The scripts for construction of enzymatic and thermodynamic constrained GEMs in a single Pyomo modelling framework.

The scripts were written and tested with Python 3.5.5.

The core libraries essential for the pipeline including:

1. Cobrapy toolkit: version --0.13.3 (recommend, because the latest version has removed a required function of "convert_to_irreversible")；
2. Pyomo package: version --5.7；
3. Gurobi solver: version --9.0.2;

In addition，the Pandas and related packages.

The packages used to run the pipeline was listed in requirements.txt. To install the requirements using pip, run the following code at command-line:

$ pip install -r requirements.txt

To create a stand-alone environment named ETGEMs with Python 3.5.5 and all the required package versions (especially for cobrapy is also available), run the following code:

$ conda create -n ETGEMs python=3.5.5

$ conda activate ETGEMs

$ pip install -r requirements.txt

$ python -m ipykernel install --user --name ETGEMs --display-name "ETGEMs"

You can read more about using conda environments in the Managing Environments section of the conda documentation.

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

• ETGEMs_function.py

  ——Pyomo template model and functions definition file used for following analysis：

  Get_Figure1.ipynb

  Get_Figure2.ipynb

  Get_Table D.ipynb

  Get_Table E.ipynb

Xue Yang,Zhitao Mao,Xin Zhao,Ruoyu Wang,Peiji Zhang,Jingyi Cai,Chaoyou Xue, Hongwu Ma, Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models,Metabolic Engineering, 2021; https://doi.org/10.1016/j.ymben.2021.06.005

Xue Yang,Zhitao Mao,Jianfeng Huang,Ruoyu Wang,Huaming Dong,Yanfei Zhang,Hongwu Ma, Improving pathway prediction accuracy of constraints-based metabolic network models by treating enzymes as microcompartments,Synthetic and Systems Biotechnology, 2023; https://doi.org/10.1016/j.synbio.2023.09.002