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PARALLEL COMPUTING FOR BIOINFORMATICS Models, Case Studies and Enabling Technologies Albert Y. Zomaya The University of Sydney, Australia Table of Contents Chp. Title Authors Contact Author 0 Preface A.Y. Zomaya zomaya@it.usyd.edu.au ALGORITHMS & MODELS 1. Parallel and Evolutionary Approaches to Computational Biology Nouhad Rizk Nouhad Rizk Computer Science Department Notre dame University p.o.box 72zouk mihael Zouk Mosbeh - Lebanon nrizk@ndu.edu.lb 2. Parallel Monte Carlo Simulation of HIV Molecular Evolution in Response to Immune Surveillance Jack da Silva Jack da Silva Discipline of Genetics School of Molecular & Biomedical Science Gate 8, Victoria Drive The University of Adelaide Adelaide, SA 5005 AUSTRALIA jack.dasilva@adelaide.edu.au 3. Differential Evolutionary Algorithms for in vivo dynamic analysis of glycolysis and pentose phosphate pathway in Escherichia coli Andrei Doncescu Andrei Doncescu Groupe DISCO Laboratory of Analysis and Architecture of Systems LAAS CNRS 8001 Avenue du Colonel Roche 31007 Toulouse France adoncesc@laas.fr 4. Compute Intensive Simulations for Cellular Models Kevin Burrage Prof Kevin Burrage Director Advanced Computational Modelling Centre c/o Department of Mathematics Priestley Building (Bldg 69) University of Queensland Queensland 4072 Australia kb@maths.uq.edu.au 5. Parallel Computation in Simulating Diffusion and Deformation in Human Brain Jun Zhang Jun Zhang Department of Computer Science, University of Kentucky Lexington, Kentucky, USA jzhang@cs.uky.edu SEQUENCE ANALYSIS AND MICROARRAYS 6. Computational Molecular Biology Azzedine Boukerche A. Boukerche 800 King Edward Avn SITE, University of Ottawa Ottawa, ONT K1N-6N5 Canada tel: 613-301-9476 boukerch@site.uottawa.ca 7. Special-Purpose Computing for Biological Sequence Analysis Heiko Schroder Bertil Schmidt Bertil Schmidt School of Computer Engineering Nanyang Technological University N4-02a-32 Nanyang Avenue Singapore 639798 Singapore ASBSchmidt@ntu.edu.sg heiko@cs.rmit.edu.au 8. Multiple Sequence Alignment in Parallel on a Cluster of Workstations Amitava datta Amitava Datta School of Computer Science & Software Engineering, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia datta@csse.uwa.edu.au 9. Searching Sequence Databases using High Performance BLASTs Chau-Wen Tseng Chau-Wen Tseng Department of Computer Science University of Maryland at College Park tseng@cs.umd.edu 10. Parallel Implementations of Local Sequence Alignment: Hardware and Software Vipin Chaudhary Vipin Chaudhary 2630 Creek Bend Drive Troy, MI 48098, USA vipin@wayne.edu 11. Parallel Computing in the Analysis of Gene Expression Relationships Martino, Robert Dr. Robert Martino 7996 Aladdin Drive Laurel, Maryland 20723 Robert.Martino@nih.gov 12. Parallel Algorithms for Solving the Fragment Assembly Problem in DNA Strands Enrique Alba Enrique Alba E.T.S.I. Inform?tica (3.2.12) Campus de Teatinos 29071, M?laga SPAIN eat@lcc.uma.es 13. A Cooperative Genetic Algorithm for Knowledge Discovery in MicroArray Experiments El-Ghazali Talbi E-G. Talbi LIFL - University of Lille Bat.M3 Cité scientifique 59655 Villeneuve d'Ascq France talbi@lifl.fr PHYLOGENETICS 14. Parallel and Distributed Computation of Large Phylogenetic Trees Alexandros P. Stamatakis Dr. Alexandros Stamatakis Institute of Computer Science Foundation for Research and Technology-Hellas Institute of Computer Science Foundation for Research and Technology-Hellas P.O. Box 1385, Heraklion, Crete, GR-711 10 Greece Tel: +30 2810 391672 Mobile: +30 697 stamatak@in.tum.de 15. Phylogenetic Parameter Estimation on COWs Heiko Schmidt Heiko Schmidt Institut fuer Bioinformatik HHU Duesseldorf Universitaetsstr. 