Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes

Contents

• System requirements
• Installation guide
• Demo
• Instructions for use

System requirements

Installation of the 'glove' package requires either Linux (Ubuntu 16+) or Max OSX operating systems. Recommended computer specs:

RAM: 16+ GB CPU: 4+ cores (base speed 2.3+ GHz).

Installation Guide

We recommend installing the Anaconda Python distribution (https://www.anaconda.com/download)

Once Python is installed, run the installation file for glove in the terminal:

python setup.py install

Installation should take less than a minute to install all dependencies (numpy, pandas, jax, jaxlib)

DEMO

Following successful installation, please see the tutorial Jupyter notebook, "GLOVE tutorial.ipynb"

Instructions for use

The glove package is intended for use with synthetic microbial community data to perform Bayesian parameter estimation and experimental design. Please refer to the tutorial for reference on data formatting guidelines and code execution.