NCSI: Using Bioinformatics to Study Wildlife Microbiomes

Status	Completed
Mentor Name	Steven Kimble
Mentor's XSEDE Affiliation	Research Allocation, Teaching Allocation
Mentor Has Been in XSEDE Community	3-4 years
Project Title	Using Bioinformatics to Study Wildlife Microbiomes
Summary	Almost every organism studied to date has a microbiome, the collection of bacteria, viruses, and tiny plants and animals that live in an on other creatures (the "hosts"). Though these microbiota can have important interactions with the host, such as helping them fight disease or digest vitamins, they are poorly understood in most species. The primary goal of this project is to better understand the microbiomes of threatened wildlife species such as turtles and frogs via bioinformatic explorations of vast amounts of DNA sequence data. Using high-powered computing resources, these analyses can teach us much about the microbial communities that inhabit these species.
Job Description	Student duties will be threefold: 1. Use of high-powered computing resources to analyze DNA sequence data: Student will use mostly command line-driven software to load and analyze DNA sequence files. Code and tutorials may or may not be available for some steps so students will need to be self-driven to troubleshoot on their own. Experience with LINUX or R or other command line computer languages is highly desirable as student will be expected to improve and apply their computational skills. 2. Periodic communication with the PI: Student will have regular meetings with the PI and will need to present progress reports and discuss the science at meetings. Student should be comfortable discussing the scientific method, scientific ideas, and be a reliable communicator. Experience with independent research highly desirable as student will be tasked with specific projects but with their own intellectual contribution. 3. Preparation of a manuscript for submission to a peer-reviewed journal for publication: Student will be expected to search the literature, develop hypotheses, and write a rough draft of a manuscript reporting the results of their analyses. Experience with manuscript preparation highly desirable. There will be multiple sources of frustration: failed experiments, contamination, ambiguous results and limited resources, but this mirrors the reality of authentic scientific research. In exchange, students will get to experience real sciencing, from hypothesis development to data analysis to scientific communication.
Computational Resources	Most computation required for this project will be with a research allocation of compute resources on the NSF's XSEDE EXPANSE cluster of supercomputers.
Contribution to Community	This project will contribute to the XSEDE community by employing advanced digital NSF resources to train an undergraduate student and explore the microbiomes of wild organisms.
Position Type	Apprentice
Training Plan	Student computational skills will be assessed at onset and training plan tailored accordingly, but in general will include the use of previously developed tutorials and online training, inclusion in discussions of project development, and hands-on tutoring as needed.
Student Prerequisites/Conditions/Qualifications	Students should have completed some upper-level coursework in some combination of genetics, ecology, or microbiology. Students with experience in LINUX or other computer languages preferred. Also, students with undergraduate independent research experience or and manuscript preparation preferred.
Duration	Semester
Start Date	01/31/2022
End Date	05/24/2022