Develop a data portal for the organization of molecular and imaging data

Submission information

Submission Number: 157

Submission ID: 1768

Submission UUID: 6676ffbb-c33a-461e-8b7c-2f675413e27d

Submission URI: /form/project

Created: Wed, 11/02/2022 - 07:01

Completed: Wed, 11/02/2022 - 07:01

Changed: Thu, 06/13/2024 - 14:38

Remote IP address: 173.69.40.16

Submitted by: Gaurav Khanna

Language: English

Is draft: No

Webform: Project

Project Title Develop a data portal for the organization of molecular and imaging data

Program CAREERS

Project Image

Tags archiving (266), aws (20), bioinformatics (277), biology (515), Cloud (687), Data Storage (670), docker (35), genomics (537)

Status Complete

Project Leader

Project Leader Ying Zhang

Email yingzhang@uri.edu

Mobile Phone {Empty}

Work Phone {Empty}

Project Personnel

Mentor(s) Ying Zhang, Gaurav Khanna

Student-facilitator(s) Andrew Lefebvre

Mentee(s) {Empty}

Project Information

Project Description Microorganisms play important roles in nutrient cycling, energy production, and ecosystem health. The collection of microorganisms, also known as the “microbiomes”, are central participants of plant-soil interactions, bioproduct synthesis, environmental sustainability, and human health. The study of microbiomes has long been inhibited by lack of laboratory cultivated microbial isolates. This problem has been alleviated over the past decade through the rapid advancement and adaptation of metagenomics, a sequencing technology that determines the genomic composition of mixed microbial populations encompassing hundreds to thousands of genomes as a whole.

In this project, we will aim to develop a data portal to facilitate the organization of laboratory and field sampling data. The data will be organized into a relational database, and an interactive user interface will be developed to facilitate data input and data retrieval. The database will be deployed to a cloud server.

Project Information Subsection

Project Deliverables {Empty}

Student Research Computing Facilitator Profile Prior experiences with relational database design and deployment; familiarity with MySQL, python, and other toolkits for web interface development; experiences with cloud server deployment.

Mentee Research Computing Profile {Empty}

Student Facilitator Programming Skill Level Some hands-on experience

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Project Institution University of Rhode Island -- Bay Campus

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Anchor Institution CR-University of Rhode Island

Preferred Start Date {Empty}

Start as soon as possible. No

Project Urgency Already behind3Start date is flexible

Expected Project Duration (in months) 6

Launch Presentation

bburnett_project_launch - Repaired.pdf

Launch Presentation Date 02/08/2023

Wrap Presentation

Careers.project.wrap_.mov

Wrap Presentation Date {Empty}

Project Milestones

Milestone Title: Milestone #1
Milestone Description: determine project scope, Cloud/VM access, launch presentation, git project
Completion Date Goal: 2023-02-01
Milestone Title: Milestone #2
Milestone Description: organize data set, finalize relational database schema
Completion Date Goal: 2023-03-01
Milestone Title: Milestone #3
Milestone Description: complete working prototype
Completion Date Goal: 2023-05-01
Milestone Title: Milestone #4
Milestone Description: extensive testing and debugging
Completion Date Goal: 2023-06-01
Milestone Title: Milestone #5
Milestone Description: wrap up development, update project git and documentation, wrap presentation.
Completion Date Goal: 2023-06-30

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Planned Portal Contributions (if any) {Empty}

Planned Publications (if any) {Empty}

What will the student learn? {Empty}

What will the mentee learn? {Empty}

What will the Cyberteam program learn from this project? {Empty}

HPC resources needed to complete this project? {Empty}

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Final Report

What is the impact on the development of the principal discipline(s) of the project? As part of the development of this project it will assist the speed and organization of sequencing Foram information within that lab.

What is the impact on other disciplines? This will not have much impact on other disciplines, but for future maintenance of the system there will be substantial framework for continued use and development.

Is there an impact physical resources that form infrastructure? {Empty}

Is there an impact on the development of human resources for research computing? {Empty}

Is there an impact on institutional resources that form infrastructure? {Empty}

Is there an impact on information resources that form infrastructure? {Empty}

Is there an impact on technology transfer? {Empty}

Is there an impact on society beyond science and technology? {Empty}

Lessons Learned The 2 most important lessons learned are to keep things simple when possible (don’t over engineer something) and to try to get as much information on parameters of a project before working on it.

Overall results The outcome of this project results in an useful and maintainable database application.