1, Geb. 25.02.02 D-40225 Duesseldorf Germany phone: ++49 +211/81-11 914 fax: ++49 +211/81-15 767 hschmidt@cs.uni-duesseldorf.de 16. High-Performance Phylogeny Reconstruction Under Maximum Parsimony David Bader, Bernard Moret, Tiffani Williams, and Mi Yan Tiffani Williams Radcliffe Institute 34 Concord Avenue Cambridge, MA, 02138 USA tlw@cs.unm.edu PROTEIN FOLDING 17. Protein Folding with the Parallel Replica Exchange Molecular Dynamics Method Ruhong Zhou Ruhong Zhou Computational Biology Center IBM Thomas J. Watson Research Center Yorktown Heights, NY 10598 ruhongz@us.ibm.com 18. High Performance Alignment Methods for Protein Threading Nicola Yanev Nicola Yanev FMI, University of Sofia, 5, J. Bouchier str., 1126 Sofia, Bulgaria choby@math.bas.bg 19. PARALLEL EVOLUTIONARY COMPUTATIONS IN DISCERNING PROTEIN STRUCTURES Gary Lamont Professor Gary B. Lamont DEPARTMENT OF ELECTRICAL AND COMPUTER ENGINEERING GRADUATE SCHOOL OF ENGINEERING AND MANAGEMENT AIR FORCE INSTITUTE OF TECHNOLOGY (AIR UNIVERSITY) AFIT/ENG BLDG. 641, RM. 220 2950 HOBSON WAY, WRIGHT-PATTERSON AFB DAYTON, OH 45433-7765 Gary.Lamont@afit.edu PLATFORMS & ENABLING TECHNOLOGIES 20. An Overview of Grid Technology in Bio- and Health-Informatics A.Y. Zomaya Albert Y. Zomaya School of Information Technologies Sydney University Sydney, NSW 2006 Australia zomaya@it.usyd.edu.au 21. Parallel Algorithms for Bioinformatics Shahid H. Bokhari, Jon Sauer Shahid Bokhari 275-S DHA Lahore 54792 Pakistan phone 92-42-5734471 sbokhari@wol.net.pk 22. Cluster and Grid Infrastructure for Computational Chemistry and Biochemistry David Abramson David Abramson School of Computer Science and Software Engineering Monash University Clayton, Victoria 3800 Australia davida@csse.monash.edu.au 23. Distributed Workflows in Bioinformatics Arun Krishnan Arun Krishnan, Research Scientist and Team Leader, Bioinformatics Institute, 30, Biopolis Street, #07-01, Matrix, Singapore - 138671 arun@bii.a-star.edu.sg 24. Molecular Structure Determination on a Computational and Data Grid Russ Miller Dr. Russ Miller Center for Computational Research, 9 Norton Hall State University of New York Buffalo, NY 14260 miller@cse.Buffalo.EDU 25. GIPSY: A Problem Solving Environment for Bioinformatics applications Rajendra Joshi Dr. Rajendra R. Joshi Scientific & Engineering Computing Group Centre for Development of Advanced Computing University of Pune Campus, Ganeshkhind PUNE-411007, Maharashtra INDIA rajendra@cdacindia.com 26. TaskSpaces: A Software Framework for Parallel Bioinformatics on Computational Grids Hans De Sterck Hans De Sterck Department of Applied Mathematics University of Waterloo 200 University Ave W. Waterloo, Ontario N2L 3G1 Canada hdesterck@math.uwaterloo.ca 27. The Organic Grid: self-organizing computation on desktop Grids Mario Lauria Mario Lauria Dept of Computer Science & Engineering 2015 Neil Ave #395 Columbus, OH 43210-1277 USA lauria@cis.ohio-state.edu 28. FPGA Computing in modern bioinformatics Simmler Harald Harald Simmler Bgm.-Horlacherstr. 86 67067 Ludwigshafen Germany harald.simmler@acconovis.com 29. Virtual Microscopy: Distributed Image Storage, Retrieval, Analysis, and Visualization Joel Saltz Joel Saltz 3168 Graves Hall 333 W 10th Avenue Columbus OH 43210 614-292-4778 Joel.Saltz@osumc.edu
Library of Congress Subject Headings for this publication:
Bioinformatics.
Computational biology.
Parallel processing (Electronic computers).