Reimport MFA data after calculation in INCA

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.

[1]:

import pandas as pd
import numpy as np
import time
import ast
import sys
import escher
from BFAIR.INCA import INCA_reimport

[2]:

filename = 'data/MFA_modelInputsData/TestFile.mat'
simulation_info = pd.read_csv('data/MFA_modelInputsData/Re-import/experimentalMS_data_I.csv')
simulation_id = 'WTEColi_113C80_U13C20_01'

Stepwise import

[3]:

reimport_data = INCA_reimport()

[4]:

# Succession of functions
info = reimport_data.extract_file_info(filename)
parallel, non_stationary = reimport_data.det_simulation_type(simulation_info)
m, f = reimport_data.data_extraction(filename)
model_info = reimport_data.extract_model_info(m)
simulationParameters = reimport_data.extract_sim_params(simulation_id, info, m, filename)
fittedData = reimport_data.extract_base_stats(f, simulation_id, info)
f_mnt_info = reimport_data.get_fit_info(f)
fittedMeasuredFluxes, fittedMeasuredFragments = reimport_data.sort_fit_info(f_mnt_info, simulation_info, fittedData)
f_mnt_res_info = reimport_data.get_residuals_info(f, simulation_info)
fittedMeasuredFluxResiduals, fittedMeasuredFragmentResiduals = reimport_data.sort_residual_info(f_mnt_res_info, simulation_info, fittedData)
f_par_info = reimport_data.get_fitted_parameters(f, simulation_info)
fittedFluxes, fittedFragments = reimport_data.sort_parameter_info(f_par_info, simulation_info, fittedData)

Alternative shortcut

There is also a summary function that performes all the custom re-import functions subsequently

[5]:

reimport_data_directly = INCA_reimport()

[6]:

fittedData2, fittedFluxes2, fittedFragments2, fittedMeasuredFluxes2, fittedMeasuredFragments2, fittedMeasuredFluxResiduals2, fittedMeasuredFragmentResiduals2, simulationParameters2 = reimport_data_directly.reimport(filename, simulation_info, simulation_id)

Output

[7]:

fittedData

[7]:
fitted_echi2 fitted_alf fitted_chi2 fitted_dof simulation_id simulation_dateAndTime used_ comment_
0 66.500689 0.05 30848.845497 91 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 True None 
[8]:

fittedFluxes

[8]:
simulation_id simulation_dateAndTime rxn_id flux flux_stdev flux_lb flux_ub flux_units fit_alf fit_chi2s fit_cor fit_cov free used_ comment_
0 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 26dap_DASH_MSYN 2.295040e-01 0.002608 0.224392 0.234616 mmol*gDCW-1*hr-1 0.05 None None None False True None
1 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 ACONTa_ACONTb 2.074886e+00 16996.864976 1.185984 1000.000000 mmol*gDCW-1*hr-1 0.05 None None None False True None
2 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 ACONTa_ACONTb_reverse 8.690514e-07 15432.592032 0.000000 28.927600 mmol*gDCW-1*hr-1 0.05 None None None True True None
3 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 AKGDH 1.423617e-01 7673.615592 0.000000 1.919800 mmol*gDCW-1*hr-1 0.05 None None None False True None
4 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 ALATA_L 3.435520e-01 0.003904 0.335900 0.351204 mmol*gDCW-1*hr-1 0.05 None None None False True None
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
92 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 TPI 2.175603e+00 25620.656341 0.000000 1000.000000 mmol*gDCW-1*hr-1 0.05 None None None False True None
93 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 TPI_reverse 8.689299e-07 24739.593649 0.000000 1000.000000 mmol*gDCW-1*hr-1 0.05 None None None True True None
94 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 TrpSYN 3.801600e-02 0.000432 0.037169 0.038863 mmol*gDCW-1*hr-1 0.05 None None None False True None
95 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 TyrSYN 9.222400e-02 0.001048 0.090170 0.094278 mmol*gDCW-1*hr-1 0.05 None None None False True None
96 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 ValSYN 2.830080e-01 0.003216 0.276705 0.289311 mmol*gDCW-1*hr-1 0.05 None None None False True None

