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Table of Contents Table of Contents Volume I Foreword ........................................................................................................................................xxxvii Preface ................................................................................................................................................... xl Acknowledgment ................................................................................................................................ xlv Section I Infrastructures and Services for HealthGrids and BioGrids Chapter I SHARE: A European Healthgrid Roadmap ............................................................................................ 1 Mark Olive, University of the West of England, UK Hanene Boussi Rahmouni, University of the West of England, UK Tony Solomonides, University of the West of England, UK Vincent Breton, IN2P3, CNRS, Clermont-Ferrand, France Nicolas Jacq, HealthGrid (International) Yannick Legré, HealthGrid (International), IN2P3, CNRS, Clermont-Ferrand, France Ignacio Blanquer, Universidad Politécnica de Valencia, Spain Vicente Hernandez, Universidad Politécnica de Valencia, Spain Isabelle Andoulsi, Universitaires Notre-Dame de la Paix, Belgium Jean Herveg, Universitaires Notre-Dame de la Paix, Belgium Celine Van Doosselaere, European Health Management Association (International) Petra Wilson, European Health Management Association (International) Alexander Dobrev, Empirica GmbH, Germany Karl Stroetmann, Empirica GmbH, Germany Veli Stroetmann, Empirica GmbH, Germany Chapter II Types of Resources and their Discovery in HealthGrids ...................................................................... 30 Aisha Naseer, Brunel University, UK Lampros K. Stergioulas, Brunel University, UK Chapter III Data Provenance in Scientific Workflows ............................................................................................. 46 Khalid Belhajjame, University of Manchester, UK Paolo Missier, University of Manchester, UK Carole A. Goble, University of Manchester, UK Chapter IV Provenance Tracking and End-User Oriented Query Construction ...................................................... 60 Bartosz Balis, Institute of Computer Science AGH, Poland Marian Bubak, Institute of Computer Science AGH, Poland & University of Amsterdam, The Netherlands Michal Pelczar, ACC CYFRONET AGH, Poland Jakub Wach, ACC CYFRONET AGH, Poland Chapter V Data Protection and Data Security Regarding Grid Computing in Biomedical Research .................... 76 Yassene Mohammed, Georg-August-University, Germany Fred Viezens, Georg-August-University, Germany Frank Dickmann, Georg-August-University, Germany Jürgen Falkner, Fraunhofer Institute for Industrial Engineering IAO, Germany Thomas Lingner, Georg-August-University, Germany Dagmar Krefting, University Medicine Berlin, Germany Ulrich Sax, Georg-August-University, Germany Chapter VI Parallel, Distributed, and Grid-Based Data Mining: Algorithms, Systems, and Applications ............. 90 Moez Ben HajHmida, Faculty of Sciences of Tunis, Tunisia Antonio Congiusta, University of Calabria, Italy & University of Salerno, Italy Section II Grids for Genomics and Proteomics Chapter VII High Performance BLAST Over the Grid .......................................................................................... 121 Vincent Breton, IN2P3, CNRS, Clermont-Ferrand, France Eddy Caron, Université de Lyon, LIP, CNRS-ENS-Lyon-UCBL-INRIA, France Frédéric Desprez, INRIA, Université de Lyon, LIP, CNRS-ENS-Lyon-UCBL-INRIA, France Gaël Le Mahec, CNRS, IN2P3, UBP Clermont-Ferrand, France Chapter VIII Functional Genomics Applications in GRID ...................................................................................... 149 Luciano Milanesi, Istituto di Tecnologie Biomediche – Consiglio Nazionale delle Ricerche, Italy Ivan Merelli, Istituto di Tecnologie Biomediche – Consiglio Nazionale delle Ricerche, Italy Gabriele Trombetti, Istituto di Tecnologie Biomediche – Consiglio Nazionale delle Ricerche, Italy Paolo Cozzi, Istituto di Tecnologie Biomediche – Consiglio Nazionale delle Ricerche, Italy Alessandro Orro, Istituto di Tecnologie Biomediche – Consiglio Nazionale delle Ricerche, Italy Chapter IX PheGee@Home: A Grid-Based Tool for Comparative Genomics ...................................................... 168 Bertil Schmidt, Nanyang Technological University, Singapore Chen Chen, Nanyang Technological University, Singapore Weiguo Liu, Nanyang Technological University, Singapore Wayne P. Mitchell, Experimental Therapeutics Centre (ETC), Singapore Chapter X High-Throughput GRID Computing for Life Sciences ...................................................................... 