 1000.000000 mmol*gDCW-1*hr-1 \n", "2 8.690514e-07 15432.592032 0.000000 28.927600 mmol*gDCW-1*hr-1 \n", "3 1.423617e-01 7673.615592 0.000000 1.919800 mmol*gDCW-1*hr-1 \n", "4 3.435520e-01 0.003904 0.335900 0.351204 mmol*gDCW-1*hr-1 \n", ".. ... ... ... ... ... \n", "92 2.175603e+00 25620.656341 0.000000 1000.000000 mmol*gDCW-1*hr-1 \n", "93 8.689299e-07 24739.593649 0.000000 1000.000000 mmol*gDCW-1*hr-1 \n", "94 3.801600e-02 0.000432 0.037169 0.038863 mmol*gDCW-1*hr-1 \n", "95 9.222400e-02 0.001048 0.090170 0.094278 mmol*gDCW-1*hr-1 \n", "96 2.830080e-01 0.003216 0.276705 0.289311 mmol*gDCW-1*hr-1 \n", "\n", " fit_alf fit_chi2s fit_cor fit_cov free used_ comment_ \n", "0 0.05 None None None False True None \n", "1 0.05 None None None False True None \n", "2 0.05 None None None True True None \n", "3 0.05 None None None False True None \n", "4 0.05 None None None False True None \n", ".. ... ... ... ... ... ... ... \n", "92 0.05 None None None False True None \n", "93 0.05 None None None True True None \n", "94 0.05 None None None False True None \n", "95 0.05 None None None False True None \n", "96 0.05 None None None False True None \n", "\n", "[97 rows x 15 columns]" ] }, "execution_count": 15, "metadata": {}, "output_type": "execute_result" } ], "source": [ "fittedFluxes" ] }, { "cell_type": "code", "execution_count": 16, "metadata": {}, "outputs": [], "source": [ "fluxes = {}\n", "for i, rxn in fittedFluxes.iterrows():\n", " fluxes[rxn['rxn_id']] = rxn['flux']" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Then we can check if there is a suitable map available (if not it will have to be added)" ] }, { "cell_type": "code", "execution_count": 17, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "[{'organism': 'Saccharomyces cerevisiae',\n", " 'map_name': 'iMM904.Central carbon metabolism'},\n", " {'organism': 'Homo sapiens',\n", " 'map_name': 'RECON1.Inositol retinol metabolism'},\n", " {'organism': 'Homo sapiens', 'map_name': 'RECON1.Glycolysis TCA PPP'},\n", " {'organism': 'Homo sapiens', 'map_name': 'RECON1.Tryptophan metabolism'},\n", " {'organism': 'Homo sapiens', 'map_name': 'RECON1.Carbohydrate metabolism'},\n", " {'organism': 'Homo sapiens',\n", " 'map_name': 'RECON1.Amino acid metabolism (partial)'},\n", " {'organism': 'Escherichia coli', 'map_name': 'iJO1366.Nucleotide metabolism'},\n", " {'organism': 'Escherichia coli',\n", " 'map_name': 'iJO1366.Fatty acid biosynthesis (saturated)'},\n", " {'organism': 'Escherichia coli',\n", " 'map_name': 'iJO1366.Nucleotide and histidine biosynthesis'},\n", " {'organism': 'Escherichia coli', 'map_name': 'e_coli_core.Core metabolism'},\n", " {'organism': 'Escherichia coli', 'map_name': 'iJO1366.Central metabolism'},\n", " {'organism': 'Escherichia coli',\n", " 'map_name': 'iJO1366.Fatty acid beta-oxidation'}]" ] }, "execution_count": 17, "metadata": {}, "output_type": "execute_result" } ], "source": [ "escher.list_available_maps()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "And then we are ready to display the fluxes" ] }, { "cell_type": "code", "execution_count": 18, "metadata": {}, "outputs": [], "source": [ "b = escher.Builder('e_coli_core.Core metabolism',\n", " reaction_data= fluxes).display_in_notebook()" ] }, { "cell_type": "code", "execution_count": 19, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", " \n", " \n", "\n", " \n", " \n", " \n", " \n", "\n", "\n", "\n", "
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