97 rows × 15 columns

[9]:

fittedFragments

[9]:
simulation_id simulation_dateAndTime experiment_id sample_name_abbreviation time_point fragment_id fragment_mass fit_val fit_stdev fit_units fit_alf fit_cor fit_cov free used_ comment_
97 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 3pg_c_C3H6O7P_MRM 185.049463 0.464103 0.017405 norm 0.05 None None True True None
98 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 6pgc_c_C6H12O10P_MRM 275.127544 0.139491 0.029912 norm 0.05 None None True True None
99 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 akg_c_C4H5O3_MRM 101.080880 0.014567 0.001620 norm 0.05 None None True True None
100 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 akg_c_C5H5O5_MRM 145.090430 7.003159 0.342067 norm 0.05 None None True True None
101 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 asp_DASH_L_c_C3H6NO2_MRM 88.085379 0.380567 0.012953 norm 0.05 None None True True None
102 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 asp_DASH_L_c_C4H6NO4_MRM 132.094929 0.352042 0.016582 norm 0.05 None None True True None
103 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 dhap_c_C3H6O6P_MRM 169.050058 0.321554 0.033352 norm 0.05 None None True True None
104 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 fdp_c_C6H13O12P2_MRM 339.108057 0.044915 0.004312 norm 0.05 None None True True None
105 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 g6p_c_C6H12O9P_MRM 259.128139 0.109670 0.025212 norm 0.05 None None True True None
106 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 glc_DASH_D_c_C2H3O2_MRM 59.044113 0.648814 0.016425 norm 0.05 None None True True None
107 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 glc_DASH_D_c_C6H11O6_MRM 179.148221 0.007728 0.001388 norm 0.05 None None True True None
108 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 glu_DASH_L_c_C5H6NO3_MRM 128.106264 0.143175 0.005395 norm 0.05 None None True True None
109 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 glu_DASH_L_c_C5H8NO4_MRM 146.121551 0.143175 0.005395 norm 0.05 None None True True None
110 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 icit_c_C5H3O3_MRM 111.075738 0.556731 0.078481 norm 0.05 None None True True None
111 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 icit_c_C6H7O7_MRM 191.115862 0.659628 0.078770 norm 0.05 None None True True None
112 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 mal_DASH_L_c_C4H3O4_MRM 115.064403 0.376196 0.010982 norm 0.05 None None True True None
113 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 mal_DASH_L_c_C4H5O5_MRM 133.079690 0.376196 0.010982 norm 0.05 None None True True None
114 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 met_DASH_L_c_C5H10NO2S_MRM 148.203423 0.190092 0.026700 norm 0.05 None None True True None
115 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 met_DASH_L_c_CH3S_MRM 47.099363 0.484876 0.030054 norm 0.05 None None True True None
116 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 pep_c_C3H4O6P_MRM 167.034176 0.468839 0.021512 norm 0.05 None None True True None
117 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 phe_DASH_L_c_C9H10NO2_MRM 164.181583 2.970986 0.417026 norm 0.05 None None True True None
118 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 phe_DASH_L_c_C9H7O2_MRM 147.151057 2.970986 0.417026 norm 0.05 None None True True None
119 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 prpp_c_C5H12O14P3_MRM 389.061948 0.283507 0.015233 norm 0.05 None None True True None
120 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 pyr_c_C3H3O3_MRM 87.054258 0.442824 0.009992 norm 0.05 None None True True None
121 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 s7p_c_C7H14O10P_MRM 289.154166 0.297171 0.028618 norm 0.05 None None True True None
122 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 succ_c_C4H3O3_MRM 99.064998 0.236633 0.014982 norm 0.05 None None True True None
123 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 succ_c_C4H5O4_MRM 117.080285 0.236633 0.014982 norm 0.05 None None True True None
124 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 thr_DASH_L_c_C2H4NO2_MRM 74.058757 0.518172 0.078920 norm 0.05 None None True True None
125 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 thr_DASH_L_c_C4H8NO3_MRM 118.111406 0.278460 0.058629 norm 0.05 None None True True None 
[10]:

