/ecCGL1

Construction and application of the Corynebacterium glutamicum enzyme‐constrained model

Primary LanguageJupyter Notebook

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

Install dependencies using pip:

pip install --update .

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.