From genes to personalized healthcare : grid solutions for the life sciences ; proceedings of HealthGrid 2007 00 / edited by Nicolas Jacq .... [et al.]

356 Pages·2007·7.655 MB·English

by  N. Jacqet

FROM GENES TO PERSONALIZED HEALTHCARE:
GRID SOLUTIONS FOR THE LIFE SCIENCES
Studies in Health Technology and
Informatics
This book series was started in 1990 to promote research conducted under the auspices of the EC
programmes’ Advanced Informatics in Medicine (AIM) and Biomedical and Health Research
(BHR) bioengineering branch. A driving aspect of international health informatics is that
telecommunication technology, rehabilitative technology, intelligent home technology and many
other components are moving together and form one integrated world of information and
communication media. The complete series has been accepted in Medline. Volumes from 2005
onwards are available online.
Series Editors:
Dr. J.P. Christensen, Prof. G. de Moor, Prof. A. Famili, Prof. A. Hasman, Prof. L. Hunter,
Dr. I. Iakovidis, Dr. Z. Kolitsi, Mr. O. Le Dour, Dr. A. Lymberis, Prof. P.F. Niederer,
Prof. A. Pedotti, Prof. O. Rienhoff, Prof. F.H. Roger France, Dr. N. Rossing,
Prof. N. Saranummi, Dr. E.R. Siegel, Dr. P. Wilson, Prof. E.J.S. Hovenga,
Prof. M.A. Musen and Prof. J. Mantas
Volume 126
Recently published in this series
Vol. 125. J.D. Westwood, R.S. Haluck, H.M. Hoffman, G.T. Mogel, R. Phillips, R.A. Robb and
K.G. Vosburgh (Eds.), Medicine Meets Virtual Reality 15 – in vivo, in vitro, in silico:
Designing the Next in Medicine
Vol. 124. A. Hasman, R. Haux, J. van der Lei, E. De Clercq and F.H. Roger France (Eds.),
Ubiquity: Technologies for Better Health in Aging Societies – Proceedings of
MIE2006
Vol. 123. D. Uyttendaele and P.H. Dangerfield (Eds.), Research into Spinal Deformities 5
Vol. 122. H.-A. Park, P. Murray and C. Delaney (Eds.), Consumer-Centered Computer-
Supported Care for Healthy People – Proceedings of NI2006 – The 9th International
Congress on Nursing Informatics
Vol. 121. L. Bos, L. Roa, K. Yogesan, B. O’Connell, A. Marsh and B. Blobel (Eds.), Medical
and Care Compunetics 3
Vol. 120. V. Hernández, I. Blanquer, T. Solomonides, V. Breton and Y. Legré (Eds.),
Challenges and Opportunities of HealthGrids – Proceedings of Healthgrid 2006
Vol. 119. J.D. Westwood, R.S. Haluck, H.M. Hoffman, G.T. Mogel, R. Phillips, R.A. Robb and
K.G. Vosburgh (Eds.), Medicine Meets Virtual Reality 14 – Accelerating Change in
Healthcare: Next Medical Toolkit
Vol. 118. R.G. Bushko (Ed.), Future of Intelligent and Extelligent Health Environment
Vol. 117. C.D. Nugent, P.J. McCullagh, E.T. McAdams and A. Lymberis (Eds.), Personalised
Health Management Systems – The Integration of Innovative Sensing, Textile,
Information and Communication Technologies
ISSN 0926-9630
From Genes to Personalized
HealthCare: Grid Solutions for
the Life Sciences
Proceedings of HealthGrid 2007
Edited by
Nicolas Jacq
HealthGrid, France
Henning Müller
University and Hospitals of Geneva, Switzerland
Ignacio Blanquer
Universidad Politécnica de Valencia, Spain
Yannick Legré
CNRS-IN2P3, France
Vincent Breton
CNRS-IN2P3, France
Dominique Hausser
Observatoire technologique, Switzerland
Vicente Hernández
Universidad Politécnica de Valencia, Spain
Tony Solomonides
University of the West of England, Bristol, United Kingdom
and
Martin Hofmann-Apitius
Fraunhofer Institut für Algorithmen und Wissenschaftliches Rechnen SCAI, Germany
Amsterdam • Berlin • Oxford • Tokyo • Washington, DC
© 2007 The authors and IOS Press.
All rights reserved. No part of this book may be reproduced, stored in a retrieval system,
or transmitted, in any form or by any means, without prior written permission from the publisher.
ISBN 978-1-58603-738-3
Library of Congress Control Number: 2007924025
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The publisher is not responsible for the use which might be made of the following information.