fittedMeasuredFluxes

[10]:
simulation_id simulation_dateAndTime experiment_id sample_name_abbreviation rxn_id fitted_sres used_ comment_
0 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc Ec_Biomass_INCA 6.309539e-24 True None
1 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc EX_ac_LPAREN_e_RPAREN_ 8.846925e-23 True None
2 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc EX_glc_LPAREN_e_RPAREN_ 6.518208e-23 True None 
[11]:

fittedMeasuredFragments

[11]:
simulation_id simulation_dateAndTime experiment_id sample_name_abbreviation fragment_id fitted_sres used_ comment_
3 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 3pg_c_C3H6O7P_MRM 1587.763805 True None
4 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 6pgc_c_C6H12O10P_MRM 1563.596778 True None
5 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc akg_c_C4H5O3_MRM 1216.643767 True None
6 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc akg_c_C5H5O5_MRM 807.498659 True None
7 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc asp_DASH_L_c_C3H6NO2_MRM 1073.129640 True None
8 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc asp_DASH_L_c_C4H6NO4_MRM 913.677204 True None
9 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc dhap_c_C3H6O6P_MRM 458.596502 True None
10 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc fdp_c_C6H13O12P2_MRM 1405.172021 True None
11 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc g6p_c_C6H12O9P_MRM 946.401789 True None
12 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc glc_DASH_D_c_C2H3O2_MRM 423.003283 True None
13 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc glc_DASH_D_c_C6H11O6_MRM 2212.963611 True None
14 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc glu_DASH_L_c_C5H6NO3_MRM 1912.009969 True None
15 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc glu_DASH_L_c_C5H8NO4_MRM 1912.009969 True None
16 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc icit_c_C5H3O3_MRM 363.128831 True None
17 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc icit_c_C6H7O7_MRM 379.700785 True None
18 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc mal_DASH_L_c_C4H3O4_MRM 3211.350094 True None
19 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc mal_DASH_L_c_C4H5O5_MRM 3211.350094 True None
20 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc met_DASH_L_c_C5H10NO2S_MRM 1493.029733 True None
21 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc met_DASH_L_c_CH3S_MRM 306.906314 True None
22 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc pep_c_C3H4O6P_MRM 588.864673 True None
23 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc phe_DASH_L_c_C9H10NO2_MRM 152.138718 True None
24 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc phe_DASH_L_c_C9H7O2_MRM 152.138718 True None
25 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc prpp_c_C5H12O14P3_MRM 222.820659 True None
26 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc pyr_c_C3H3O3_MRM 542.990231 True None
27 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc s7p_c_C7H14O10P_MRM 524.879652 True None
28 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc succ_c_C4H3O3_MRM 1535.567686 True None
29 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc succ_c_C4H5O4_MRM 1535.567686 True None
30 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc thr_DASH_L_c_C2H4NO2_MRM 86.390543 True None
31 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc thr_DASH_L_c_C4H8NO3_MRM 109.554083 True None 
[12]:

fittedMeasuredFluxResiduals

[12]:
simulation_id simulation_dateAndTime experiment_id sample_name_abbreviation time_point rxn_id res_data res_fit res_peak res_stdev res_val res_msens res_esens used_ comment_
0 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 Ec_Biomass_INCA 0.704 0.704 None 0.008 2.511880e-12 None None True None
1 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 EX_ac_LPAREN_e_RPAREN_ 2.130 2.130 None 0.500 9.405809e-12 None None True None
2 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 EX_glc_LPAREN_e_RPAREN_ 7.400 7.400 None 0.200 -8.073542e-12 None None True None 
[13]:

