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:
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Cobrapy toolkit: version --0.13.3 (recommend, because the latest version has removed a required function of "convert_to_irreversible")；
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Pyomo package: version --5.7；
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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.txtTo 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:
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ETGEMs_function.py
——Pyomo template model and functions definition file used for following analysis：