NCSI: RNA Comparative Analysis of Covid-19 Strains

Status	Completed
Mentor Name	Stephen Wheat
Mentor's XSEDE Affiliation	Campus Champion
Mentor Has Been in XSEDE Community	4-5 years
Project Title	RNA Comparative Analysis of Covid-19 Strains
Summary	This is a continuation on the Spring 2021 Covid analytics project. The objective is to assess the fine-grained similarities of the 70,000 samples and to derive a means to expand that to the more than 200,000 samples now available. The key question is whether the fine-grained dissimilarities can be clustered and create a mutation tree that could be mapped across the world.
Job Description	The student(s) will work with BioChem and CSC research professors, doing coding, large-scale capacity job runs, data pre- and post-processing. The coding will also involve R development, BI tool scripts, and other visualization scripts to facilitate insight into the nature of the similarity clusters. The scope of the work is that of a "Apprentice". Weekly tasks with frequent engagement with the PIs will be given. The intention is to have an intensive learning opportunity beyond the classroom while developing results of importance to the research community.
Computational Resources	This project will use ORU's own HPC cluster, Titan, which provides regional services in OK on the OneOklahoma Friction Free Network (OFFN). By the time the Fall semester starts, Titan will an additional 80+ nodes.
Contribution to Community	This project provides undergraduate research experience, growing future leaders whose potential graduate work will be that much more strong and capable. The results will contribute to insights regarding long-term after affects of the virus and give that much more insight into what it would take to prepare for the next pandemic.
Position Type	Apprentice
Training Plan	This project involves 3 CSC faculty and a BioChem faculty. Each will provide time and expertise to guide the direction of the work and answer questions. The team will meet weekly for two hours to work through the prior week's accomplishments and to ensure the goals of the next week are clear. In that weekly session, training on the use of various tools (e.g., R) will be provided in a contextual basis (aka learning as needed for the tasks at hand).
Student Prerequisites/Conditions/Qualifications	Given the Apprentice level, the students will need prior experience with HPC SLURM environments and be experienced in C++. The student should be well familiar with Unix command-line environment and storage organization and strong in networking skills. Strong communication skills with inquisitive and proactive pursuit; traits self motivating. Seek help when it is needed versus floundering.
Duration	Semester
Start Date	08/25/2021
End Date	11/26/2021