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, University “Magna Græcia” of Catanzaro, Italy

Section V Collaborative Grids for Healthcare and Clinical Applications

Chapter XXII Grid Technologies in Epidemiology...... 426 Ignacio Blanquer, Universidad Politécnica de Valencia, Spain Vicente Hernández, Universidad Politécnica de Valencia, Spain Chapter XXIII IntegraEPI: Epidemiologic Surveillance on the Grid...... 444 Fabrício Alves Barbosa da Silva, Universidade de Lisboa, Portugal Henrique Fabrício Gagliardi, Instituto de Ensino Superior COC, Brasil Eduardo Gallo, APRAESPI, Brasil Maria Antónia Madope, Ford Foundation Alumni Association, Moçambique Virgílio Cavicchioli Neto, Universidade Federal de São Paulo, Brasil Ivan Torres Pisa, Universidade Federal de São Paulo, Brasil Domingos Alves, Universidade de São Paulo, Brasil

Chapter XXIV Gridifying Biomedical Applications in the Health-e-Child Project...... 469 David Manset, maat Gknowledge, France Frederic Pourraz, maat Gknowledge, France Alexey Tsymbal, Siemens AG, Germany Jerome Revillard, maat Gknowledge, France Konstantin Skaburskas, CERN, Switzerland Richard McClatchey, University of the West of England, UK Ashiq Anjum, University of the West of England, UK Alfonso Rios, maat Gknowledge, Spain Martin Huber, Siemens AG, Germany

Chapter XXV e-Infrastructures Fostering Multi-Centre Collaborative Research into the Intensive Care Management of Patients with Brain Injury...... 494 Richard O. Sinnott, University of Glasgow, UK Ian Piper, Southern General Hospital, Glasgow, UK

Section VI Grid-Based Virtual Laboratories for Bioinformatics and E-Science

Chapter XXVI Semantic Integration for Research Environments...... 514 Tomasz Gubala, University of Amsterdam, The Netherlands & ACC CYFRONET AGH, Poland Marian Bubak, Institute of Computer Science AGH, Poland & University of Amsterdam, The Netherlands Peter M.A. Sloot, Informatics Institute, University of Amsterdam, The Netherlands Chapter XXVII Virtual Laboratory for Collaborative Applications...... 531 Marian Bubak, Institute of Computer Science AGH, Poland & University of Amsterdam, The Netherlands Maciej Malawski, Institute of Computer Science AGH, Poland Tomasz Gubala, ACC CYFRONET AGH, Poland & University of Amsterdam, The Netherlands Marek Kasztelnik, ACC CYFRONET AGH, Poland Piotr Nowakowski, ACC CYFRONET AGH, Poland Daniel Harezlak, ACC CYFRONET AGH, Poland Tomasz Bartynski, University of Amsterdam, The Netherlands & ACC CYFRONET AGH, Poland Joanna Kocot, ACC CYFRONET AGH, Poland Eryk Ciepiela, ACC CYFRONET AGH, Poland Wlodzimierz Funika, Institute of Computer Science AGH, Poland Dariusz Krol, ACC CYFRONET AGH, Poland Bartosz Balis, Institute of Computer Science AGH, Poland Matthias Assel, University of Stuttgart, Germany Alfredo Tirado-Ramos, University of Amsterdam, The Netherlands

Chapter XXVIII Leveraging the Power of the Grid with Opal...... 552 Sriram Krishnan, University of California San Diego, USA Luca Clementi, University of California San Diego, USA Zhaohui Ding, Jilin University, China Wilfred Li, University of California San Diego, USA

Chapter XXIX The LIBI Grid Platform for Bioinformatics...... 577 The LIBI Grid Platform Developers, Italy

Section VII Building and Deploying HealthGrids

Chapter XXX UNICORE: A Middleware for Life Sciences Grids...... 615 Piotr Bała, ICM University of Warsaw & N. Copernicus University, Poland Kim Baldridge, University of Zurich, Switzerland Emilio Benfenati, Istituto Mario Negri, Italy Mosè Casalegno, Istituto Mario Negri, Italy Uko Maran, University of Tartu, Estonia Łukasz Mirosław, University of Zürich, Switzerland Vitaliy Ostropytskyy, University of Ulster, UK Katharina Rasch, Technische Universität Dresden, Germany Sulev Sild, University of Tartu, Estonia Robert Schöne, Technische Universität Dresden, Germany Bernd Schuller, Research Centre Juelich, Germany Nadya Williams, University of Zürich, Switzerland Chapter XXXI A Grid Paradigm for e-Science Applications...... 644 Livia Torterolo, University of Genoa, Italy Luca Corradi, University of Genoa, Italy Barbara Canesi, University of Genoa, Italy Marco Fato, University of Genoa, Italy Roberto Barbera, University of Catania, Italy & INFN-Catania, Italy Salvatore Scifo, Consorzio Cometa of Catania, Italy Antonio Calanducci, INFN-Catania, Italy Diego Scardaci, INFN (National Institute of Nuclear Physics), Italy Giordano Scuderi, Unico Informatica s.r.l, Catania, Italy

Chapter XXXII gLibrary/DRI: A Grid-Based Platform to Host Multiple Repositories for Digital Content...... 664 Roberto Barbera, University of Catania, Italy & INFN-Catania, Italy Antonio Calanducci, INFN-Catania, Italy Juan Manuel González Martín, maat Gknowledge, Spain Francisco Prieto Castrillo, CETA-CIEMAT, Spain Raúl Ramos Pollán, CETA-CIEMAT, Spain Manuel Rubio del Solar, CETA-CIEMAT, Spain Dorin Tcaci, maat Gknowledge, Spain

Section VIII Selected Readings

Chapter XXXIII Porting Applications to Grids and Clouds...... 688 Wolfgang Gentzsch, Duke University, USA

Chapter XXXIV Evaluating a Bio-Inspired Approach for the Design of a Grid Information System: The SO-Grid Portal...... 712 Agostino Forestiero, Institute of High Performance Computing and Networking CNR-ICAR, Italy Carlo Mastroianni, Institute of High Performance Computing and Networking CNR-ICAR, Italy Fausto Pupo, Institute of High Performance Computing and Networking CNR-ICAR, Italy Giandomenico Spezzano, Institute of High Performance Computing and Networking CNR-ICAR, Italy Chapter XXXV Large-Scale Co-Phylogenetic Analysis on the Grid...... 731 Heinz Stockinger, Swiss Institute of Bioinformatics, Switzerland Alexander F. Auch, University of Tübingen, Germany Markus Göker, University of Tübingen, Germany Jan Meier-Kolthoff, University of Tübingen, Germany Alexandros Stamatakis, Ludwig-Maximilians-University Munich, Germany

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