BIOINFOGRID: Bioinformatics Grid Application for life science MILANESI, Luciano National Research Council Institute of Biomedical Technologies)

EGEE User Forum March 2006, Geneve 2 Project descriptions Bioinformatics Grid Application for life science (BIOINFOGRID) project. The BIOINFOGRID projects proposes to combine the Bioinformatics services and applications for molecular biology users with the Grid Infrastructure created by EGEE. In the BIOINFOGRID initiative we plan to evaluate genomics, transcriptomics, proteomics and molecular dynamics applications studies based on GRID technology. BIOINFOGRID will evaluate the Grid usability in wide variety of applications, and explore and exploit common solutions.

EGEE User Forum March 2006, Geneve 3 DNA High Throughput Sequencing DNA High Throughput Sequencing MSMS EST HTS Microsatellite SNP’s Microarray High Throughput Data Project

EGEE User Forum March 2006, Geneve 4 A typical gene lab can produce 100 terabytes of information a year, the equivalent of 1 million encyclopedias. Few biologists have the computational skills needed to fully explore such an astonishing amount of data; nor do they have the skills to explore the exploding amount of data being generated from clinical trials. The immense amount of data that are available, and the knowledge is the tip of the data iceberg. Bioinformatics: Emerging Opportunities and Emerging Gaps11 Paula E.Stephan and Grant Black Introduction

EGEE User Forum March 2006, Geneve 5 The grid application aspects. The massive potential of Grid technology will be indispensable when dealing with both the complexity of models and the enormous quantity of data, for example, in searching the human genome or when carry out simulations of molecular dynamics for the study of new drugs. The BIOINFOGRID projects proposes to combine the Bioinformatics services and applications for molecular biology users with the Grid Infrastructure created by EGEE Enabling Grids for E-sciencE

EGEE User Forum March 2006, Geneve 6 Proteins (Proteomics) Microarray (Trascriptomics) Gene & SNPs (Genomics) Data Integration

EGEE User Forum March 2006, Geneve 7 Applications in GRID Genomics Applications in GRID Analysis of the W3H task system for GRID. GRID analysis of cDNA data. GRID analysis of the NCBI and Ensembl databases. GRID analysis of rule-based multiple alignments. Proteomics Applications in GRID Pipeline analysis for protein functional domain analysis. Surface proteins analysis in GRID platform. Transcriptomics and Phylogenetics Applications in GRID Data analysis specific for microarray and allow the GRID user to store and search this information, with direct access to the data files stored on Data Storage element on GRID servers

EGEE User Forum March 2006, Geneve 8 Database and Functional Genomics Applications to manage and access biological database by GRID to cluster gene products by their functionality as an alternative to the normally used comparison by sequence similarity. Molecular Dynamics Applications to improve the scalability of Molecular Dynamics simulations. to perform simulation folding and aggregation of peptides and small proteins, to investigate structural properties of proteins and protein-DNA complexes and to study the effect of mutations in proteins of biomedical interest. to perform a challenge of the Wide In Silico Docking On Malaria. Applications in GRID

EGEE User Forum March 2006, Geneve 9 ID MURA_BACSU STANDARD; PRT; 429 AA. DE PROBABLE UDP-N-ACETYLGLUCOSAMINE 1- CARBOXYVINYLTRANSFERASE DE (EC ) (ENOYLPYRUVATE TRANSFERASE) (UDP-N- ACETYLGLUCOSAMINE DE ENOLPYRUVYL TRANSFERASE) (EPT). Genetics applications in GRID

EGEE User Forum March 2006, Geneve 10 Database Applications UI RB Farm2 SE Data flow for local database creation Normal grid job data flow Temporal distribution of a working database

EGEE User Forum March 2006, Geneve 11 Transcriptomics & Phylogenetics Data analysis specific for microarray and allow the GRID user to store and search this information, with direct access to the data files stored on Data Storage element on GRID servers and to discovery new cluster motifs Candidate Motifs Gene expression

EGEE User Forum March 2006, Geneve 12 Bioinformatics Data challenge

EGEE User Forum March 2006, Geneve 13

EGEE User Forum March 2006, Geneve 14 CREDITS Suhai Sándor (DKFZ) Germany Mazzucato, Mirco (INFN), Italy Breton Vincent (CNRS/IN2P3), France. Giorgio Maggi (INFN), Italy Legre Yannick (CNRS/IN2P3), France. Francesco Beltrame (DIST), Italy Lio’ Pietro (UNIVERSITY OF CAMBRIDGE), UK Meloni Giovanni (CILEA), Italy Giselle Andreas (CNR-ITB), Italy Ivan Merelli (CNR-ITB), Italy