Developing Biomedical Applications in the Framework of EELA

Developing Biomedical Applications in the Framework of EELA

Gabriel Aparicio (Universidad Politécnica de Valencia, Spain), Fernando Blanco (CIEMAT, Spain), Ignacio Blanquer (Universidad Politécnica de Valencia, Spain), César Bonavides (UNAM Campus Morelos, Mexico), Juan Luis Chaves (Universidad de los Andes, Venezuela), Miguel Embid (CIEMAT, Spain) and Álvaro Hernández (Universidad de los Andes, Venezuela)
DOI: 10.4018/978-1-60566-184-1.ch020
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Abstract

In the last years an increasing demand for Grid Infrastructures has resulted in several international collaborations. This is the case of the EELA Project, which has brought together collaborating groups of Latin America and Europe. One year ago, the authors presented this e-infrastructure used, among others, by the biomedical groups for the studies of oncological analysis, neglected diseases, sequence alignments and computational phylogenetics. After this period, the achieved advances and the scientific results are summarized in this chapter
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Background

The realization of a common interoperable Grid testbed from existing resources in Latin America and Europe, distributed over 15 resource centers, was the first problem to overcome. For this purpose, the testbed was built upon the network infrastructure provided by GÉANT in Europe and RedCLARA in Latin America and interfacing with European and Latin American National Research and Education Networks (NREN).

The Pilot Testbed is organized in three layers: at the highest level, the EELA Operations Centre (old Grid Operations Centre) coordinates the interaction between the subordinate CORE Services Centers (CSC) and the Resource Centers (RCs) which provide computing power and data storage. At the base level we have the Additional Service Providers (ASPs) which provide support for services needed by proper operation of the Pilot Testbed but not directly related to the middleware utilized, such as Certification Authority management and Virtual Organization Management Services (VOMS) and File Catalogues.

EELA has integrated more than 1,500 computing cores and 60 TB of data storage available to the project users and has been accepted as member of The Americas Grid Policy Management Authority (TAGPMA), as well as new national Latin American Certification Authorities have been accredited too. EELA has two distinct VOs (EELA and EDTEAM) and accepts two particular High Energy Physics VOs (Alice and LHCb), accounting for 4 VO setups. EELA provides network services through standard modeling processes thus ensuring the required quality of service.

As EELA has adopted the gLite Middleware (see http://whitepaper.healthgrid.org) identifies five key areas: Genomics; Proteomics; Medical Imaging; Human Body Simulation; and Epidemiology. These issues apply to the whole society and, in particular, to the Latin American countries.

Key Terms in this Chapter

GATE: C++ platform based on the Monte Carlo GEANT4 software, which models nuclear medicine applications, such as Positron Emission Tomography (PET), Single Photon Emission Computed Tomography (SPECT) or radiotherapy dosimetry

EELA Infrastructure Grid: This grid pools, shares and reuses infrastructure resources such as hardware, software, storage and networks across multiple applications between Europe and Latin America

Grid Computing: A style of computing that dynamically pools IT resources together for use based on resource need. It allows organizations to provision and scale resources as needs arise, thereby preventing the underutilization of resources (computers, networks, data archives, instruments).

Phylogeny: A reconstruction of the evolutionary history of a group of organisms used throughout the life sciences

EMBOSS: Free Open Source software analysis package which covers several molecular biology tools.

BiG: BLAST in Grids uses the Basic Local Alignment Search tool to find regions of local similarity between sequences by comparing nucleotide or protein sequences to databases and by calculating the statistical significance of matches.

Wisdom: Wide in Silico Docking of Malaria is the proposition of new inhibitors by means of periodic Data-Challenges and further analysis

Applications Grid: It shares and reuses application codes but uses software technologies like service oriented architectures that facilitate sharing business logic among multiple applications.

