The process for enzyme-constrained model construction.

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

Install dependencies using pip:

pip install --update .

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.