MFA using INCA in MATLAB - now all in Python!¶

This is an example notebook that makes use of functions that can write a MATLAB script that runs an MFA analysis using INCA. INCA is a MATLAB software. To make it easier for users, MATLAB can be run here in the notebook using an engine. See the instructions below on how to use this notebook.

Prerequisites¶

MATLAB¶

Get a free academic licence and install MATLAB from https://www.mathworks.com. Then, install the engine API following the guide provided under this link. In short, you will have to go to your MATLAB root folder (find your installation and open that folder) and go to “/extern/engines/python” and run “python setup.py install” from the command line.

INCA¶

“INCA (Isotopomer Network Compartmental Analysis) is a MATLAB-based software package for isotopomer network modeling and metabolic flux analysis.” You can read more about it in Young, 2014.

You have to get a free academic licence for INCA from the Vanderbilt University website (the second option is the relevant one) and install it. Note the path to the base directory of your INCA installation, you will need it later.

Import customized functions for INCA utilization¶

[1]:

from BFAIR.INCA import INCA_script
import pandas as pd
import numpy as np
import time
import ast
import matlab.engine

Academic license - for non-commercial use only - expires 2021-05-28
Using license file /Users/matmat/gurobi.lic

Initialize the script¶

[2]:

INCA_script = INCA_script()

Import the data¶

[3]:

# measured fragments/MS data, tracers and measured fluxes should be limited to one experiment

atomMappingReactions_data_I = pd.read_csv('data/MFA_modelInputsData/data_stage02_isotopomer_atomMappingReactions2.csv')
modelReaction_data_I = pd.read_csv('data/MFA_modelInputsData/data_stage02_isotopomer_modelReactions.csv')
atomMappingMetabolite_data_I = pd.read_csv('data/MFA_modelInputsData/data_stage02_isotopomer_atomMappingMetabolites.csv')
measuredFluxes_data_I = pd.read_csv('data/MFA_modelInputsData/data_stage02_isotopomer_measuredFluxes.csv')
experimentalMS_data_I = pd.read_csv('data/MFA_modelInputsData/data-1604345289079.csv')
tracer_I = pd.read_csv('data/MFA_modelInputsData/data_stage02_isotopomer_tracers.csv')

Exclude data for irreleavnt experiments and models¶

[4]:

# The files need to be limited by model id and mapping id, I picked "ecoli_RL2013_02" here
atomMappingReactions_data_I = INCA_script.limit_to_one_model(atomMappingReactions_data_I, 'mapping_id', 'ecoli_RL2013_02')
modelReaction_data_I = INCA_script.limit_to_one_model(modelReaction_data_I, 'model_id', 'ecoli_RL2013_02')
atomMappingMetabolite_data_I = INCA_script.limit_to_one_model(atomMappingMetabolite_data_I, 'mapping_id', 'ecoli_RL2013_02')
measuredFluxes_data_I = INCA_script.limit_to_one_model(measuredFluxes_data_I, 'model_id', 'ecoli_RL2013_02')

# Limiting fluxes, fragments and tracers to one experiment
measuredFluxes_data_I = INCA_script.limit_to_one_experiment(measuredFluxes_data_I, 'experiment_id', 'WTEColi_113C80_U13C20_01')
experimentalMS_data_I = INCA_script.limit_to_one_experiment(experimentalMS_data_I, 'experiment_id', 'WTEColi_113C80_U13C20_01')
tracer_I = INCA_script.limit_to_one_experiment(tracer_I, 'experiment_id', 'WTEColi_113C80_U13C20_01')

Generate the MATLAB script¶

Save it in your working directory. The last argument in the script_generator function will name your future .mat file

[7]:

script = INCA_script.script_generator(
    modelReaction_data_I,
    atomMappingReactions_data_I,
    atomMappingMetabolite_data_I,
    measuredFluxes_data_I,
    experimentalMS_data_I,
    tracer_I
)
INCA_script.save_INCA_script(script, "testscript")
runner = INCA_script.runner_script_generator('TestFile', 10)
INCA_script.save_runner_script(runner=runner, scriptname="testscript")

There is no stoichimetriy given for: ATPM
There is no stoichimetriy given for: Ec_Biomass_INCA
There is no stoichimetriy given for: EX_nh4_LPAREN_e_RPAREN_
There is no stoichimetriy given for: EX_o2_LPAREN_e_RPAREN_
There is no stoichimetriy given for: EX_so4_LPAREN_e_RPAREN_
There is no stoichimetriy given for: FADR_NADH_CYTBD_HYD_ATPS4r
There is no stoichimetriy given for: NADH_CYTBD_HYD_ATPS4r
There is no stoichimetriy given for: NADTRHD_THD2pp
There is no stoichimetriy given for: NADTRHD_THD2pp_reverse

Provide the path to you INCA installation, your working directory and the name of the previously generated MATLAB script¶

[6]:

INCA_base_directory = # ADD YOUR BASE DIRECTORY HERE, e.g. "/Users/Username/Documents/INCAv1.9"
script_folder = %pwd
matlab_script = "testscript"
runner_script = matlab_script + "_runner"

INCA will be started and your script run in MATLAB. This will produce the .mat file specified above¶

[7]:

INCA_script.run_INCA_in_MATLAB(INCA_base_directory, script_folder, matlab_script, runner_script)

--- 270.8612148761749 seconds -

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