Parallel Computing for Bioinformatics and Computational Biology

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.