Biological Software and Databases  

  MEMBERSDr BOUIGE Philippe / BOUSSIN Marie-Christine / DEMEY Sylvain / DEVEAUD Éric / JOLY Nicolas / JONES Louis / Dr LETONDAL Catherine / Dr MAUFRAIS Corinne / MÉNAGER Hervé / NÉRON Bertrand / QUEVILLON Emmanuel / RÉMY Blandine

  Annual Report

The “Biological Software and Databases” Group is in charge of the installation, maintenance and interfacing of biological software for researchers, as well as the release to a choice of international biological databanks. We ensure the concept of scientific databases that enable the placement of laboratory results online. The new interfaces of presentation of biological software operate since January 2008.

Software for biology:

The whole software available for biology is divided into 150 packets including about 750 programs. Installation, release and maintenance of this software are the main part of our activities. The software is installed on a new cluster updated during the year 2006. To give friendly access to this software, we have constructed 240 Web interfaces that help the researchers to start programs. The project Mobyle enables us to achieve a friendly portal sharing all our bioinformatics analysis software. This portal is available to the campus and outside, and is comparable to the services provided by the NCBI, the EBI or the SIB to the researchers worldwide.

Biological databanks:

Biological databanks are updated with an automate developed here. It periodically searches the original banks and gives access to local copies. The important data volume remains the most difficult constraint to manage. The space used on disks for the whole formats represents 4 TB. Today 34 banks, including Embl, GenBank, RefSeq, Uniprot, Nrprot, Genpept, Pdb, Interpro are available.


New features were added to the server Genolist : the application “Find Target” searches for the presence or absence of genes of reference in one or several genomes. A tool “Bibliolist” was developed to update and validate the bibliography to insert in GenoList. To put bibliographic references into a genome, BiblioList searches the base PubMed either under the gene name, or the description keywords or the gene function. The results are validated by the annotator. It is possible to use the tool “BiblioList” for any other databases of organisms that administrate the bibliography.

We maintain the database system ARPAS for the CRBIP. This system is used by 22 collections of organisms at the Campus.


The acquisition of skills in statistics for multiple correspondence analysis, functional analysis and hierarchical classification enabled a scientific collaboration with the Yersinia Research Unit and resulted in a publication.

Bioinformatics training courses:

Sessions of two weeks are run per year for the autonomous and critical use of biological data analysis software. The students concerned are about of thirty researchers, technicians or trainees. Initiation to bio-informatics is included in the Genome Analysis course and in the Cellular and Molecular Genetics course.

Work group “High-Throughput Sequencing”:

In June 2008, we have set up with the bioinformatics teams of the platforms “Genomics”, “DNA Micro-arrays” and “Genome Analysis and Integration” a work group to install and test the data analysis software required by this technology. Such a multi-disciplinary group increases the efficiency and shortens the delay to answer the software demands of biologists involved in this field.

Keywords: bioinformatics, biological software, databases


d'Enfert C, Goyard S, Rodriguez-Arnaveilhe S, Frangeul L, Jones L, Tekaia F, Bader O, Albrecht A, Castillo L, Dominguez A, Ernst JF, Fradin C, Gaillardin C, Garcia-Sanchez S, de Groot P, Hube B, Klis FM, Krishnamurthy S, Kunze D, Lopez MC, Mavor A, Martin N, Moszer I, Onesime D, Perez Martin J, Sentandreu R, Valentin E, Brown AJ. 2005. CandidaDB: a genome database for Candida albicans pathogenomics. Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D353-7. PMID: 15608215

Néron B, Tufféry P, Letondal C. 2005. Mobyle : a Web portal framework for bioinformatics analyses. Communication and poster presented at NETTAB, October 2005 - Naples, Italy.

Stinear TP, Seemann T, Pidot S, Frigui W, Reysset G, Garnier T, Meurice G, Simon D, Bouchier C, Ma L, Tichit M, Porter JL, Ryan J, Johnson PD, Davies JK, Jenkin GA, Small PL, Jones LM, Tekaia F, Laval F, Daffe M, Parkhill J, Cole ST. 2007. Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer. Genome Res. 17(2):192-200. PMID: 17210928

Tabard A, Mackay WE, Roussel N, Letondal C. 2007. PageLinker: integrating contextual bookmarks within a browser. in Proceedings of the CHI 2007 conference on Human factors in computing systems : 337-346, 28 April - 3 May 2007 - San Jose, California, USA. ISBN:978-1-59593-593-9

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Activity Reports 2009 - Institut Pasteur
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