Parallel programming in the classroom : analysis of genome data

Mike Morris Assistant Professor Department of Chemistry, Computer and Physical Sciences Southeastern Oklahoma State University Mike Morris' degrees are in math, but he has always said he wound up on the business end of a computer. He taught Computer Science (CS) in the early 80s after working as an Operations Research Analyst for Conoco in Ponca City OK. Mike left teaching and spent 15 years doing various things in the CS industry before returning to Southeastern Oklahoma State to once again teach CS, where he remains today. ____________________________________________________________________________________________ Karl Frinkle Professor Department of Mathematics Southeastern Oklahoma State University Karl Frinkle is an applied mathematician who earned his PhD from the University of New Mexico. He is deeply interested in numerical simulations, and most recently in parallel programming. Karl joined the SE Mathematics department in 2005, and thoroughly enjoys teaching parallel programming courses with Mike Morris through the CS department. ____________________________________________________________________________________________Presented at the Oklahoma Supercomputing Symposium 2015, September 23, 2015.Over the course of a semester, students enrolled in an HPC seminar class created a suite of human genome analysis tools on the Beowulf clusters that they and other students built. The analysis tools were written with C and MPI and subsequently interfaced with a LAMP (Linux, Apache, MySQL, and PHP) website through the use of scripts. The output was visualized with the help of Google Charts. We will discuss the technical details of this project and demonstrate how these tools can be used to analyze multiple human genomes simultaneously. Presented at: 2015 Oklahoma Supercomputing Symposium Wednesday September 23 2015, 8:00am-5:00pm Thurman J. White Forum Building, 1704 Asp Ave., Norman OK 73072N