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Architecture Exploration Of Fpga Based Accelerators For Bioinformatics Applications
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Book Synopsis Architecture Exploration of FPGA Based Accelerators for BioInformatics Applications by : B. Sharat Chandra Varma
Download or read book Architecture Exploration of FPGA Based Accelerators for BioInformatics Applications written by B. Sharat Chandra Varma and published by Springer. This book was released on 2016-03-02 with total page 133 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Bioinformatics: FPGA-based accelerators for bioinformatics applications by :
Download or read book Bioinformatics: FPGA-based accelerators for bioinformatics applications written by and published by . This book was released on 2013 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis FPGA Based Accelerators for Financial Applications by : Christian De Schryver
Download or read book FPGA Based Accelerators for Financial Applications written by Christian De Schryver and published by Springer. This book was released on 2015-07-30 with total page 288 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers the latest approaches and results from reconfigurable computing architectures employed in the finance domain. So-called field-programmable gate arrays (FPGAs) have already shown to outperform standard CPU- and GPU-based computing architectures by far, saving up to 99% of energy depending on the compute tasks. Renowned authors from financial mathematics, computer architecture and finance business introduce the readers into today’s challenges in finance IT, illustrate the most advanced approaches and use cases and present currently known methodologies for integrating FPGAs in finance systems together with latest results. The complete algorithm-to-hardware flow is covered holistically, so this book serves as a hands-on guide for IT managers, researchers and quants/programmers who think about integrating FPGAs into their current IT systems.
Book Synopsis Tree-based Heterogeneous FPGA Architectures by : Umer Farooq
Download or read book Tree-based Heterogeneous FPGA Architectures written by Umer Farooq and published by Springer Science & Business Media. This book was released on 2012-05-17 with total page 198 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a new FPGA architecture known as tree-based FPGA architecture, due to its hierarchical nature. This type of architecture has been relatively unexplored despite their better performance and predictable routing behavior, as compared to mesh-based FPGA architectures. In this book, we explore and optimize the tree-based architecture and we evaluate it by comparing it to equivalent mesh-based FPGA architectures.
Book Synopsis FPGA-BASED Hardware Accelerators by : Iouliia Skliarova
Download or read book FPGA-BASED Hardware Accelerators written by Iouliia Skliarova and published by Springer. This book was released on 2019-05-30 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book suggests and describes a number of fast parallel circuits for data/vector processing using FPGA-based hardware accelerators. Three primary areas are covered: searching, sorting, and counting in combinational and iterative networks. These include the application of traditional structures that rely on comparators/swappers as well as alternative networks with a variety of core elements such as adders, logical gates, and look-up tables. The iterative technique discussed in the book enables the sequential reuse of relatively large combinational blocks that execute many parallel operations with small propagation delays. For each type of network discussed, the main focus is on the step-by-step development of the architectures proposed from initial concepts to synthesizable hardware description language specifications. Each type of network is taken through several stages, including modeling the desired functionality in software, the retrieval and automatic conversion of key functions, leading to specifications for optimized hardware modules. The resulting specifications are then synthesized, implemented, and tested in FPGAs using commercial design environments and prototyping boards. The methods proposed can be used in a range of data processing applications, including traditional sorting, the extraction of maximum and minimum subsets from large data sets, communication-time data processing, finding frequently occurring items in a set, and Hamming weight/distance counters/comparators. The book is intended to be a valuable support material for university and industrial engineering courses that involve FPGA-based circuit and system design.
Book Synopsis ITNG 2021 18th International Conference on Information Technology-New Generations by : Shahram Latifi
Download or read book ITNG 2021 18th International Conference on Information Technology-New Generations written by Shahram Latifi and published by Springer Nature. This book was released on 2021-06-04 with total page 515 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume represents the 18th International Conference on Information Technology - New Generations (ITNG), 2021. ITNG is an annual event focusing on state of the art technologies pertaining to digital information and communications. The applications of advanced information technology to such domains as astronomy, biology, education, geosciences, security, and health care are the among topics of relevance to ITNG. Visionary ideas, theoretical and experimental results, as well as prototypes, designs, and tools that help the information readily flow to the user are of special interest. Machine Learning, Robotics, High Performance Computing, and Innovative Methods of Computing are examples of related topics. The conference features keynote speakers, a best student award, poster award, service award, a technical open panel, and workshops/exhibits from industry, government and academia. This publication is unique as it captures modern trends in IT with a balance of theoretical and experimental work. Most other work focus either on theoretical or experimental, but not both. Accordingly, we do not know of any competitive literature.
