Bioremediation of a Coastal Oil Spill: A Case Study Using a Community Genome-Scale Metabolic Model

This repo contains the supplementary Jupyter Notebook of the perspective article: Applications of marine microbial community models in the nature-based economy. In this notebook, we demonstrate the use of a community genome-scale metabolic model (cGEM) to simulate the bioremediation of a coastal oil spill.

Running the notebook locally

1. Clone this repository to your local machine, set up a virtual environment, and install the dependencies:

git clone
cd
python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

2. Start a Jupyter Notebook server:

jupyter notebook

3. Open the notebook oil_spill.ipynb and run the cells.

License

This work is license under the Apache License, Version 2.0. See the LICENSE file for details.