PRINTED IN THE NETHERLANDS
From Genes to Personalized HealthCare: Grid Solutions for the Life Sciences v
N. Jacq et al. (Eds.)
IOS Press, 2007
© 2007 The authors and IOS Press. All rights reserved.
Introduction
HealthGrid 2007 (http://geneva2007.healthgrid.org) is the fifth edition of this open
forum for the integration of grid technologies and their applications in the biomedical,
medical, and biological domains to pave the path towards an international research area
in the HealthGrid field. The main objective of the HealthGrid conference and of the
HealthGrid Association is the exchange and discussion of ideas, technologies, solutions
and requirements that interest the grid and the life-science communities to foster the
integration of grids into health. Participation is encouraged for grid middleware and
grid application developers, biomedical and health informatics users, and security and
policy makers to participate in a set of multidisciplinary sessions with a common focus
on the application in the health domain.
HealthGrid conferences have been organized on an annual basis. The first confer-
ence, held in 2003 in Lyon (http://lyon2003.healthgrid.org), reflected the need to in-
volve all actors – physicians, scientists and technologists – who might play a role in the
application of grid technology to health, whether healthcare or bio-medical research.
The second conference, held in Clermont-Ferrand in January 2004 (http://clermont2004.
healthgrid.org) reported research and work in progress from a large number of projects.
The third conference in Oxford (http://oxford2005.healthgrid.org) had a major focus on
the results and deployment strategies in healthcare. The fourth conference in Valencia
(http://valencia2006.healthgrid.org) aimed at consolidating the collaboration among
biologists, healthcare professionals and grid technology experts. This fifth conference
will focus on the five domains defined by the European Commission as application
areas for grids in the biomedical field: molecules, cells, organs, individuals, and popu-
lations. For each of these five domains, an invited speaker will give a state of the art
address followed by concrete projects. The conference venue in a hospital setting
should also help to locate healthgrid research where it undoubtedly belongs, in the
biomedical field. Potential users need to be shown that grids have now gone beyond
hype and can show concrete applications that demonstrate the success of the technol-
ogy.
The conference includes a number of high-profile keynote presentations comple-
mented by a set of high quality peer reviewed papers. The number of contributions to
this conference has increased from previous occasions, reaching the number of 55
submissions of papers, demonstrations and posters from principal authors coming from
21 countries (ordered by the number of contributions: Italy, Switzerland, United King-
dom, Germany, USA, France, Spain, Poland, Russia, Taiwan, Australia, Belgium, Bra-
zil, Cuba, Cyprus, Czech Republic, Greece, Hungary, Portugal, Romania, and Ukraine).
Considering the affiliations of all the authors of the papers, the number of contributing
countries is extended to 22 countries with Venezuela. These proceedings have been
organized in eight chapters. Five chapters focus on state of the art of the grid research
and use at molecule, cell, organ, individual and population levels. Two chapters present
security and imaging papers. The last chapter includes the best poster contributions.
vi
From among the themes of the conference, it may be thought that molecules pre-
sent the most amenable target for a healthgrid approach. Although this may be true, it is
far from obvious. Even in applications such as BLAST which treat symbolic ‘words’ in
a molecular alphabet, there are a great many problems to be addressed, both when
searching for large query strings and in seeking to maintain an appropriate ‘rollback’
distributed database, as Trombetti et al. show. Two papers, by Andreas Quandt et al.
and by Zosso et al., apply grids in ‘tandem mass spectrometry’ a highly demanding
application for protein identification. It is equally good to see applications to screening
in Malaria (Jean Salzemann et al.) and early detection of Alzheimer’s (Nabil Abden-
nadher et al.), while the application to sleep disorders in their full breadth (Sebastian
Canisius et al.) demonstrates the considerable breadth of application that is possible on
a grid platform. Hernandez et al. provide an overview of the substantial progress that
has been made in the field in the wake of large platform projects.
By contrast, applications in the cellular and organ domains appear to present as
much difficulty in conceiving possible projects as in devising grid deployment schemes.
Sinnott et al. identify and are in part motivated by the intrinsic value of microarray data
as a major issue, while Roberta Alfieri et al. consider a mathematical model of the cell
cycle – two extremes in the exploration of cell issues. Marienne Hibbert et al. describe
a molecular medicine model and Emerson and Rossi discuss a simulation of the human
immune system. Among organs, Andrés Gómez et al. demonstrate a radiotherapy tool
and Blanquer Espert et al. explore the management of DICOM objects on a grid.
The domain of the individual is highly attractive, since it provides an entry point to
the whole HealthGrid project and the possible grid health record. Two papers by the
SHARE collaboration provide outline ‘road maps’ for the creation of viable healthgrids.
