Physical Sciences and Mathematics Commons^™

Evaluating Reproducibility In Computational Biology Research, Morgan Oneka

Honors Projects

For my Honors Senior Project, I read five research papers in the field of computational biology and attempted to reproduce the results. However, for the most part, this proved a challenge, as many details vital to utilizing relevant software and data had been excluded. Using Geir Kjetil Sandve's paper "Ten Simple Rules for Reproducible Computational Research" as a guide, I discuss how authors of these five papers did and did not obey these rules of reproducibility and how this affected my ability to reproduce their results.

Graphics Processor Based Implementation Of Bioinformatics Codes, Andrew Bellenir, Christian Trefftz, Greg Wolffe

Student Summer Scholars Manuscripts

We created a powerful computing platform based on video cards with the goal of accelerating the performance of bioinformatics codes. To satisfy the demands of the video gaming industry, modern graphics processing units (GPUs) have become very advanced computational devices, using a large set of stream processors to render multiple pixels in parallel. Recently, computer scientists have taken interest in a GPU's ability to execute a single instruction on multiple data (SIMD computation) for general applications, as opposed to graphics processing only. This is known as general purpose computation on a graphics processing unit, or GPGPU.

Our project was comprised …