187 Giulia De Sario, Istituto di Tecnologie Biomediche, CNR, Italy Angelica Tulipano, Istituto di Tecnologie Biomediche, CNR, Italy Giacinto Donvito, INFN, Sezione di Bari, Italy Giorgio Maggi, INFN Bari, Italy & Università e Politecnico di Bari, Italy Andreas Gisel, Istituto di Tecnologie Biomediche, CNR, Italy Chapter XI Management and Analysis of Mass Spectrometry Proteomics Data on the Grid ............................... 206 Mario Cannataro, University Magna Graecia of Catanzaro, Italy Pietro Hiram Guzzi, University Magna Graecia of Catanzaro, Italy Giuseppe Tradigo, University Magna Graecia of Catanzaro, Italy Pierangelo Veltri, University Magna Graecia of Catanzaro, Italy Chapter XII High-Throughput Data Analysis of Proteomic Mass Spectra on the SwissBioGrid .......................... 228 Andreas Quandt, Swiss Institute of Bioinformatics, Switzerland Sergio Maffioletti, ETH Zurich (Swiss National Supercomputing Centre), Switzerland Cesare Pautasso, University of Lugano, Switzerland Heinz Stockinger, Swiss Institute of Bioinformatics, Switzerland Frederique Lisacek, Swiss Institute of Bioinformatics, Switzerland Peter Kunszt, ETH Zurich (Swiss National Supercomputing Centre), Switzerland Chapter XIII Data Mining in Proteomics Using Grid Computing ........................................................................... 245 Fotis E. Psomopoulos, Aristotle University of Thessaloniki, Greece Pericles A. Mitkas, Aristotle University of Thessaloniki, Greece Section III Grid-Based Bioinformatics Environments Chapter XIV ProGenGrid: A Grid Problem Solving for Bioinformatics ................................................................. 269 Maria Mirto, University of Salento, Lecce, Italy & SPACI Consortium, Italy Italo Epicoco, University of Salento, Lecce, Italy & SPACI Consortium, Italy Massimo Cafaro, University of Salento, Lecce, Italy & SPACI Consortium, Italy Sandro Fiore, University of Salento, Lecce, Italy & SPACI Consortium, Italy, Marco Passante, University of Salento, Lecce, Italy & SPACI Consortium, Italy Alessandro Negro, University of Salento, Lecce, Italy & SPACI Consortium, Italy Giovanni Aloisio, University of Salento, Lecce, Italy & SPACI Consortium, Italy Chapter XV A Graphical Workflow Modeler for Docking Process in Drug Discovery ......................................... 292 Qiang Wang, Harbin Institute of Technology, China Yunming Ye, Harbin Institute of Technology, China Kunqian Yu, Chinese Academy of Science (CAS), China Joshua Zhexue Huang, University of Hong Kong, China Chapter XVI BioSimGrid Biomolecular Simulation Database ................................................................................ 307 Kaihsu Tai, University of Oxford, UK Mark S. P. Sansom, University of Oxford, UK Chapter XVII Molecular Structure Determination on the Grid ................................................................................. 327 Russ Miller, Hauptman-Woodward Medical Research Institute, USA & SUNY-Buffalo, USA Charles M. Weeks, Hauptman-Woodward Medical Research Institute, USA Section IV Grids for Medical Informatics Chapter XVIII Aspects of Visualization and the Grid in a Biomedical Context ......................................................... 347 Ian Greenshields, University of Connecticut, USA Gamal El-Sayed, University of Connecticut, USA Volume II Chapter XIX Grid Analysis of Radiological Data .................................................................................................... 363 Cécile Germain-Renaud, Université Paris-Sud, CNRS, France Vincent Breton, IN2P3, CNRS, Clermont-Ferrand, France Patrick Clarysse, CNRS; Inserm; INSA-Lyon; Université Lyon 1, France Bertrand Delhay, CNRS; Inserm; INSA-Lyon; Université Lyon 1, France Yann Gaudeau, Université Strasbourg; CNRS, France Tristan Glatard, Université de Lyon; CREATIS-LRMN, France Emmanuel Jeannot, INRIA; CNRS; Université Henri Poincaré, France Yannick Legré, CNRS; Université Blaise Pascal, France Johan Montagnat, CNRS; Université Nice Sophia-Antipolis, France Jean Marie Moureaux, CNRS; Université Henri Poincaré, France Angel Osorio, CNRS, France Xavier Pennec, INRIA Sophia-Antipolis, France Joël Schaerer, CNRS; Inserm; INSA-Lyon; Université Lyon 1, France Romain Texier, CNRS; Université Nice Sophia-Antipolis, France Chapter XX Grid Computing in 3D Electron Microscopy Reconstruction ............................................................ 392 J.R. Bilbao Castro, University of Almería. Spain I. García Fernández, University of Almería. Spain J.J. Fernández, University of Almería. Spain Chapter XXI Hybrid Mock Circulatory System to Test Cardiovascular Prostheses on the Grid ............................. 410 Francesco Maria Colacino, University “Magna Græcia” of Catanzaro, Italy & University of Calabria, Italy Maurizio Arabia, University of Calabria, Italy Gionata Fragomeni,
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