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Architecture Exploration of FPGA Based Accelerators for BioInformatics Applications [electronic resource] / by B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan.

By: Varma, B. Sharat Chandra [author.].
Contributor(s): Paul, Kolin [author.] | Balakrishnan, M [author.] | SpringerLink (Online service).
Material type: materialTypeLabelBookSeries: Springer Series in Advanced Microelectronics: 55Publisher: Singapore : Springer Singapore : Imprint: Springer, 2016Edition: 1st ed. 2016.Description: XV, 122 p. 54 illus., 40 illus. in color. online resource.Content type: text Media type: computer Carrier type: online resourceISBN: 9789811005916.Subject(s): Engineering | Bioinformatics | Electronics | Microelectronics | Electronic circuits | Engineering | Circuits and Systems | Computational Biology/Bioinformatics | Electronics and Microelectronics, InstrumentationAdditional physical formats: Printed edition:: No titleDDC classification: 621.3815 Online resources: Click here to access online
Contents:
Introduction -- Related Work -- Methodology for Implementing Accelerators -- FPGA based Acceleration of Protein Docking -- FPGA based Acceleration of De Novo Genome Assembly -- Design of Accelerators with HEBs -- System Level Design Space Exploration -- Future Directions.
In: Springer eBooksSummary: 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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Introduction -- Related Work -- Methodology for Implementing Accelerators -- FPGA based Acceleration of Protein Docking -- FPGA based Acceleration of De Novo Genome Assembly -- Design of Accelerators with HEBs -- System Level Design Space Exploration -- Future Directions.

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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