GNN encodings of bovine metabolities towards anti-methanogenicity

Published: 10 September 2024| Version 1 | DOI: 10.17632/y9h3rhphtz.1
Contributor:
Ratul Chowdhury

Description

This project focuses on analyzing and visualizing the complex molecular structures present in milk and bovine metabolites. We use Graph Neural Networks (GNNs) to generate molecular embeddings from SMILES string and t-SNE for dimensionality reduction and visualization. We utilize two metabolite databases: The Milk Composition Database (MCDB) - 2,360 entries The Bovine Metabolome Database (BMDB) - 51,682 entries Sample - 16 selected MCR molecules Note: The MCDB database is included in the metabolites folder of this repository. Due to its large size, the BMDB is not incorporated directly into this repository. The databses are publicly available here: https://metabolomicscentre.ca/software-databases/databases/. Bovine metabolome database can also be accessed from: https://iastate.box.com/s/8xz7ipb6rxqdfgfpcurxyq0ynd5l9g29

Files not available for this dataset

This contains only metadata

Steps to reproduce

All steps are given in detail in PI Chowdhury's lab GitHub page - https://github.com/ChowdhuryRatul/Methanogenesis-GNN

Institutions

Iowa State University

Categories

Enzyme Inhibitor, Molecular Computing

Funders

Licence