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Table of Contents
Foreword
Ruth E. Shaw
Preface
Emmanuel Udoh, Frank Zhigang Wang
Acknowledgment
Emmanuel Udoh
Chapter 1
Emmanuel Udoh, Frank Zhigang Wang, Vineet R. Khare
This chapter presents a historical record of the advent of Grid with a recourse to some basic definitions commonly accepted by most researchers. It... Sample PDF
Overview of Grid Computing
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Chapter 2
Eric Aubanel
The problem of load balancing parallel applications is particularly challenging on computational grids, since the characteristics of both the... Sample PDF
Resource-Aware Load Balancing of Parallel Applications
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Chapter 3
Enis Afgan, Purushotham Bangalore
Grid computing has emerged as the next generation computing platform. Because of the resource heterogeneity that exists in the grid environment... Sample PDF
Assisting Efficient Job Planning and Scheduling in the Grid
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Chapter 4
Kuo-Chan Huang, Po-Chi Shih, Yeh-Ching Chung
Most current grid environments are established through collaboration among a group of participating sites which volunteer to provide free computing... Sample PDF
Effective Resource Allocation and Job Scheduling Mechanisms for Load Sharing in a Computational Grid
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Chapter 5
Tevfik Kosar
As the data requirements of scientific distributed applications increase, the access to remote data becomes the main performance bottleneck for... Sample PDF
Data-Aware Distributed Batch Scheduling
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Chapter 6
Gianni Pucciani, Flavia Donno, Andrea Domenici, Heinz Stockinger
Data replication is a well-known technique used in distributed systems in order to improve fault tolerance and make data access faster. Several... Sample PDF
Consistency of Replicated Datasets in Grid Computing
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Chapter 7
Ming Wu, Xian-He Sun
Rapid advancement of communication technology has changed the landscape of computing. New models of computing, such as business-on-demand, Web... Sample PDF
Quality of Service of Grid Computing
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Chapter 8
QoS in Grid Computing  (pages 75-83)
Zhihui Du, Zhili Cheng, Xiaoying Wang, Chuang Lin
This chapter first summarizes popular terms of QoS related concepts and technologies in grid computing, including SLA, End-to-End QoS Provision and... Sample PDF
QoS in Grid Computing
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Chapter 9
Kris Bubendorfer, Ben Palmer, Ian Welch
A Grid resource broker is the arbiter for access to a Grid’s computational resources and therefore its performance and functionality has a... Sample PDF
Trust and Privacy in Grid Resource Auctions
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Chapter 10
Sandro Fiore, Alessandro Negro, Salvatore Vadacca, Massimo Cafaro, Giovanni Aloisio, Roberto Barbera
Grid computing is an emerging and enabling technology allowing organizations to easily share, integrate and manage resources in a distributed... Sample PDF
An Architectural Overview of the GRelC Data Access Service
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Chapter 11
Man Wang, Zhihui Du, Zhili Cheng
Resource Management System (RMS), which manages the Grid resources and matches the applications’ requests to the proper resources, is one of the... Sample PDF
Adaptive Resource Management in Grid Environment
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Chapter 12
Vineet R. Khare, Frank Zhigang Wang
The need for a dynamic and scalable expansion of the grid infrastructure and resources and other scalability issues in terms of execution efficiency... Sample PDF
Bio-Inspired Grid Resource Management
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Chapter 13
Yuhui Deng, Frank Zhigang Wang, Na Helian
Storage Grid is a new model for deploying and managing the heterogeneous, dynamic, large-scale, and geographically distributed storage resources.... Sample PDF
Service Oriented Storage System Grid
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Chapter 14
Dominic Cherry, Maozhen Li, Man Qi
This chapter presents MediaGrid, a distributed storage system for archiving broadcast media contents. MediaGrid utilizes storage resources donated... Sample PDF
A Distributed Storage System for Archiving Broadcast Media Content
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Chapter 15
Maozhen Li, Man Qi, Bin Yu
The computational grid is rapidly evolving into a service-oriented computing infrastructure that facilitates resource sharing and large-scale... Sample PDF
Service Discovery with Rough Sets
