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U N A M. B i o i n f o r m a t i c s / B i o m e d i c a l A p p l i c a t i o n s i n E E L A. e – s c i e n c e M e x i c o , 8 th E E L A W o r k s h o p. Mexico, D.F., october 22 – 26, 2007. César Bonavides-Martínez. Overview. Introduction

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B i o i n f o r m a t i c s / B i o m e d i c a l A p p l i c a t i o n s i n E E L A

e – s c i e n c e M e x i c o , 8th E E L A W o r k s h o p

Mexico, D.F., october 22 – 26, 2007.

César Bonavides-Martínez

  • Introduction
  • Objectives for the Bio-informatics/medical Work Package (3.1)
  • Categories for the bioinformatics/biomedical applications in EELA
  • Selected bioinformatics/biomedical applications in EELA
  • WISDOM case (a simple big sample)
  • Conclusions
  • Bioinformatics refers to the use of computers and the information sciences (such as mathematics and statistics) to help life science data analysis (biological and medical).
  • Bioinformatics evolves so fast that biologist, computer, and even the bioinformatician scientists, frequently find themselves in trouble to keep up to date with the continuous growth of technologies, applications, tools and databases.
  • There is a need to set up computer infrastructures that could allow the bioinformaticians to concentrate in their research work rather than thinking on issues such as:
    • computer resources,
    • installation/configuration of tools and/or applications
    • downloading, storing and updating databases
  • Such tasks have been frequently demonstrated to be accomplished easier by the use of computer GRID infrastructures.
  • The HealthGrid project identified 5 key areas which apply to the whole society:
    • Genomics
    • Proteomics
    • Medical Imaging
    • Human Body Simulation
    • Epidemiology
  • EELA tries to differentiate the needs/relevancy of certain applications between Europe and Latin America, and aims for the development/improvement of those research needs.
objectives for the bioinformatics biomedical part of the project
Objectives for the Bioinformatics/biomedical part of the project
  • To deploy Grid applications for the biomedical Latin American community.
  • To foster physicians and biologists to improve their scientific position.
  • To improve research and excellence in Latin America.
  • To increase the use of Grids in this community.
eela categories for the bioinformatics biomedical applications
EELA. Categories for the bioinformatics/biomedical applications
  • Bioinformatics applications, where we can find genomic, genetic or proteomic analysis.
  • Computational biochemical processes, which are applied to molecular biology and chemical interactions.
  • Biomodels simulation, used to simulate structural, flow or electrical biomodels.
  • Medical imaging, for image post-processing and sharing.
eela selected bioinformatics biomedical applications
EELA. Selected bioinformatics/biomedical applications

EELA Project partners selected applications in the first three areas:

1) Bioinformatics applications:

  • BLAST (Basic Local Alignment Searching Tool)
  • Phylogeny (MrBayes)
  • EMBOSS (European Molecular Biology Open Software Suite)
eela selected bioinformatics biomedical applications1
EELA. Selected bioinformatics/biomedical applications

Applications already deployed in EGEE were integrated into EELA with low effort on porting and configuration.

2) Computational biochemical processes:

  • WISDOM (Wide In Silico Docking of Malaria)

3) Biomedical simulation:

  • GATE (GEANT4 Application to Tomographic Emission)
wisdom case a simple big sample
WISDOM Case (a simple big sample)
  • In the First Biomed “Data Challenge” (Coordinated Experiment on Malaria) 46 Million Ligands were Docked in 39 Days Using EGEE Grid.
  • 72751 Jobs were Executed From 9 UIs on the 1758 CPUs Available for the Data Challenge and Organized Through 58 CEs and 12 RBs.
  • 1,5 Terabytes Were Produced and are Being Analysed by the Experts.
  • This same process would have taken about 80 Years in a Single CPU PC.

“Gridification” of applications is not an easy task, but is an essential part for the use of any Grid infrastructure. EELA Project has provided mechanisms for achieving both gridification and dissemination of biomed applications.

The results obtained so far demonstrate EELA’s efficiency and usability in both application deployment and scientific research support.

The EELA e-infrastructure allows various collaborative groups in Latin America to use more powerful computational resources than those available on their centres.