Parallel Computing for Bioinformatics and Computational Biology (eBook, PDF)

Models, Enabling Technologies, and Case Studies
Redaktion: Zomaya, Albert Y.

• Format: PDF

Produktbeschreibung

Discover how to streamline complex bioinformatics applications with parallel computing This publication enables readers to handle more complex bioinformatics applications and larger and richer data sets. As the editor clearly shows, using powerful parallel computing tools can lead to significant breakthroughs in deciphering genomes, understanding genetic disease, designing customized drug therapies, and understanding evolution. A broad range of bioinformatics applications is covered with demonstrations on how each one can be parallelized to improve performance and gain faster rates of computation. Current parallel computing techniques and technologies are examined, including distributed computing and grid computing. Readers are provided with a mixture of algorithms, experiments, and simulations that provide not only qualitative but also quantitative insights into the dynamic field of bioinformatics. Parallel Computing for Bioinformatics and Computational Biology is a contributed work that serves as a repository of case studies, collectively demonstrating how parallel computing streamlines difficult problems in bioinformatics and produces better results. Each of the chapters is authored by an established expert in the field and carefully edited to ensure a consistent approach and high standard throughout the publication. The work is organized into five parts: * Algorithms and models * Sequence analysis and microarrays * Phylogenetics * Protein folding * Platforms and enabling technologies Researchers, educators, and students in the field of bioinformatics will discover how high-performance computing can enable them to handle more complex data sets, gain deeper insights, and make new discoveries.

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Produktdetails

• Verlag: John Wiley & Sons
• Seitenzahl: 816
• Erscheinungstermin: 28. Juli 2006
• Englisch
• ISBN-13: 9780471756491
• Artikelnr.: 37353919

Autorenporträt

ALBERT Y. ZOMAYA is the CISCO Systems Chair Professor of Internetworking, School of Information Technologies, The University of Sydney, and Deputy Director for Information Technology of the Sydney University Biological Informatics and Technology Centre. Professor Zomaya has been the Chair of the IEEE Technical Committee on Parallel Processing and has been awarded the IEEE Computer Society's Meritorious Service Award. He is an IEEE fellow.

Inhaltsangabe

Preface. Contributors. Acknowledgments. PART I: ALGORITHMS AND MODELS. 1
Parallel and Evolutionary Approaches to Computational Biology (Nouhad J.
Rizk). References. 2 Parallel Monte Carlo Simulation of HIV Molecular
Evolution in Response to Immune Surveillance (Jack da Silva). References. 3
Differential Evolutionary Algorithms for In Vivo Dynamic Analysis of
Glycolysis and Pentose Phosphate Pathway in Escherichia coli (Christophe
Chassagnole). References. 4 Compute-Intensive Simulations for Cellular
Models (K. Burrage). References. 5 Parallel Computation in Simulating
Diffusion and Deformation in Human Brain (Ning KangI0. References. PART II:
SEQUENCE ANALYSIS AND MICROARRAYS. 6 Computational Molecular Biology
(Azzedine Boukerche). References. 7 Special-Purpose Computing for
Biological Sequence Analysis (Bertil Schmidt). References. 8 Multiple
Sequence Alignment in Parallel on a Cluster ofWorkstations (Amitava Datta).
References. 9 Searching Sequence Databases Using High-Performance BLASTs
(Xue Wu). References. 10 Parallel Implementations of Local Sequence
Alignment: Hardware and Software (Vipin Chaudhary). References. 11 Parallel
Computing in the Analysis of Gene Expression Relationships (Robert L.
Martino). References. 12 Assembling DNA Fragments with a Distributed
Genetic Algorithm (Gabriel Luque). References. 13 A Cooperative Genetic
Algorithm for Knowledge Discovery in Microarray Experiments (Mohammed
Khabzaoui). References. PART III: PHYLOGENETICS. 14 Parallel and
Distributed Computation of Large Phylogenetic Trees (Alexandros
Stamatakis). References. 15 Phylogenetic Parameter Estimation on COWs
(Ekkehard Petzold). References. 16 High-Performance Phylogeny
Reconstruction Under Maximum Parsimony (Tiffani L. Williams). References.
PART IV: PROTEIN FOLDING. 17 Protein Folding with the Parallel Replica
Exchange Molecular Dynamics Method (Ruhong Zhou). References. 18
High-Performance Alignment Methods for Protein Threading (R. Andonov).
References. 19 Parallel Evolutionary Computations in Discerning Protein
Structures (Richard O. Day). References. PART V: PLATFORMS AND ENABLING
TECHNOLOGIES. 20 A Brief Overview of Grid Activities for Bioinformatics and
Health Applications (Ali Al Mazari). References. 21 Parallel Algorithms for
Bioinformatics (Shahid H. Bokhari). References. 22 Cluster and Grid
Infrastructure for Computational Chemistry and Biochemistry (Kim K.
Baldridge). References. 23 DistributedWorkflows in Bioinformatics (Arun
Krishnan). References. 24 Molecular Structure Determination on a
Computational and Data Grid (Russ Miller). References. 25 GIPSY: A
Problem-Solving Environment for Bioinformatics Applications (Rajendra R.
Joshi). References. 26 TaskSpaces: A Software Framework for Parallel
Bioinformatics on Computational Grids (Hans De Sterck). References. 27 The
Organic Grid: Self-Organizing Computational Biology on Desktop Grids (Arjav
J. Chakravarti). References. 28 FPGA Computing in Modern Bioinformatics (H.
Simmler). References. 29 Virtual Microscopy: Distributed Image Storage,
Retrieval, Analysis, and Visualization (T. Pan). References. Index.

Rezensionen

"...this book presents researchers in computational biology, bioinformatics, mathematics, statistics, and computer science with the opportunity to explore this interdisciplinary research area..." - Computing Reviews.com, September 27, 2006

"...clearly written and understandable...researchers and students in the related areas will find the style and format familiar and the content valuable." (E-STREAMS, September 2007)

"...a building block on computational biology concepts to help researchers and students work on more innovative ideas." (IEEE Distributed Systems Online, March 2007)

"...a good overview of the current state of computing in these areas." (CHOICE, November 2006)

"...this book presents researchers in computational biology, bioinformatics, mathematics, statistics, and computer science with the opportunity to explore this interdisciplinary research area..." (Computing Reviews.com, September 27, 2006)