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Paris, February 1, 2005

Embrace : standardizing access to bioinformatic data in Europe

Embrace is a European bioinformatics network project that begins on February 1. It has received funding of 8.28 million euros from the European Commission for five years and involves 16 partners from 11 countries, including three CNRS teams (1). Its goal is to standardize access to the vast quantities data from genome projects and their study methods so that researchers can consult it and use it easily.

Since the time of the first sequencing of the human genome in 2001, biologists have been generating more and more bioinformatic data. To store it, they have created more and more databases, but there is as yet no standardization in this field. As a result, the data is not always presented in the same way. Furthermore, the access protocols are always different, as are the algorithms for handling the unprocessed data based on the latest progress in molecular biology which allow us to identify genes and predict their function. Bioinformatics is not limited to the design of computer systems for storing biological data: it also involves analyzing this data.

 

Europe decided to finance Embrace to address researchers' needs for storage and processing of biological data. This network, to which CNRS belongs (1), will allow researchers to pool their data themselves, in a standardized form, and to consult their colleagues' data. Through Embrace they will be able to work on this data using the software provided.

 

Embrace will use a “grid technology” by which a large number of geographically separated computers work in a network to provide substantial storage and calculation capacity. A grid operates like an electricity network that provides current through a standard outlet: the users do not need to know how electricity is generated, nor how it gets to their sockets. They just need to be able to plug in their appliances. In the same way, with Embrace, users of bioinformatic data will connect to the web site of the grid and will be guided step by step. They will have easy access to the latest versions of the data. The suppliers, who will be fewer than the users, will handle the upgrading of the grid's standards and functions.

 

From 2001 to 2004, the European Datagrid project demonstrated the feasibility of grid technology for the pooling of computer resources. Its extension, Egee, now provides the scientific community with a set of 10,000 processors at more than 80 sites in Europe. Grid software adapted to bioinformatic issues was also developed within the framework of these two projects.  CNRS developed the GPSA gateway, dedicated to the analysis of protein sequences, and it was also involved in several French projects including Gripps (to seek patterns in protein sequences) and Rugbi (to predict the structure of proteins). Embrace will benefit from the experience gained in the development of this software. 

 

The 16 partners in the Embrace project are divided into five groups, each one handling a particular task: the European Bioinformatics Institute (EBI), the coordinator of Embrace, will integrate the databases and reference algorithms in Embrace so that biologists can start using them immediately. These will include the American database Medline and the Swiss Swissprot database for example. CNRS is responsible for selection and for the technology watch; it will make sure that Embrace benefits from the latest developments in terms of grids and that the options chosen are the ones best suited to bioinformatics. The University of Uppsala, in Sweden, will test Embrace's response to some “typical questions”, for instance: What genes favor the appearance of cancers? Does the hepatitis C virus become more dangerous in the course of its mutations? The University of Nijmegen in the Netherlands will coordinate promotion of the grid with biology researchers and will train them to integrate their data.

 

(1) The three participating teams are the Institute of Protein Biology and Chemistry (IBCP) of Lyons, the Calculation Center of Lyons and the Particle Physics Laboratory (LPC) of Clermont-Ferrand.

Contacts:

Researcher Contacts:
Christophe Blanchet (IBCP)
Telephone: 04 72 72 26 71
E-mail: christophe.blanchet@ibcp.fr
Vincent Breton (LCP)
Telephone: 04 73 40 72 19
E-mail: breton@clermont-in2p3.fr

Press contact:
Claire Le Poulennec
Telephone: 01 44 96 49 88, E-mail: claire.le-poulennec@cnrs-dir.fr

Life Sciences Department Contact:
Nathalie Gibelin
Telephone: 01 44 96 40 28, E-mail: nathalie.gibelin@cnrs-dir.fr

National Institute of Nuclear Physics and Particle Physics Contact:
Christina Cantrel
Telephone: 01 44 96 47 60, E-mail: Ccantrel@admin.in2p3.fr


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