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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