Biological Software and Databases  


  HEADCAUDRON Bernard / caudron@pasteur.fr
  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 maintenance and access to a choice of international biological databanks. We provide the concept of scientific databases that enable the placement of laboratory results online. The interfaces used to present the biological software were redesigned. In 2007, the group took part in teaching activities.

Software for biology:

The whole software available for biology is divided into 135 packets including about 700 programs. Installation, release and maintenance of this software is the essential 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 250 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 3200 Go. Today 36 banks, including Embl, GenBank, RefSeq, Uniprot, Nrprot, Genpept, Pdb, Interpro are available.

Databases:

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 enable the interrogation of bibliographical references in a genome. It searches the base PubMed either under the gene name, or the description keywords or the gene function. The results are validated by the labeller. We administrate the database system ARPAS for the CRBIP.

Stastistics :

Acquisition of skills in statistics in match and functional analysis and hierarchical classification for a scientific collaboration.

Bioinformatics training sessions:

A training session is held each year, during 2 weeks by about thirty researchers, technicians or trainees for the autonomous and critical use of biological data analysis software. Initiation to bio-informatics is included in the Genome Analysis course and that of Cellular and Molecular Genetics.

Teaching :

The Bioinformatics course aims at giving the biologists autonomy in the creation of software tools. The theoretical part introduces the informatics bases that are used for the achievement of bioinformatics project training.

Keywords: bioinformatics, biological software, databases



  Publications

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



  Web Site

More informations on our web site




Activity Reports 2007 - Institut Pasteur
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