1. IST-2006-026409 www.eu-eela.org E-infrastructure shared between Europe and Latin America Biomedical Applications in EELA Esther Montes Prado CIEMAT (Spain) ICT for Biomedical Sciences 2006 Brussels, 29.06.2006

2. IST-2006-026409 E-infrastructure shared between Europe and Latin America www.eu-eela.org Brussels, ICT for Biomedical Sciences 2006 2 Funded by the European Commission, the EELA project is building a digital bridge between the existing e-Infrastructures in Europe (EGEE) and those emerging in Latin America (LA), throughout the creation of network of collaboration sharing a Grid infrastructure to support development and test of advanced applications of general interest (Biomedicine among other applications). EELA aims to position LA countries at the same level of European developments, in terms of e-Infrastructures. EELA focus will be in Grid infrastructure and some e-Science Applications. Therefore, three main objectives have been defined: the creation of a human collaboration network; the creation of a pilot e-Infrastructure in LA interoperable with EGEE in the EU; and the identification and promotion of a sustainable framework for e-Science. Introduction

3. IST-2006-026409 E-infrastructure shared between Europe and Latin America www.eu-eela.org Brussels, ICT for Biomedical Sciences 2006 3 Context: –The biomedical applications being deployed on the pilot EELA infrastructure have been identified from current existing ones already in use in EGEE, and from the expertise and research activity of the LA and EU partners in EELA. –The target of the biomedical part of EELA is to deploy Grid applications for the biomedical LA community to improve their research excellence and to foster the use of Grids in this community. –Applications are selected considering their relevance for LA partners from the portfolio of existing and new applications. Project: –Two applications from the portfolio of mature EGEE biomedical applications have been selected by LA partners: GATE and WISDOM. –Two new applications were identified from the specifics needs of LA partners: BLAST and Phylogenetics. –EELA has joined the Ibero-American Portal of Bioinformatics. Objectives

4. IST-2006-026409 E-infrastructure shared between Europe and Latin America www.eu-eela.org Brussels, ICT for Biomedical Sciences 2006 4 GATE GATE: Géant4 Application for Tomographic Emission –GATE is a C++ platform based on the Monte Carlo Geant4 software designed to model nuclear medicine applications (PET, SPECT). This platform is also adequate for radiotherapy and brachytherapy treatment planning. –The objective of GATE is to use the Grid environment to reduce the computing time of Monte Carlo simulations in order to provide higher accuracy in a reasonable period of time. –The main benefit of using the Grid is that it has enabled medical users to access to realistic Monte Carlo simulations for their research in radiotherapy planning. The EELA Grid provide of enough computational resources to deal with the large requirements that this processing has. –GATE is already installed on several EELA’s partners sites.

5. IST-2006-026409 E-infrastructure shared between Europe and Latin America www.eu-eela.org Brussels, ICT for Biomedical Sciences 2006 5 WISDOM WISDOM: Wide In Silico Docking On Malaria –The objective of WISDOM is the creation of new inhibitors for a family of proteins produced by Plasmodium falciparum. This protozoan parasite causes malaria. –This application consists on the deployment of a high throughput virtual screening in the perspective of in silico drug discovery for neglected diseases. –Interest of EELA partners: selection of new targets for malaria; study of new targets for new parasitory diseases; and contribution with resources for the WISDOM data challenge. –The benefit of Grids is the reduction of the development cycle of new drugs for neglected diseases by providing in silico simulations of the selection of the adequate reactors for specific targets and the needed infrastructure to deal with the computational power required.

6. IST-2006-026409 E-infrastructure shared between Europe and Latin America www.eu-eela.org Brussels, ICT for Biomedical Sciences 2006 6 BLAST BLAST: Basic Local Alignment Searching Tool –BLAST finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. –The process of finding homologous of sequences is computionally-intensive. The size of available non-redundant databases increases daily. Since databases are periodically updated, the periodically update of the previous studies is convenient. –The use of Grid will allow to increase the number of fragments to be analysed and the periodical update of this information. –A Grid service for running MPIBlast on the EELA grid, and using the Ibero-American portal of Bioinformatics (CECALC- ULA), has been developed.

7. IST-2006-026409 E-infrastructure shared between Europe and Latin America www.eu-eela.org Brussels, ICT for Biomedical Sciences 2006 7 PHYLOGENY (MrBayes) Phylogeny with MrBayes program: –A phylogeny is a reconstruction of the evolutionary history of a group of organisms. –Bayesian inference is a powerful mathematical method which is implemented in the MrBayes program for estimating phylogenetic trees that are based on the “a posteriori” probability distribution of the trees. –The phylogenetic tools are widely demanded by LA bioinformatics community. –A Grid service for the parallelised version of MrBayes application will be developed and a simple interface will be deployed on the Ibero-American Portal of Bioinformatics. This Grid-enabled service will make use of EELA resources to run phylogenetic studies at high performance.

8. IST-2006-026409 E-infrastructure shared between Europe and Latin America www.eu-eela.org Brussels, ICT for Biomedical Sciences 2006 8 Bioinformatics portal Ibero-American Portal of Bioinformatics: –http://portal-bio.ula.vehttp://portal-bio.ula.ve –This portal is installed at the National Centre for Scientific Computation (CeCalCULA) of the Universidad of Los Andes (ULA) in Venezuela. –It is an initiative for the dissemination of findings in the Bioinformatics area in Venezuela and in other Spanish speaking countries. It was developed before EELA starting date. –It aims to create on-line academic and research communities. It has several on-line applications for registered users. –By joining EELA, it is expected to increase the number or users and running applications (mpiBLAST and parallelised MrBayes mentioned at previous slides). –The linkage of the portal to EELA is neccesary to deal with the computational demad stimated.

9. IST-2006-026409 E-infrastructure shared between Europe and Latin America www.eu-eela.org Brussels, ICT for Biomedical Sciences 2006 9 Thanks Thanks for your kind attention…