1- Scientific context and project objectives

One of the latest advances in life sciences is the development of DNA biochips. These high-speed molecular biology tools were initially developed for global studies of the expression of an organism’s genes (transcriptome). Numerous other application programs have been developed, such as the specific detection of mutations in DNA sequences and the characterisation of microorganisms in environmental samples. The significant development of this new technology in biology laboratories requires the creation of an effective information system. The quantities of data to manage are considerable, for the development of a DNA biochip depends on the use of genome data (more than 100 Gigabases in international databases, still growing exponentially). It is then necessary to use processing in silico (algorithms developed in a laboratory) in order to design the biochip, analyse the processing results and process the information. Not only that, all of the experimental parameters must be archived (experimenter, biological sample, deposit plan, marking type, etc.). Lastly, the images produced must be stored without being compressed to avoid any loss of information and analysed to extract the information that is biologically relevant (data extraction, statistics, data classification, data search).

2- Project description

The purpose of this project is to create an information system for biologists on the design and analysis of different types of biochips. It will make it possible to keep all the information on biochip design and experiments and make this easier to analyse. Conservation and traceability in accordance with MIAME (Minimum Information About a Microarray Experiment) requirements are key (MIAME). Such an information system will make it easier to submit chip experiment results to public databases (type ArrayExpress). This is in fact required to publish the results of chips in different international reviews. This project will be based on the 2004-2007 dynamic multi-training plan on the genome and epigenetic control sponsored by Dr. Chantal Vaury, on which 6 research teams from the University of Auvergne and 6 teams from Blaise Pascal University are working. An application program software is currently being installed to extract biochip data (Genepix, Acuity). The effective information system for biochips targeted in the LifeGrid call for projects will be open to other research teams on the Clermont-Ferrand site who would like to develop the DNA biochip approach. This is particularly the case for the ERT CIDAM (Prof. Monique Alric), which hopes to study the bacterial diversity of the human intestine.

3- Public or controlled use

The system implemented will be for public use. It will be via secured access (users must register) and may not be duplicated to other platforms. The data generated will be the property of the laboratories and businesses having commissioned the research contracts.

4- Expected results

The benefits in terms of enhancement are evident through the research activities of the various partners. What’s more, the new algorithms developed as part of the team’s research work are undergoing APP (French Agency of Programme Protection) protection. A file has also been submitted for the Ministry’s call for projects entitled “National competition to assist the creation of innovative technology businesses”, an emerging category with Abdel Belkorchia as the project sponsor ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it : this email address is protected against spam robots. You have to activate Javascript to see it). Abdel is currently completing a thesis at the Aurillac University Technology Institute. Note that the Aurillac basin will be a partner in the development of the information system. A bioinformatics cluster has been installed at the Aurillac Institute and unique bioinformatics training programmes in France (two-year post-A level diploma, Vocational three-year degree) are administered in line with socio-economic needs. More generally, in the context of point 7.2 of the document describing the ex programme E-nnovegne and more precisely the creation of a biomedical resource centre, this programme is part of the more extensive medical research platform of the university hospital centre, the Jean Perrin Centre, the Blaise Pascal and Auvergne Universities and the French National Institute for Agricultural Research (INRA), comprising Inserm Units 384 and 484, the Inserm Clinical Investigation Centre (CIC), the Clinical Pharmacology Centre (CPC), the Pain Treatment and Assessment Centre (CETD), the Cancéropole, the National Reference Centre for Leucodystrophy Prevention, the Protist Biology Laboratory mixed research unit CNRS 6023, the small animal imagery platform and INRA’s metabolome platform. The purpose is to standardise and professionalise data exchange between the various research bodies, whether they be public or private.

LifeGrid, the regional information system