Book Synopsis Robotic Computing on FPGAs by : Shaoshan Liu
Download or read book Robotic Computing on FPGAs written by Shaoshan Liu and published by Springer Nature. This book was released on 2022-05-31 with total page 202 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a thorough overview of the state-of-the-art field-programmable gate array (FPGA)-based robotic computing accelerator designs and summarizes their adopted optimized techniques. This book consists of ten chapters, delving into the details of how FPGAs have been utilized in robotic perception, localization, planning, and multi-robot collaboration tasks. In addition to individual robotic tasks, this book provides detailed descriptions of how FPGAs have been used in robotic products, including commercial autonomous vehicles and space exploration robots.
Book Synopsis Artificial Intelligence Applications and Reconfigurable Architectures by : Anuradha D. Thakare
Download or read book Artificial Intelligence Applications and Reconfigurable Architectures written by Anuradha D. Thakare and published by John Wiley & Sons. This book was released on 2023-03-21 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: ARTIFICIAL INTELLIGENCE APPLICATIONS and RECONFIGURABLE ARCHITECTURES The primary goal of this book is to present the design, implementation, and performance issues of AI applications and the suitability of the FPGA platform. This book covers the features of modern Field Programmable Gate Arrays (FPGA) devices, design techniques, and successful implementations pertaining to AI applications. It describes various hardware options available for AI applications, key advantages of FPGAs, and contemporary FPGA ICs with software support. The focus is on exploiting parallelism offered by FPGA to meet heavy computation requirements of AI as complete hardware implementation or customized hardware accelerators. This is a comprehensive textbook on the subject covering a broad array of topics like technological platforms for the implementation of AI, capabilities of FPGA, suppliers’ software tools and hardware boards, and discussion of implementations done by researchers to encourage the AI community to use and experiment with FPGA. Readers will benefit from reading this book because It serves all levels of students and researcher’s as it deals with the basics and minute details of Ecosystem Development Requirements for Intelligent applications with reconfigurable architectures whereas current competitors’ books are more suitable for understanding only reconfigurable architectures. It focuses on all aspects of machine learning accelerators for the design and development of intelligent applications and not on a single perspective such as only on reconfigurable architectures for IoT applications. It is the best solution for researchers to understand how to design and develop various AI, deep learning, and machine learning applications on the FPGA platform. It is the best solution for all types of learners to get complete knowledge of why reconfigurable architectures are important for implementing AI-ML applications with heavy computations. Audience Researchers, industrial experts, scientists, and postgraduate students who are working in the fields of computer engineering, electronics, and electrical engineering, especially those specializing in VLSI and embedded systems, FPGA, artificial intelligence, Internet of Things, and related multidisciplinary projects.
Book Synopsis Reconfigurable and Adaptive Computing by : Nadia Nedjah
Download or read book Reconfigurable and Adaptive Computing written by Nadia Nedjah and published by CRC Press. This book was released on 2018-10-09 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt: Reconfigurable computing techniques and adaptive systems are some of the most promising architectures for microprocessors. Reconfigurable and Adaptive Computing: Theory and Applications explores the latest research activities on hardware architecture for reconfigurable and adaptive computing systems. The first section of the book covers reconfigurable systems. The book presents a software and hardware codesign flow for coarse-grained systems-on-chip, a video watermarking algorithm for the H.264 standard, a solution for regular expressions matching systems, and a novel field programmable gate array (FPGA)-based acceleration solution with MapReduce framework on multiple hardware accelerators. The second section discusses network-on-chip, including an implementation of a multiprocessor system-on-chip platform with shared memory access, end-to-end quality-of-service metrics modeling based on a multi-application environment in network-on-chip, and a 3D ant colony routing (3D-ACR) for network-on-chip with three different 3D topologies. The final section addresses the methodology of system codesign. The book introduces a new software–hardware codesign flow for embedded systems that models both processors and intellectual property cores as services. It also proposes an efficient algorithm for dependent task software–hardware codesign with the greedy partitioning and insert scheduling method (GPISM) by task graph.
Book Synopsis Applied Reconfigurable Computing. Architectures, Tools, and Applications by : Fernando Rincón
Download or read book Applied Reconfigurable Computing. Architectures, Tools, and Applications written by Fernando Rincón and published by Springer Nature. This book was released on 2020-03-25 with total page 408 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the proceedings of the 16th International Symposium on Applied Reconfigurable Computing, ARC 2020, held in Toledo, Spain, in April 2020. The 18 full papers and 11 poster presentations presented in this volume were carefully reviewed and selected from 40 submissions. The papers are organized in the following topical sections: design methods & tools; design space exploration & estimation techniques; high-level synthesis; architectures; applications.
