Computational pipelines for the analysis of plastic-degrading genes

Project Title: Computational pipelines for the analysis of plastic-degrading genes
Program:
CAREERS (323)

Project Image: https://support.access-ci.org/system/files/webform/project/3985/anthrax-image-protein-units-drug-factor-unit.jpg
Tags:
bioinformatics (277), biology (515), workflow (365), workforce-development (337)

Status: Complete
Project Leader
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Project Leader:
Ying Zhang

Email: yingzhang@uri.edu
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Project Personnel
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Mentor(s):
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Student-facilitator(s):
Aidan McCrillis (19738)

Mentee(s):
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Project Information
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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 Information Subsection
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Project Deliverables:
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Student Research Computing Facilitator Profile:
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Project Institution: University of Rhode Island
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Anchor Institution: CR-University of Rhode Island
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Start as soon as possible.: No
Project Urgency: Already behind3Start date is flexible
Expected Project Duration (in months): 6
Launch Presentation: https://support.access-ci.org/system/files/webform/project/3985/Aidan.Careers.project.launch.pptx
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Wrap Presentation: https://support.access-ci.org/system/files/webform/project/3985/2024-06-12-Careers_Wrap_Presentation.pptx
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Project Milestones:
- Milestone Title: Milestone #1
  Milestone Description: Determine project scope, Snakemake work environment, launch presentation.
  Completion Date Goal: 2023-10-30
- Milestone Title: Milestone #2
  Milestone Description: Bioinformatics tool assembly and testing, finalize pipeline design.
  Completion Date Goal: 2023-11-30
- Milestone Title: Milestone #3
  Milestone Description: Complete working prototype, project git
  Completion Date Goal: 2023-12-30
- Milestone Title: Milestone #4
  Milestone Description: Extensive testing and debugging, application and data analysis.
  Completion Date Goal: 2024-02-28
- Milestone Title: Milestone #5
  Milestone Description: Wrap up development, update project git and documentation, wrap presentation
  Completion Date Goal: 2024-03-30

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What will the student learn?:
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Final Report
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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.

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Is there an impact on technology transfer?:
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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.