LITBIO

Introduction

The main objective of the Laboratory of Interdisciplinary Technologies in Bioinformatics (LITBIO) is to support Bioinformatics applications for Genomics and Proteomics research at an international level.

The goal of Bioinformatics is the creation of novel knowledge by analyzing genomic, proteomic and transcriptomic data to suggest further experiments that provide insight into the molecular basis of life. The data generated by various genome sequencing projects form the basis for extracting information about regulatory modules and networks and interpreting genotypic and phenotypic data.

A number of supercomputers are being developed for human genome analysis and they are being increasingly deployed worldwide. More efficient algorithms and richer analysis toolsets change the way that scientists approach biomedical discovery. The creation of a robust computational platforms and the design of advanced data-mining software for the analysis of large data sets in collaboration with the scientists generating experimental data is a need that is clearly perceived.

LITBIO aims to satisfy this need by providing a reliable resource in terms of computation, knowledge and personnel capable of carrying out and coordinating the various types of high-performance informatics that are necessary for all kinds of biomedical research, development and technology transfer.

LITBIO will actively cooperate and interface with the production departments of Biotechnological, Pharmaceutical and Informatics Industries dedicated to addressing key issues in biomedical research.

LITBIO aims at being highly proactive in the training of Bioinformatics professionals with specific competence in resource integration and data-mining of medical information from large data sets.

LITBIO will establish a distributed network between European Centres for Bioinformatics resources and databases that will offer users the ability to find useful information from bibliographic and genome data, factual or image databases and full text scientific journal information.

Strategy

The partners participating in the project and their national and international collaborators will strengthen the quality of the laboratory. Incentives based on common research between public and private organizations will produce product new products that can be the subject of patent applications.

To achieve the goal of this project, the supercomputer created for Bioinformatics applications will be installed at the inter-university centre CILEA (http://www.cilea.it) and eventually interconnected with other important Bioinformatics resources (e.g. CEINGE, IST, CNR, CASPUR, CINECA).

• Development of a bioinformatics supercomputer with a throughput of at least 1.2Tflops
• Implementation of programs for the analysis of entire genomes
• Implementation of programs for the analysis of functional genomics, gene analysis and promoter regions
• Analysis of gene expression by means of micro array, for the analysis of EST, SNP, mutations
• Metabolic Networks
• Programs for genome comparison and phylogenetic analysis
• Implementation of dedicated programs for proteomic analysis
• Integrated platform for the study of proteomics and the identification of new proteins
• Programs for querying proteomic databases of data produced by mass spectrometry
• Programs for studying proteins-proteins and DNA-protein interactions
• Prediction of protein structures
• Molecular dynamics programs for drug development.
• GRID Computing and Supercomputing
  Development of a network between the main European resources based on GRID. In this way the programs of the main European centres will be available to registered clients with secure and automated procedures. A Supercomputing platform will be available for all industrial and academic organizations that seek large quantities of computing resources.
• Data Mining and scientific literature
  A specific platform will be available for the analysis of the enormous quantity of data obtained from genomic studies and scientific publications. This platform will allow new methodologies based on Data Mining for searching scientific information in on-line literature in biomedical and biotechnological documentation. In connection with the developed databases by the laboratory, the CILEA will release to all the research units the CDL services (CILEA Digital Library) in particular Medline, Protein Data Bank, ISI Web of Knowledge, Elsevier, American Chemical Society, Kluwer, Institute of Physics, Nature, Springer, Wiley, Oxford University Press, Blackwell, Chemical Abstracts, Beilstein CrossFire, etc.