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© 2016

Architecture Exploration of FPGA Based Accelerators for BioInformatics Applications

Benefits

  • Offers techniques to carry out design space exploration of FPGA based accelerators

  • Presents a methodology to study benefits of HEBs in FPGAs in the context of application acceleration

  • Shows FPGA based acceleration of two important bioinformatics applications

Book

Part of the Springer Series in Advanced Microelectronics book series (MICROELECTR., volume 55)

Table of contents

  1. Front Matter
    Pages i-xv
  2. B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan
    Pages 1-8
  3. B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan
    Pages 9-28
  4. B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan
    Pages 29-38
  5. B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan
    Pages 39-54
  6. B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan
    Pages 55-79
  7. B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan
    Pages 81-99
  8. B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan
    Pages 101-116
  9. B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan
    Pages 117-120
  10. Back Matter
    Pages 121-122

About this book

Introduction

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.

Keywords

BioInformatics FPGA FPGA Accelerators HEB design Hard embedded blocks Velvet de novo

Authors and affiliations

  1. 1.Elect&Elctro Engg,Chow Yei Ching BldgThe University of Hong KongHong KongHong Kong
  2. 2.Computer Science & EngineeringIndian Institute of Technology DelhiDelhiIndia
  3. 3.Computer Science and EngineeringIndian Institute of Technology DelhiNew DelhiIndia

About the authors

B. Sharat Chandra Varma is Research Associate in the Department of Electrical & Electronic Engineering at The University of Hong Kong, Hong Kong. He obtained his PhD from IIT Delhi, New Delhi. He completed his B.E. (2003) from Visvesvaraya Technological University Karnataka and MSc. (2007) from Manipal University, Karnataka. His research interest areas are re-configurable computing, FPGA, hardware-software co-design, hardware accelerators, and computer architecture. Dr. Varma has over 10 years of research and industrial experience and has several journal publications to his credit.

Kolin Paul is presently Associate Professor with the department of Computer Science and Engineering at Indian Institute of Technology Delhi, New Delhi. His academic degrees include M.Sc. (1995) from Jadavpur University and Ph.D. (2002) from Bengal Engineering College, Calcutta, India. Dr. Paul has several papers published in refereed journal and conference proceedings.

M. Balakrishnan is a Professor in the CSE Department at IIT Delhi, New Delhi, India. He completed his PhD in 1984 from IIT Delhi. He has 16 journal articles, 63 refereed conference publications, one book chapter and two patents to his credit. Dr. Balakrishnan has been a part of many research projects and consultancies from leading EDA/VLSI companies. He is a reviewer for major international journals, a member of key academic bodies. He has supervised 8 PhDs, 3 MS(R) and 78 M.Tech students. His areas of specialization are behavioral and system level synthesis, system level design and modeling, computer architecture, hardware-software co-design, embedded system design, and assistive devices for the visually impaired.

Bibliographic information

  • Book Title Architecture Exploration of FPGA Based Accelerators for BioInformatics Applications
  • Authors B. Sharat Chandra Varma
    Kolin Paul
    M. Balakrishnan
  • Series Title Springer Series in Advanced Microelectronics
  • Series Abbreviated Title Spr. Ser. Microelectronics
  • DOI https://doi.org/10.1007/978-981-10-0591-6
  • Copyright Information Springer Science+Business Media Singapore 2016
  • Publisher Name Springer, Singapore
  • eBook Packages Engineering Engineering (R0)
  • Hardcover ISBN 978-981-10-0589-3
  • Softcover ISBN 978-981-10-9203-9
  • eBook ISBN 978-981-10-0591-6
  • Series ISSN 1437-0387
  • Series E-ISSN 2197-6643
  • Edition Number 1
  • Number of Pages XV, 122
  • Number of Illustrations 14 b/w illustrations, 40 illustrations in colour
  • Topics Circuits and Systems
    Computational Biology/Bioinformatics
    Electronics and Microelectronics, Instrumentation
  • Buy this book on publisher's site
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