Submission information
Submission Number: 180
Submission ID: 3985
Submission UUID: 399fee51-c671-4acd-8572-060c448fd732
Submission URI: /form/project
Created: Sat, 08/26/2023 - 06:41
Completed: Sat, 08/26/2023 - 06:44
Changed: Thu, 06/13/2024 - 14:36
Remote IP address: 104.28.39.76
Submitted by: Gaurav Khanna
Language: English
Is draft: No
Webform: Project
| Project Title | Computational pipelines for the analysis of plastic-degrading genes |
|---|---|
| Program | CAREERS |
| Project Image |
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| Tags | bioinformatics (277), biology (515), workflow (365), workforce-development (337) |
| Status | Complete |
| Project Leader | Ying Zhang |
| yingzhang@uri.edu | |
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| Mentor(s) | |
| Student-facilitator(s) | Aidan McCrillis |
| Mentee(s) | |
| 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. |
| Project Deliverables | |
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| Student Research Computing Facilitator Profile | |
| Mentee Research Computing Profile | |
| Student Facilitator Programming Skill Level | |
| Mentee Programming Skill Level | |
| Project Institution | University of Rhode Island |
| Project Address | |
| Anchor Institution | CR-University of Rhode Island |
| Preferred Start Date | |
| Start as soon as possible. | No |
| Project Urgency | Already behind3Start date is flexible |
| Expected Project Duration (in months) | 6 |
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| What will the student learn? | |
| What will the mentee learn? | |
| What will the Cyberteam program learn from this project? | |
| HPC resources needed to complete this project? | |
| Notes | |
| What is the impact on the development of the principal discipline(s) of the project? | This project will help to streamline the identification of potential plastic degrading genes and proteins and help to create reproducible results that can easily be built upon by other researchers. |
| What is the impact on other disciplines? | This probably won't have a large impact on other disciplines but will allow people outside bioinformatics to use this pipeline without having a comprehensive knowledge of the packages and modules that were used in the pipeline. |
| Is there an impact physical resources that form infrastructure? | |
| Is there an impact on the development of human resources for research computing? | |
| Is there an impact on institutional resources that form infrastructure? | |
| Is there an impact on information resources that form infrastructure? | |
| Is there an impact on technology transfer? | |
| Is there an impact on society beyond science and technology? | This project will help to further knowledge about plastic degrading proteins with the aim of helping to solve the problem of plastic pollution and finding a way to degrade the plastics that are in the ocean. |
| Lessons Learned | I think I gained a lot of valuable knowledge in the process of building a workflow and what considerations should be taken to make a product that is usable for other people. I also gained a lot of experience with dealing with large sets of bioinformatics data and how to make sense of such a large dataset. |
| Overall results | The overall result of the project I worked on is a workflow that allows for the identification and sorting of potential plastic degrading genes. |