Book Synopsis Reconfigurable Computing: Architectures, Tools, and Applications by : Roger Woods
Download or read book Reconfigurable Computing: Architectures, Tools, and Applications written by Roger Woods and published by Springer. This book was released on 2008-08-29 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: Coverage in this proceedings volume includes DNA and string processing applications, reconfigurable computing hardware and systems, image processing, run-time behavior, instruction set extension, as well as random number generation and financial computation.
Book Synopsis Research Infrastructures for Hardware Accelerators by : Yakun Sophia Shao
Download or read book Research Infrastructures for Hardware Accelerators written by Yakun Sophia Shao and published by Springer Nature. This book was released on 2022-05-31 with total page 85 pages. Available in PDF, EPUB and Kindle. Book excerpt: Hardware acceleration in the form of customized datapath and control circuitry tuned to specific applications has gained popularity for its promise to utilize transistors more efficiently. Historically, the computer architecture community has focused on general-purpose processors, and extensive research infrastructure has been developed to support research efforts in this domain. Envisioning future computing systems with a diverse set of general-purpose cores and accelerators, computer architects must add accelerator-related research infrastructures to their toolboxes to explore future heterogeneous systems. This book serves as a primer for the field, as an overview of the vast literature on accelerator architectures and their design flows, and as a resource guidebook for researchers working in related areas.
Book Synopsis Bioinformatics Research and Development by : Mourad Elloumi
Download or read book Bioinformatics Research and Development written by Mourad Elloumi and published by Springer Science & Business Media. This book was released on 2008-08-31 with total page 613 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains the papers which were selected for presentation at the second Bio- formatics Research and Development (BIRD) conference held in Vienna, Austria during July 7–9, 2008. BIRD covers a wide range of topics related to bioinformatics. This year sequence analysis and alignment, pathways, networks, systems biology, protein and RNA structure and function, gene expression/regulation and microarrays, databases and data integration, machine learning and data analysis were the subjects of main interest. The decisions of the Program Committee are based on the recommendations of at least three, up to five, reviews for each paper. As a result, 30 of the 61 submitted c- tributions could be accepted for the conference. We were happy to have three invited talks presented by experienced researchers providing visitors with a good overview but also some very important insights into the fascinating domain of bioinformatics. Abstracts and more information on these talks are provided in the conference program as well as at the conference site. In the second part of this volume the selected contributions of the two workshops which were held in parallel to the main conference are presented: Workshop on - namical Aspects of Perturbation, Intervention and Transition in Biological Systems – PETRIN 2008 and Workshop on Algorithms in Molecular Biology – ALBIO 2008 Poster presentations of the BIRD conference are in the companion proceedings published by the Trauner Verlag, Linz.
Book Synopsis Exploration of FPGA Based Accelerators in Linux Host Systems by : Daniel May
Download or read book Exploration of FPGA Based Accelerators in Linux Host Systems written by Daniel May and published by . This book was released on 2021 with total page 70 pages. Available in PDF, EPUB and Kindle. Book excerpt: PCIe devices are pervasive in today's computer systems. In addition, FPGAs are increasingly finding use in data centers as accelerators for specialized computation tasks. This paper endeavors to provide a guide for future researchers to use as a springboard for future work in this area by providing working examples and documentation for various FPGA designs and host system drivers.
Book Synopsis FPGA Accelerated Bioinformatics by : Nathaniel McVicar
Download or read book FPGA Accelerated Bioinformatics written by Nathaniel McVicar and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in next-generation sequencing technology have led to increases in genomic data production by sequencing machines that outpace Moore’s law. This trend has reached the point where the time and money spent processing human and other genome sequence data could be greater than that spent producing it. Field-Programmable Gate Arrays (FPGAs) can provide a solution to this problem. Bioinformatics accelerators running on FPGAs achieve order of magnitude speedups across a variety of genomics applications important in both biological research and clinical medicine. This dissertation presents three accelerators. The first addresses the short read alignment problem, where millions of short DNA or RNA reads, with lengths on the order of 100 base pairs, are aligned to an index built from a reference genome. Our aligner combines an FPGA accelerator with the greater memory bandwidth of our host system to produce a fast and flexible short read aligner. Using this aligner, we developed a classifier to determine which of two possible species each read originated from. In a case study with RNA-Seq reads from mouse and human retinal cultures our aligner produced more accurate classification results and better performance than software-based aligners. Our second accelerator tackles the problem of non-coding RNA (ncRNA) homology search. The biologically important functions these ncRNAs perform are determined by their two- or three-dimensional structure, and ncRNAs with different sequences can perform the same functions if they share a similar structure. Homology search scores sequences using models of ncRNA families in an effort to find previously unknown members. Our accelerator greatly improves the speed of filters that identify candidate sequences using the Viterbi and CYK algorithms. The final accelerator uses the Hybrid Memory Cube (HMC), a stacked DRAM, for K-mer counting. In many areas of bioinformatics, including de novo assembly, K-mer counting is a filter with important roles including removing read errors. Our approach stores K-mer counts in a Bloom filter on the HMC leveraging the greater random access rate for increased performance over both the host and FPGA-attached DRAM. Throughout this dissertation we demonstrate that FPGA accelerators can achieve excellent speedups across a variety of genomics applications.
