Architecture exploration of FPGA based accelerators for BioInformatics applications

Sharat Chandra Varma B, Kolin Paul, M Balakrishnan

Research output: Book/ReportBook

Abstract

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.
LanguageEnglish
Volume55
DOIs
Publication statusPublished - 11 Apr 2016

Fingerprint

Bioinformatics
Particle accelerators
Field programmable gate arrays (FPGA)
Genes
Students
Proteins
Hardware
Engineers

Keywords

  • FPGA
  • reconfigurable computing
  • Hardware Acceleration
  • bioinformatics
  • Drug Design
  • Next Generation Sequencing (NGS)
  • Genome Assembly

Cite this

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title = "Architecture exploration of FPGA based accelerators for BioInformatics applications",
abstract = "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.",
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Architecture exploration of FPGA based accelerators for BioInformatics applications. / B, Sharat Chandra Varma; Paul, Kolin; Balakrishnan, M.

2016.

Research output: Book/ReportBook

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AB - 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.

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