Digital Commons Network^™

Raidx: Raid Extended For Heterogeneous Arrays, Andras Fekete

Doctoral Dissertations

The computer hard drive market has diversified with the establishment of solid state disks (SSDs) as an alternative to magnetic hard disks (HDDs). Each hard drive technology has its advantages: the SSDs are faster than HDDs but the HDDs are cheaper. Our goal is to construct a parallel storage system with HDDs and SSDs such that the parallel system is as fast as the SSDs. Achieving this goal is challenging since the slow HDDs store more data and become bottlenecks, while the SSDs remain idle. RAIDX is a parallel storage system designed for disks of different speeds, capacities and technologies. …

The Identification Of Major Factors In The Deployment Of A Science Dmz At Small Institutions, Scott A. Valcourt

Doctoral Dissertations

The Science DMZ is a network research tool offering superior large science data transmission between two locations. Through a network design that places the Science DMZ at the edge of the campus network, the Science DMZ defines a network path that avoids packet inspecting devices (firewalls, packet shapers) and produces near line-rate transmission results for large data sets between institutions. Small institutions of higher education (public and private small colleges) seeking to participate in data exchange with other institutions are inhibited in the construction of Science DMZs due to the high costs of deployment. While the National Science Foundation made …

The Paladin Suite: Multifaceted Characterization Of Whole Metagenome Shotgun Sequences, Anthony Stephen Westbrook

Master's Theses and Capstones

Whole metagenome shotgun sequencing is a powerful approach for assaying many aspects of microbial communities, including the functional and symbiotic potential of each contributing community member. The research community currently lacks tools that efficiently align DNA reads against protein references, the technique necessary for constructing functional profiles. This thesis details the creation of PALADIN – a novel modification of the Burrows-Wheeler Aligner that provides orders-of-magnitude improved efficiency by directly mapping in protein space. In addition to performance considerations, utilizing PALADIN and associated tools as the foundation of metagenomic pipelines also allows for novel characterization and downstream analysis.

The accuracy and …