fittedMeasuredFragmentResiduals

[13]:
simulation_id simulation_dateAndTime experiment_id sample_name_abbreviation time_point fragment_id fragment_mass res_data res_fit res_peak res_stdev res_val res_msens res_esens used_ comment_
3 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 3pg_c_C3H6O7P_MRM 185.049463 0.434465 0.449206 M+0 0.016856 0.874535 None None True None
4 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 6pgc_c_C6H12O10P_MRM 275.127544 0.095200 0.130680 M+0 0.028053 1.264734 None None True None
5 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 akg_c_C4H5O3_MRM 101.080880 0.013870 0.013947 M+0 0.001551 0.049918 None None True None
6 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 akg_c_C5H5O5_MRM 145.090430 0.353333 0.362609 M+1 0.017717 0.523606 None None True None
7 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 asp_DASH_L_c_C3H6NO2_MRM 88.085379 0.362688 0.368352 M+0 0.012540 0.451634 None None True None
8 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 asp_DASH_L_c_C4H6NO4_MRM 132.094929 0.326136 0.337056 M+0 0.015887 0.687353 None None True None
9 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 dhap_c_C3H6O6P_MRM 169.050058 0.285900 0.311233 M+0 0.032310 0.784057 None None True None
10 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 fdp_c_C6H13O12P2_MRM 339.108057 0.041052 0.042078 M+0 0.004040 0.253959 None None True None
11 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 g6p_c_C6H12O9P_MRM 259.128139 0.062617 0.102742 M+0 0.023661 1.695852 None None True None
12 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 glc_DASH_D_c_C2H3O2_MRM 59.044113 0.624426 0.634855 M+0 0.016085 0.648315 None None True None
13 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 glc_DASH_D_c_C6H11O6_MRM 179.148221 0.006977 0.007240 M+0 0.001300 0.202349 None None True None
14 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 glu_DASH_L_c_C5H6NO3_MRM 128.106264 0.134416 0.135597 M+0 0.005110 0.231207 None None True None
15 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 glu_DASH_L_c_C5H8NO4_MRM 146.121551 0.134416 0.135597 M+0 0.005110 0.231207 None None True None
16 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 icit_c_C5H3O3_MRM 111.075738 0.271897 0.527267 M+0 0.076534 3.336682 None None True None
17 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 icit_c_C6H7O7_MRM 191.115862 0.255439 0.617962 M+0 0.078364 4.626148 None None True None
18 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 mal_DASH_L_c_C4H3O4_MRM 115.064403 0.324639 0.360182 M+0 0.010540 3.372176 None None True None
19 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 mal_DASH_L_c_C4H5O5_MRM 133.079690 0.324639 0.360182 M+0 0.010540 3.372176 None None True None
20 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 met_DASH_L_c_C5H10NO2S_MRM 148.203423 0.116097 0.180032 M+0 0.025444 2.512787 None None True None
21 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 met_DASH_L_c_CH3S_MRM 47.099363 0.473937 0.479632 M+0 0.029731 0.191543 None None True None
22 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 pep_c_C3H4O6P_MRM 167.034176 0.439365 0.453790 M+0 0.020835 0.692360 None None True None
23 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 phe_DASH_L_c_C9H10NO2_MRM 164.181583 0.250254 0.265110 M+1 0.037267 0.398648 None None True None
24 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 phe_DASH_L_c_C9H7O2_MRM 147.151057 0.250254 0.265110 M+1 0.037267 0.398648 None None True None
25 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 prpp_c_C5H12O14P3_MRM 389.061948 0.266659 0.268503 M+0 0.014429 0.127800 None None True None
26 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 pyr_c_C3H3O3_MRM 87.054258 0.424906 0.428610 M+0 0.009673 0.382893 None None True None
27 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 s7p_c_C7H14O10P_MRM 289.154166 0.210187 0.275388 M+0 0.026767 2.435895 None None True None
28 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 succ_c_C4H3O3_MRM 99.064998 0.217845 0.226561 M+0 0.014353 0.607219 None None True None
29 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 succ_c_C4H5O4_MRM 117.080285 0.217845 0.226561 M+0 0.014353 0.607219 None None True None
30 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 thr_DASH_L_c_C2H4NO2_MRM 74.058757 0.501832 0.507023 M+0 0.077235 0.067213 None None True None
31 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 WTEColi_113C80_U13C20_01 OxicWtGlc 0 thr_DASH_L_c_C4H8NO3_MRM 118.111406 0.262139 0.266607 M+0 0.056147 0.079581 None None True None 
[14]:

simulationParameters

[14]:
cont_alpha cont_reltol cont_steps fit_nudge fit_reinit fit_reltol fit_starts fit_tau hpc_on int_maxstep ... sim_sens sim_ss sim_tunit hpc_mcr hpc_serve simulation_id simulation_dateAndTime original_filename used_ comment_
0 0.05 1.0 5.0 1.0 True 0.01 10.0 0.000001 False inf ... False True h 0.0 parfor WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 data/MFA_modelInputsData/TestFile.mat True None

