Publication Date

Winter 1-20-2021

Degree Type

Master's Project

Degree Name

Master of Science in Bioinformatics (MSBI)

Department

Computer Science

First Advisor

Philip Heller

Abstract

Space travel presents inherent risks to human health and a better understanding of space biology is required to mitigate harm in an oncoming age of increased space travel. Omics analysis will play a central role in better understanding human health in space. In this project, differential gene expression analysis was performed on GLDS-104, an open science dataset provided by NASA’s GeneLab. GeneLab’s RNA-Seq Consensus Pipeline was implemented using Nextflow, performed on San Jose State University’s College of Science High Performance Computing Cluster, and optimized for computational resource efficiency. Comparison of the Nextflow implemention developed in this project to GeneLab’s posted results for the pipeline indicate a high degree of reproducibility was achieved. The results from GLDS-104 were further analyzed to develop insights into the physiological effect of space flight on skeletal muscle and demonstrate utility of the pipeline. Among the insights discussed includes a theory suggesting the upregulation in myogenesis related genes during space flight compared to hindlimb unloading may be due to unique space flight ambulation. This project highlights the importance of connecting effective pipeline specifications, efficient workflow implementations, and high performance computing to enable space biology omics research.

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