BIOINFOGRID: Bioinformatics Grid Application for life science

1
BIOINFOGRID Bioinformatics Grid Application for
life science

• MILANESI, Luciano
• National Research Council
• Institute of Biomedical Technologies)
• luciano.milanesi_at_itb.cnr.it

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.

3
High Throughput Data Project
Microsatellite
MSMS
EST
DNA High Throughput Sequencing
Microarray
SNPs
4
Introduction

• 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 Gaps1 Paula E.Stephan and Grant Black
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
6
Data Integration
Proteins (Proteomics)
Microarray (Trascriptomics)
Gene SNPs (Genomics)
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

8
Applications in GRID

• 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.

9
Genetics applications in GRID
10
Database Applications
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

Gene expression
Candidate Motifs
12
Bioinformatics Data challenge
13
http//www.itb.cnr.it/bioinfogrid
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