Architecture Exploration of FPGA Based Accelerators for BioInformatics Applications

✍ Scribed by B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan (auth.)

Publisher: Springer Singapore
Year: 2016
Tongue: English
Leaves: 133
Series: Springer Series in Advanced Microelectronics 55
Edition: 1
Category: Library

No coin nor oath required. For personal study only.

✦ Synopsis

This book presents an evaluation methodology to design future FPGA fabrics incorporating hard embedded blocks (HEBs) to accelerate applications. This methodology will be useful for selection of blocks to be embedded into the fabric and for evaluating the performance gain that can be achieved by such an embedding. The authors illustrate the use of their methodology by studying the impact of HEBs on two important bioinformatics applications: protein docking and genome assembly. The book also explains how the respective HEBs are designed and how hardware implementation of the application is done using these HEBs. It shows that significant speedups can be achieved over pure software implementations by using such FPGA-based accelerators. The methodology presented in this book may also be used for designing HEBs for accelerating software implementations in other domains besides bioinformatics. This book will prove useful to students, researchers, and practicing engineers alike.

✦ Table of Contents

Front Matter....Pages i-xv
Introduction....Pages 1-8
Related Work....Pages 9-28
Methodology for Implementing Accelerators....Pages 29-38
FPGA-Based Acceleration of Protein Docking....Pages 39-54
FPGA-Based Acceleration of De Novo Genome Assembly....Pages 55-79
Design of Accelerators with Hard Embedded Blocks....Pages 81-99
System-Level Design Space Exploration....Pages 101-116
Future Directions....Pages 117-120
Back Matter....Pages 121-122

✦ Subjects

Circuits and Systems; Computational Biology/Bioinformatics; Electronics and Microelectronics, Instrumentation

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