Biological Software and Databases


  HEADCAUDRON Bernard / caudron@pasteur.fr
  MEMBERSDr BOUIGE Philippe / DEVEAUD Éric / JOLY Nicolas / JONES Louis / JORGE Catherine
Dr LETONDAL Catherine / Dr MAUFRAIS Corinne / MÉNAGER Hervé / NÉRON Bertrand


  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 to place laboratory results online. The interfaces used to present the biological software are in full release.

The group takes part in teaching activities.

Software for biology:

The whole software available for biology is divided into 135 packages including about 700 programs. Installation, release and maintenance of this software are under our responsibility. The software has been installed on the new cluster. To give a friendly access to this software, we have constructed 380 web interfaces that help the researchers to start programs. This service is comparable to that one provided by the NCBI, the EBI or the SIB.

The project Mobyle that intends improving the current portal of bioinformatics analysis is at 90 % of its implementation. This activity employs 6 persons whose efforts contribute to finalize the cluster installation.

Biological databanks: (N. Joly)

Biological databases are updated with an automate that has been developed in the group, to search periodically the original banks and give access to local copies. The important data volume remained the most difficult constrain to manage. The space used on disks for the whole formats represents a total of 1700 Gb. Today 36 banks are available, including Embl, GenBank, RefSeq, Uniprot, Nrprot, Genpept, Pdb and Interpro.

Databases: (L. Jones, C. Jorge)

New databases have been added to present on the web the genomes Candida albicans, Aspergillus fumigatus, Mycobacterium smegmatis and a “biodiversity database”. A database has been developed for the Mouse Molecular Genetics Unit, to analyze, compare and label the X-chromosome regions around the mouse and bovine gene Xist.

A collaboration with the “Centre of resources in biostatistics, epidemiology and pharmaco-epidemiology” leads to the development and experimentation of data collection tools via secured databases and via the Internet adapted to the pharmaco-epidemiology research.

Bioinformatics training sessions: (C. Maufrais)

Training sessions of two weeks for the autonomous and critical use of biological data analysis software are given each year, they concern about thirty researchers, technicians or trainees. Sessions of bioinformatics initiation are part of the Genome Analysis course, the Cellular and Molecular Genetics course. In 2006, international courses have been taught in Morocco, Uruguay and Senegal.

Bioinformatics course: (C. Letondal, C. Maufrais, K. Schuerer, E. Deveaud)

This course aims at giving the biologists autonomy in the creation of software tools. After a theoretical part that introduces the informatics bases and implies about twenty lecturers in total (half of them belongs to the Institut Pasteur), 16 trainees could put into practice their knowledge to the completion of a bioinformatics project, a real problem, set either by the student laboratory or by one of the lecturers.



  Web Site

More informations on our web site


  Publications

Publications 2006 of the unit on Pasteur's references database




Activity Reports 2006 - Institut Pasteur
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