Bioinformatics (eBook, PDF)

High Performance Parallel Computer Architectures
Redaktion: Schmidt, Bertil

• Format: PDF

Produktbeschreibung

Written by internationally renowned experts, this book introduces emerging parallel architectures, their corresponding programming paradigms, and their bioinformatics applications. Providing two introductory chapters to supply necessary background on sequential bioinformatics algorithms and parallel architectures-such as multi-cores, Cell B.E., GPUs, FPGAs-it then presents parallelization strategies and performance evaluations for numerous state-of-the-art bioinformatics algorithms and tools. Topics include pairwise sequence alignment, multiple sequence alignment, BLAST, motif finding, and pattern matching. The book also covers sequence assembly, hidden Markov models, molecular dynamics, and evolutionary tree reconstruction.

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Produktdetails

• Verlag: Taylor & Francis eBooks
• Seitenzahl: 370
• Erscheinungstermin: 15. Juli 2010
• Englisch
• ISBN-13: 9781439814895
• Artikelnr.: 57533962

Autorenporträt

Bertil Schmidt is Associate Professor at the School of Computer Engineering at Nanyang Technological University (NTU), Singapore. Prior to that, he was faculty member at the University of New South Wales and Senior Researcher at the University of Melbourne, Australia. At NTU he also held appointments as Program Director M.Sc. in Bioinformatics and Deputy Director of BMERC. Before coming to Singapore, he held research appointments at the Karlsruhe Institute of Technology (KIT) and RWTH Aachen. Bertil has been involved in the design and implementation of parallel algorithms and architectures for over a decade. He has worked extensively with fine-grained (e.g. GPUs, FPGAs, Cell BE), coarse-grained (clusters, grids) as well as hybrid parallel architectures. He has successfully applied these technologies to various domains including bioinformatics, image processing, multimedia video compression, and cryptography. He has published more than 35 journal papers in leading journals such as Journal of VLSI Signal Processing, Microelectronic Engineering, IEEE Transactions on Circuits and Systems II, IEEE Transactions on Parallel and Distributed Systems, IEEE Transactions on IT in Biomedicine, Journal of Parallel and Distributed Computing, Parallel Computing, Concurrency and Computation: Practice and Experience, Future Generation Computer Systems, Bioinformatics, BMC Bioinformatics, Autoimmunity, and Computer Physics Communications.

Inhaltsangabe

Algorithms for Bioinformatics.Introduction to GPGPUs and Massively Threaded
Programming. FPGA: Architecture and Programming. Parallel Algorithms for
Alignments on the Cell BE. Orchestrating the Phylogenetic Likelihood
Function on Emerging Parallel Architectures. Parallel Bioinformatics
Algorithms for CUDA-enabled GPUs. CUDA Error Correction Method for
High-Throughput Short-Read Sequencing Data. FPGA Acceleration of Seeded
Similarity Searching. Seed-Based Parallel Protein Sequence Comparison
Combining Multithreading, GPU, and FPGA Technologies. Database Searching
with Profi le Hidden Markov Models on Reconfi gurable and Many-Core
Architectures. COPACOBANA: A Massively Parallel FPGA-Based Computer
Architecture. Accelerating String Set Matching for Bioinformatics Using
FPGA Hardware. Reconfigurable Neural System and its Application to Dimeric
Protein Binding Site Identification. Parallel FPGA Search Engine for
Protein Identification. Index.