Jenny Ure et al. took schizophrenia as a case study for a series of workshops to under-
stand what it might take to create appropriate ontologies for data integration. Michal
Kosiedowski et al. discuss a grid-based Electronic Medical Library and Shu-Hui
Hung et al. consider the merits of the treatment of asthma in a grid system. Stefan
Rüping et al. seek to extend workflow management for knowledge discovery from
combined clinical and genomic data towards a fuller electronic health record. Giovanni
Aloisio et al. treat the paradigm of Service-Oriented Architecture in bioinformatics.
Thus we arrive at the population domain, where Fabricio Silva et al. report on a
grid-based epidemic surveillance system in Brazil for essentially slow evolving dis-
eases. Tiberiu Stef-Praun et al. present the Swift system of workflow description and
execution.
Apart from these five domains, two topical areas are considered in depth: security
and imaging. In security, in two separate papers Jean Herveg and Luigi Lo Iacono ex-
plore familiar questions of data protection and of pseudonymization respectively, pro-
viding a theoretical perspective against which some practical proposals by Petr Holub
et al. on the Access Grid model and Harald Gjermundrød et al. on the EGEE model can
be compared. In imaging, we have papers on Globus MEDICUS (Stephan G. Erberich
et al.) which federates DICOM devices through a grid architecture and KnowARC
(Henning Müller et al.) on facilitating grid networks for the biomedical research com-
munity. Finally, Adina Riposan et al. report on the successful use of multimodal work-
flows in diabetic retinopathy research.
vii
ACKNOWLEDGEMENTS
The editors express their gratitude to the program committee and the reviewers; each
paper was read by at least two reviewers, including the editors. The editors want to
thank for the remarkable work that the staff of the HealthGrid association has invested
in these conference proceedings and on the organisation of the conference, particularly
Yannick Legré.
Opinions expressed in these proceedings are those of individual authors and editors,
and not necessarily those of their institutions.
viii
Healthgrid 2007 Programme Committee (last name alphabetical order)
Chairman:
Martin Hofmann-Apitius Fraunhofer Institut für Algorithmen und
Wissenschaftliches Rechnen SCAI, Germany
Howard Bilofsky University of Pennsylvania, USA
Ignacio Blanquer Universidad Politécnica de Valencia, Spain
Vincent Breton Centre National de la Recherche Scientifique, France
Anca Bucur Philips Research, The Netherlands
Jose Maria Carazo Centro Nacional de Biotecnología, Spain
Bastien Chopard University of Geneva, Switzerland
Manuel Doblaré University of Zaragoza, Spain
Alejandro Frangi Pompeu Fabra University, Spain
Fabrizio Gagliardi Microsoft, Switzerland
Dominique Hausser Observatoire technologique, Switzerland
Patricia Hernandez Swiss Institute of Bioinformatics, Switzerland
Vicente Hernandez-Garcia Universidad Politécnica de Valencia, Spain
Chun-Hsi Huang University of Connecticut, USA
Emmanuel Ifeachor University of Plymouth, United Kingdom
Alfonso Jaramillo École Polytechnique, France
Nicolas Jacq HealthGrid, France
Wang Jun Beijing Genomic Institute, China PRC
Mary Kratz University of Michigan, USA
Peter Kunszt Swiss National Supercomputing Center, Switzerland
Jimison Lavindrasana University of Geneva, Switzerland
Yannick Legré Centre National de la Recherche Scientifique, France
Richard McClatchey University of the West of England, Bristol, United
Kingdom
Fernando Martin-Sanchez Institute of Health Carlos III, Madrid, Spain
Carlos Martinez Generalitat Valenciana, Spain
Luciano Milanesi Consiglio Nazionale delle Ricerche, Istituto di
Tecnologie Biomediche (CNR-ITB), Italy
Steffen Moeller University of Lübeck, Germany
Johan Montagnat Institut National de Recherche en Informatique et
Automatique, France
Georges de Moor State University of Ghent, Belgium
Henning Müller University and Hospitals of Geneva, Switzerland
Luis Núñez de Villavicencio Universidad de los Andes, Venezuela
Armando Padhila Faculdade de Engenharia da Universidade do Porto,
Portugal
Christian R. Pellegrini University of Geneva, Switzerland
Michael Podvinec University of Basel, Switzerland
Simon Robinson Empirica GmbH, Germany
Andres Santos Universidad Politécnica de Madrid, Spain
Ferran Sanz Universitat Pompeu Fabra, Spain
Tony Solomonides University of the West of England, Bristol, United
Kingdom
ix
Antonio Sousa Instituto de Engenharia Electrónica e Telemática de
Aveiro, Portugal
Alfredo Tirado-Ramos University of Amsterdam, The Netherlands
Petra Wilson CISCO, Belgium
Zhiwei Xu Institute of Computing Technology, China PRC