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 |
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| Tags | archiving (266), aws (20), bioinformatics (277), biology (515), Cloud (687), Data Storage (670), docker (35), genomics (537) |
| Status | Complete |
| Project Leader | Ying Zhang |
| yingzhang@uri.edu | |
| Mobile Phone | |
| Work Phone | |
| Mentor(s) | Ying Zhang, Gaurav Khanna |
| Student-facilitator(s) | Andrew Lefebvre |
| Mentee(s) | |
| 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 Deliverables | |
| Project Deliverables | |
| 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 | |
| Student Facilitator Programming Skill Level | Some hands-on experience |
| Mentee Programming Skill Level | |
| Project Institution | University of Rhode Island -- Bay Campus |
| 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 |
| Launch Presentation | |
| Launch Presentation Date | 02/08/2023 |
| Wrap Presentation | |
| Wrap Presentation Date | |
| Project Milestones |
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| Github Contributions | |
| Planned Portal Contributions (if any) | |
| Planned Publications (if any) | |
| 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? | 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? | |
| 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? | |
| 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. |