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Chapter 16
Irfan Habib, Ashiq Anjum, Richard McClatchey
Due to some barriers to adoption we have not seen a proliferation of Grid Computing technologies throughout e-Science or other domains. This chapter... Sample PDF
On the Pervasive Adoption of Grid Technologies: A Grid Operating System
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Chapter 17
Kurt Vanmechelen, Jan Broeckhove, Wim Depoorter, Khalid Abdelkader
As grid computing technology moves further up the adoption curve, the issues of dealing with conflicting user requirements formulated by different... Sample PDF
Pricing Computational Resources in Grid Economies
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Chapter 18
Rosario M. Piro
Large, geographically distributed and heterogeneous computing infrastructures, such as the Grid, often span multiple organizations and... Sample PDF
Resource Usage Accounting in Grid Computing
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Chapter 19
Frans Arickx, Jan Broeckhove, Peter Hellinckx, David Dewolfs, Kurt Vanmechelen
Quantum structure or scattering calculations often belong to a class of computational problems involving the aggregation of a set of matrices... Sample PDF
Grid-Based Nuclear Physics Applications
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Chapter 20
Gabriel Aparicio, Fernando Blanco, Ignacio Blanquer, César Bonavides, Juan Luis Chaves, Miguel Embid, Álvaro Hernández
In the last years an increasing demand for Grid Infrastructures has resulted in several international collaborations. This is the case of the EELA... Sample PDF
Developing Biomedical Applications in the Framework of EELA
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Chapter 21
Gerald Schaefer, Roger Tait
Efficient approaches to computationally intensive image processing tasks are currently highly sought after. In this chapter, the authors show how a... Sample PDF
Distributed Image Processing on a Blackboard System
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Chapter 22
Daniele Andreotti, Armando Fella, Eleonora Luppi
The BaBar experiment uses data since 1999 in examining the violation of charge and parity (CP) symmetry in the field of high energy physics. This... Sample PDF
Simulated Events Production on the Grid for the BaBar Experiment
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Chapter 23
Diego Liberati
A framework is proposed that creates, uses, and communicates information, whose organizational dynamics allows performing a distributed cooperative... Sample PDF
A Framework for Semantic Grid in E-Science
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Chapter 24
Roberto Barbera, Valeria Ardizzone, Leandro Ciuffo
The Grid INFN virtual Laboratory for Dissemination Activities (GILDA) is a fully working Grid test-bed devoted to training and dissemination... Sample PDF
Grid INFN Virtual Laboratory for Dissemination Activities (GILDA)
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Chapter 25
Dirk Gorissen, Tom Dhaene, Piet Demeester, Jan Broeckhove
The simulation and optimization of complex systems is a very time consuming and computationally intensive task. Therefore, global surrogate modeling... Sample PDF
Grid Enabled Surrogate Modeling
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Chapter 26
Patrik Skogster
Grid computing is becoming as essential part of different business analysis. In traditional business computing infrastructures data transfer occurs... Sample PDF
GIS Grids and the Business Use of GIS Data
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Chapter 27
Gokop Goteng, Ashutosh Tiwari, Rajkumar Roy
The emerging grid technology provides a secured platform for multidisciplinary experts in the security intelligence profession to collaborate and... Sample PDF
Grid Computing: Combating Global Terrorism with the World Wide Grid
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Chapter 28
Salvatore Scifo
This chapter focuses on the efforts to design and develop a standard pure Java API to access the metadata service of the EGEE Grid middleware, and... Sample PDF
Accessing Grid Metadata through a Web Interface
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Chapter 29
Jyotsna Sharma
Efforts in Grid Computing, both in academia and industry, continue to grow rapidly worldwide for research, scientific and commercial purposes.... Sample PDF
Grid Computing Initiatives in India
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Chapter 30
Hai Jin, Li Qi, Jie Dai, Yaqin Luo
A grid system is usually composed of thousands of nodes which are broadly distributed in different virtual organizations. Owing to geographical... Sample PDF
Dynamic Maintenance in ChinaGrid Support Platform
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About the Contributors