Book Synopsis FPGA-based Implementation of Signal Processing Systems by : Roger Woods
Download or read book FPGA-based Implementation of Signal Processing Systems written by Roger Woods and published by John Wiley & Sons. This book was released on 2017-05-01 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: An important working resource for engineers and researchers involved in the design, development, and implementation of signal processing systems The last decade has seen a rapid expansion of the use of field programmable gate arrays (FPGAs) for a wide range of applications beyond traditional digital signal processing (DSP) systems. Written by a team of experts working at the leading edge of FPGA research and development, this second edition of FPGA-based Implementation of Signal Processing Systems has been extensively updated and revised to reflect the latest iterations of FPGA theory, applications, and technology. Written from a system-level perspective, it features expert discussions of contemporary methods and tools used in the design, optimization and implementation of DSP systems using programmable FPGA hardware. And it provides a wealth of practical insights—along with illustrative case studies and timely real-world examples—of critical concern to engineers working in the design and development of DSP systems for radio, telecommunications, audio-visual, and security applications, as well as bioinformatics, Big Data applications, and more. Inside you will find up-to-date coverage of: FPGA solutions for Big Data Applications, especially as they apply to huge data sets The use of ARM processors in FPGAs and the transfer of FPGAs towards heterogeneous computing platforms The evolution of High Level Synthesis tools—including new sections on Xilinx's HLS Vivado tool flow and Altera's OpenCL approach Developments in Graphical Processing Units (GPUs), which are rapidly replacing more traditional DSP systems FPGA-based Implementation of Signal Processing Systems, 2nd Edition is an indispensable guide for engineers and researchers involved in the design and development of both traditional and cutting-edge data and signal processing systems. Senior-level electrical and computer engineering graduates studying signal processing or digital signal processing also will find this volume of great interest.
Book Synopsis High-Performance Computing Using FPGAs by : Wim Vanderbauwhede
Download or read book High-Performance Computing Using FPGAs written by Wim Vanderbauwhede and published by Springer Science & Business Media. This book was released on 2013-08-23 with total page 798 pages. Available in PDF, EPUB and Kindle. Book excerpt: High-Performance Computing using FPGA covers the area of high performance reconfigurable computing (HPRC). This book provides an overview of architectures, tools and applications for High-Performance Reconfigurable Computing (HPRC). FPGAs offer very high I/O bandwidth and fine-grained, custom and flexible parallelism and with the ever-increasing computational needs coupled with the frequency/power wall, the increasing maturity and capabilities of FPGAs, and the advent of multicore processors which has caused the acceptance of parallel computational models. The Part on architectures will introduce different FPGA-based HPC platforms: attached co-processor HPRC architectures such as the CHREC’s Novo-G and EPCC’s Maxwell systems; tightly coupled HRPC architectures, e.g. the Convey hybrid-core computer; reconfigurably networked HPRC architectures, e.g. the QPACE system, and standalone HPRC architectures such as EPFL’s CONFETTI system. The Part on Tools will focus on high-level programming approaches for HPRC, with chapters on C-to-Gate tools (such as Impulse-C, AutoESL, Handel-C, MORA-C++); Graphical tools (MATLAB-Simulink, NI LabVIEW); Domain-specific languages, languages for heterogeneous computing(for example OpenCL, Microsoft’s Kiwi and Alchemy projects). The part on Applications will present case from several application domains where HPRC has been used successfully, such as Bioinformatics and Computational Biology; Financial Computing; Stencil computations; Information retrieval; Lattice QCD; Astrophysics simulations; Weather and climate modeling.
