ecCGL1

The process for enzyme-constrained model construction.

About

The pipeline was written and tested on Linux. The core libraries essential for the pipeline including: cobra, plotly (draw figures), and related packages.

Installation

1. create ECMpy environment using conda:

$ conda create -n ECMpy python=3.6.5

2. install related packages using pip:

$ conda activate ECMpy
$ pip install cobra==0.13.3
$ pip install plotly
$ pip install -U kaleido
$ pip install nbformat
$ pip install requests
$ pip install Bio
$ pip install scipy
$ pip install ipykernel
$ python -m ipykernel install --user --name ECMpy --display-name "ECMpy"

Steps to reproduce the analysis in the publication

Download all data and analysis code from github (directlt download or use git clone).

$ cd /file path/project save path/
$ git clone https://github.com/tibbdc/eciCW773.git

All results can be reproduced by executing the Jupyter Python notebooks:

• 01_model_calibration.ipynb

  • Model Calibration.

• 02_construct_ecCGL1.ipynb

  • Construction of ecCGL1.

• 03_CDF_kcat_and_mw.ipynb

  • Cumulative distribution of kcat and molecular weights.

• 04_PhPP_analysis.ipynb

  • Phenotype phase plane (PhPP) analysis.

• 05_FVA.ipynb

  • Comparative flux variability analysis.

• 06_trade-off.ipynb

  • Overflow metabolism simulation.

• 07_metabolic_engineering_targets.ipynb

  • Metabolic engineering targets prediction.

How to cite:

Jinhui Niu, Zhitao Mao, Yufeng Mao, Ke Wu,Zhenkun Shi,Qianqian Yuan,Jingyi Cai and Hongwu Ma, Construction and Analysis of an Enzyme-Constrained Metabolic Model of Corynebacterium glutamicum,Biomolecules, 2022; https://doi.org/10.3390/biom12101499