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Author: B. Sharat Chandra Varma Publisher: Springer ISBN: 9811005915 Category : Technology & Engineering Languages : en Pages : 133
Book Description
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.
Author: B. Sharat Chandra Varma Publisher: Springer ISBN: 9811005915 Category : Technology & Engineering Languages : en Pages : 133
Book Description
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.
Author: Nathaniel McVicar Publisher: ISBN: Category : Languages : en Pages :
Book Description
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.
Author: Information Resources Management Association Publisher: IGI Global ISBN: 146663605X Category : Computers Languages : en Pages : 1826
Book Description
"Bioinformatics: Concepts, Methodologies, Tools, and Applications highlights the area of bioinformatics and its impact over the medical community with its innovations that change how we recognize and care for illnesses"--Provided by publisher.
Author: Khalgui, Mohamed Publisher: IGI Global ISBN: 1609600886 Category : Computers Languages : en Pages : 652
Book Description
"This book addresses the development of reconfigurable embedded control systems and describes various problems in this important research area, which include static and dynamic (manual or automatic) reconfigurations, multi-agent architectures, modeling and verification, component-based approaches, architecture description languages, distributed reconfigurable architectures, real-time and low power scheduling, execution models, and the implementation of such systems"--
Author: Naim Majeed Harb Publisher: ISBN: Category : Languages : en Pages : 140
Book Description
Hardware accelerators have been used to accelerate various bioinformatics applic ations without altering their accuracy. These accelerators were also seen to acc elerate sophisticated algorithms where powerful computational techniques are use d to accumulate, analyze, simulate and estimate biological data. These accelerat ors are hardware accelerators mostly made up of Field Programmable Gate Array (F PGA) hybrid systems or multiple FPGA systems. One bioinformatics application in need for acceleration is the haplotype inferen ce application. This application is essential in producing maps used to identify complex diseases. It is also used in finding phylogenetic trees that provide re lationships among different populations. The main objective of this thesis is to build an FPGA-hybrid system connected to a host PC that will accelerate PHASE (one important haplotype inference applica tion) and enhance its processing time while maintaining the same accuracy and fu nctionality.
Author: Publisher: Elsevier ISBN: 0128114320 Category : Medical Languages : en Pages : 3421
Book Description
Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases
Author: Mourad Elloumi Publisher: Springer Science & Business Media ISBN: 3540706003 Category : Science Languages : en Pages : 613
Book Description
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.
Author: Anuradha D. Thakare Publisher: John Wiley & Sons ISBN: 1119857295 Category : Computers Languages : en Pages : 245
Book Description
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.
Author: Bertil Schmidt Publisher: CRC Press ISBN: 1439814899 Category : Computers Languages : en Pages : 370
Book Description
New sequencing technologies have broken many experimental barriers to genome scale sequencing, leading to the extraction of huge quantities of sequence data. This expansion of biological databases established the need for new ways to harness and apply the astounding amount of available genomic information and convert it into substantive biological
Author: B. Sharat Chandra Varma
Author: B. Sharat Chandra Varma
Author: 
Author: Nathaniel McVicar
Author: Information Resources Management Association
Author: Khalgui, Mohamed
Author: Naim Majeed Harb
Author: 
Author: Mourad Elloumi
Author: Anuradha D. Thakare
Author: Bertil Schmidt