Computational pipelines for the analysis of plastic-degrading genes

Project Information

bioinformatics, biology, workflow, workforce-development
Project Status: Complete
Project Region: CAREERS
Submitted By: Gaurav Khanna
Project Email: yingzhang@uri.edu
Project Institution: University of Rhode Island
Anchor Institution: CR-University of Rhode Island

Students: Aidan McCrillis

Project Description

The prevalence of microplastics is posing increasing problems to the environment and human health. Despite the identification of several plastic-degrading pathways, their presence and evolution among diverse microorganisms is largely unexplored.

In this project, we will develop a computational pipeline using the Snakemake workflow management system to assemble bioinformatics tools for the identification and evolutionary analysis of plastic-degrading proteins. We will also examine the abundance of these proteins by mining metagenomic data. Snakemake workflow management system is a python-based tool to create reproducible and scalable data analyses. The supported student will work with PI and other lab researchers to understand the analysis workflow and bioinformatics tools and build a computational pipeline using Snakemake. This effort will include elements of HPC, bioinformatics, python programming, and git version controls.

Additional Resources

Launch Presentation:
Wrap Presentation: 6

Project Information

bioinformatics, biology, workflow, workforce-development
Project Status: Complete
Project Region: CAREERS
Submitted By: Gaurav Khanna
Project Email: yingzhang@uri.edu
Project Institution: University of Rhode Island
Anchor Institution: CR-University of Rhode Island

Students: Aidan McCrillis

Project Description

The prevalence of microplastics is posing increasing problems to the environment and human health. Despite the identification of several plastic-degrading pathways, their presence and evolution among diverse microorganisms is largely unexplored.

In this project, we will develop a computational pipeline using the Snakemake workflow management system to assemble bioinformatics tools for the identification and evolutionary analysis of plastic-degrading proteins. We will also examine the abundance of these proteins by mining metagenomic data. Snakemake workflow management system is a python-based tool to create reproducible and scalable data analyses. The supported student will work with PI and other lab researchers to understand the analysis workflow and bioinformatics tools and build a computational pipeline using Snakemake. This effort will include elements of HPC, bioinformatics, python programming, and git version controls.

Additional Resources

Launch Presentation:
Wrap Presentation: 6