1 rows × 31 columns

Visualization

Fluxes can easily be visulaized using “Escher”

First we have to set up a dictionary containing our calculated flux values together with their corresponding reaction IDs

[15]:

fittedFluxes

[15]:
simulation_id simulation_dateAndTime rxn_id flux flux_stdev flux_lb flux_ub flux_units fit_alf fit_chi2s fit_cor fit_cov free used_ comment_
0 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 26dap_DASH_MSYN 2.295040e-01 0.002608 0.224392 0.234616 mmol*gDCW-1*hr-1 0.05 None None None False True None
1 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 ACONTa_ACONTb 2.074886e+00 16996.864976 1.185984 1000.000000 mmol*gDCW-1*hr-1 0.05 None None None False True None
2 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 ACONTa_ACONTb_reverse 8.690514e-07 15432.592032 0.000000 28.927600 mmol*gDCW-1*hr-1 0.05 None None None True True None
3 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 AKGDH 1.423617e-01 7673.615592 0.000000 1.919800 mmol*gDCW-1*hr-1 0.05 None None None False True None
4 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 ALATA_L 3.435520e-01 0.003904 0.335900 0.351204 mmol*gDCW-1*hr-1 0.05 None None None False True None
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
92 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 TPI 2.175603e+00 25620.656341 0.000000 1000.000000 mmol*gDCW-1*hr-1 0.05 None None None False True None
93 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 TPI_reverse 8.689299e-07 24739.593649 0.000000 1000.000000 mmol*gDCW-1*hr-1 0.05 None None None True True None
94 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 TrpSYN 3.801600e-02 0.000432 0.037169 0.038863 mmol*gDCW-1*hr-1 0.05 None None None False True None
95 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 TyrSYN 9.222400e-02 0.001048 0.090170 0.094278 mmol*gDCW-1*hr-1 0.05 None None None False True None
96 WTEColi_113C80_U13C20_01 2021-02-10 16:29:22 ValSYN 2.830080e-01 0.003216 0.276705 0.289311 mmol*gDCW-1*hr-1 0.05 None None None False True None

97 rows × 15 columns

[16]:

fluxes = {}
for i, rxn in fittedFluxes.iterrows():
    fluxes[rxn['rxn_id']] = rxn['flux']

Then we can check if there is a suitable map available (if not it will have to be added)

[17]:

escher.list_available_maps()

[17]:

[{'organism': 'Saccharomyces cerevisiae',
  'map_name': 'iMM904.Central carbon metabolism'},
 {'organism': 'Homo sapiens',
  'map_name': 'RECON1.Inositol retinol metabolism'},
 {'organism': 'Homo sapiens', 'map_name': 'RECON1.Glycolysis TCA PPP'},
 {'organism': 'Homo sapiens', 'map_name': 'RECON1.Tryptophan metabolism'},
 {'organism': 'Homo sapiens', 'map_name': 'RECON1.Carbohydrate metabolism'},
 {'organism': 'Homo sapiens',
  'map_name': 'RECON1.Amino acid metabolism (partial)'},
 {'organism': 'Escherichia coli', 'map_name': 'iJO1366.Nucleotide metabolism'},
 {'organism': 'Escherichia coli',
  'map_name': 'iJO1366.Fatty acid biosynthesis (saturated)'},
 {'organism': 'Escherichia coli',
  'map_name': 'iJO1366.Nucleotide and histidine biosynthesis'},
 {'organism': 'Escherichia coli', 'map_name': 'e_coli_core.Core metabolism'},
 {'organism': 'Escherichia coli', 'map_name': 'iJO1366.Central metabolism'},
 {'organism': 'Escherichia coli',
  'map_name': 'iJO1366.Fatty acid beta-oxidation'}]

And then we are ready to display the fluxes

[18]:

b = escher.Builder('e_coli_core.Core metabolism',
               reaction_data= fluxes).display_in_notebook()

[19]:

b

[19]:

[ ]: