The research of University of Tennessee, Knoxville, Assistant Professor Karen Lloyd integrates geomicrobiology, molecular biology, and geochemistry to determine how microorganisms influence marine geochemical cycles. The goal is to link uncultivated microorganisms to their geochemical functions and explore how these communities react to changing environmental conditions. Subseafloor ecosystems likely contain the majority of Earth's prokaryotic biomass, but their geochemical effects are largely untested.
In this video, Lloyd describes her collaboration with the Joint Institute for Computational Sciences (JICS) to overcome a computational obstacle to studying microbial metagenomes—genetic material recovered directly from environmental samples.
Lloyd says: "The challenge is pretty simple: what are these microbes doing? What are they capable of? What are they actually doing? How fast do they grow? What does it take for them to grow? Do they fight with each other? Do they produce new antibiotics? Do they have enzymes that have special properties? Do they have very long lives? What's their special adaptation that allows them to exist in these niches that we haven't really explored?"
An examination of the genetic information, she explains, provides a place to start in trying to characterize these abundant life forms with which we share existence but know so little about.
Lloyd is being assisted in the project by JICS computational scientist Junqi Yin, who is using HPC-BLAST, a high-throughput, highly parallel version of the NCBI Basic Local Alignment Search Tool. It is developed at JICS of the University of Tennessee and funded by the Intel® Parallel Computing Center.
Posting Date: 22 February 2016
About JICS: The Joint Institute for Computational Sciences was established by the University of Tennessee and Oak Ridge National Laboratory (ORNL) to advance scientific discovery and leading-edge engineering, and to further knowledge of computational modeling and simulation. JICS realizes its vision by taking full advantage of petascale-and-beyond computers housed at ORNL and by educating a new generation of scientists and engineers to be well-versed in the application of computational modeling and simulation for solving the most challenging scientific and engineering problems. JICS operates the National Institute for Computational Sciences (NICS) at the University of Tennessee that enables transformational research through advanced computing resources, facilities, and support, and provides education and training in high-performance computing. The center's mission is to expand the boundaries of human understanding while helping to ensure the continued leadership of the U.S. in science, technology, engineering, and mathematics. Established in 2007, NICS had the distinction of deploying Kraken, the first academic computer to break the petaflop barrier, Kraken in its prime was the National Science Foundation's flagship computing system for research. NICS is a leading academic supercomputing center and a major partner in NSF's eXtreme Science and Engineering Discovery Environment (XSEDE).