On Hardware-Accelerated Maximally-Efficient Systolic Arrays: Acceleration and Optimization of Genomics Pipelines Through Hardware/Software Co-Design

Developments in sequencing technology have drastically reduced the cost of DNA sequencing. The raw sequencing data being generated requires processing through computationally demanding suites of bioinformatics algorithms called genomics pipelines. The greatly decreased cost of sequencing has resulted in its widespread adoption, and the amount of...

Design and Experimental Evaluation of Distributed Heterogeneous Graph-Processing Systems

Graph processing is increasingly used in a variety of domains, from engineering to logistics and from scientific computing to online gaming. To process graphs efficiently, GPU-enabled graph-processing systems such as TOTEM and Medusa exploit the GPU or the combined CPU+GPU capabilities of a single machine. Unlike scalable distributed CPU-based...

Distributed heterogeneous systems for large-scale graph processing

Graph processing is increasingly popular in a variety of scientific and engineering domains. Consequently, graphs and graph-processing algorithms have become increasingly more diverse. Following the big data trend in every computer-related domain, graphs have also become increasingly larger. Processing graphs is requiring more sophisticated...

Acceleration of read alignment with coherent attached FPGA coprocessors

With the advent of Next Generation Sequencing (NGS), the cost of sequencing human DNA has decreased significantly over the past decade. This decrease in cost has attracted a great deal of attention from medical research and is now transitioning to clinical practice. Precision medicine, tailored to a persons's genetic profile, is becoming a...

Molecular Simulations of Zeolites: Heterogeneous Systems at Equilibrium and Non-Equilibrium