Archive for février, 2010

IGS – Information Génomique et Structurale

Posted on février 8, 2010 by Commentaires fermés sur IGS – Information Génomique et Structurale

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URGI – Unité de Recherche Génomique Info

Posted on février 8, 2010 by Commentaires fermés sur URGI – Unité de Recherche Génomique Info

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Pasteur – Intégration et analyse Génomique

Posted on février 8, 2010 by Commentaires fermés sur Pasteur – Intégration et analyse Génomique

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PRABIG

Posted on février 8, 2010 by Commentaires fermés sur PRABIG

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PBIL – Lyon Gerland

Posted on février 8, 2010 by Commentaires fermés sur PBIL – Lyon Gerland

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PBIL Doua

Posted on février 8, 2010 by Commentaires fermés sur PBIL Doua

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IMGT (International Immunogenetic Information System)

Posted on février 8, 2010 by Commentaires fermés sur IMGT (International Immunogenetic Information System)

IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org, is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF), major histocompatibility complex superfamily (MhcSF) and related proteins of the immune system (RPI) of human and other vertebrate species, created in 1989 by Marie-Paule Lefranc (Université Montpellier 2, CNRS). IMGT, a European project since 1992, works in close collaboration with EBI. IMGT consists of sequence databases (IMGT/LIGM-DB, a comprehensive database of IG and TR from human and other vertebrates, with translation for fully annotated sequences, IMGT/MHC-DB, IMGT/PRIMER-DB), genome database (IMGT/GENE-DB), structure database (IMGT/3Dstructure-DB), and monoclonal antibodies database, Web resources and interactive tools. The IMGT Home page http://www.imgt.org (Montpellier, France) provides a common access to all Immunogenetics data.


web site : IMGT

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BioInfo-GenoToul

Posted on février 8, 2010 by Commentaires fermés sur BioInfo-GenoToul

The resources placed at the disposal of the scientific community are:

  • competences of a data processing and bioinformatic specialist  team
  • processing capacity of infrastucture of calculation
  • storage and provision capacity of data of the servers
  • accesses to the data banks generalist or specialized
  • software of the community bioinformatics

The missions of the bioinformatic platform are declined around 9 points:

  • To offer to the local community an adapted and powerful material and software infrastructure
  • To communicate on the evolution of the hardware, software, on the various actions undertaken on the platform
  • To train the users
  • To provide a support to the other local platforms
  • To provide a support bioinformatic to the priority scientific programs of biology and bioinformatic
  • To propose an animation around the bioinformatic platform
  • To place at the disposal of the working stations “framed” near the platform
  • To answer at the requests of expertise
  • To develop programs in dialogue with the local community and other Génopoles.

Link to the official site :

Bioinfo-GenoToul

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MIG – INRA

Posted on février 8, 2010 by Commentaires fermés sur MIG – INRA

MIG is a laboratory with a strong interdisciplinary vocation that groups together mathematicians,
computer scientists, physical chemists and biologists for the analysis of genomic data.

MIG has two main tasks:

  1. to develop methods and tools for analyzing genomic data in the following fields:
    • Genome and evolution
    • Automatic text analysis, data mining
    • System biology
  2. to lend support to INRA biologists involved in genomic researches:
  • by collaborating with biologists about bioinformatics aspects of genomic projects, MIG is involved in about 20 ANR and European projects
  • by making available a bioinformatics platform that provides access to:
  • 15 servers, a cluster of 250 processors (3 Tflops/s), 50 Tb of disk, 46 biological databases, more than 100 bioinformatics softwares

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MicroScope – Genoscope – Evry

Posted on février 8, 2010 by Commentaires fermés sur MicroScope – Genoscope – Evry

Located at Genoscope – the French National Sequencing Center – our bioinformatic team ( Laboratory of Bioinformatics Analysis in Genomic and Metabolim – LABGeM) has developed the MicroScope platform to support microbial genomes (re)annotation projects and comparative analysis. The platform is RIO/IBiSA labelled since 2006.

The system published in 2006 (Vallenet et al., Nucleic Acids Research 34: 53-65) and 2009 (Vallenet et al., Database 2009:bap021) is composed of three main components: An automatic pipeline which combines a set of syntactic and functional annotation tools to predict genes and their biological functions, Genomic and metabolic databases to store the primary data, the pipeline results and the human-curated annotations, and the metabolic networks, A graphical web interface, Magnifying Genome (MaGe) which is the component accessible to our users, via a secure or a public connection to our Web server. It allows to perform relevant expert annotation to efficiently explore and compare the set of prokaryotic genomes using sophisticated query interface, comparative genomics and metabolomics (phyloprofile), etc.

Services associated with MicroScope are: the complete analysis of the novel genome(s) and *Scope project delivery, a four-day training course (http://www.genoscope.cns.fr/agc/mage/training), updates and maintenance of the MicroScope projects and a continuing support and assistance to MaGe users. The access to the platform is available upon request, with priority given to bacterial genomes being sequenced at Genoscope.

Outline :

People :
5,4 ETP : 4 ingeniors (of which 3 permanent positions) + 1,4 researchers.

Computer resources:
Applications that support the MicroScope platform run concurrently on the Genoscope computing facility. It is currently made of a cluster of 330 cores and 200 To storage.

Hosted databases :
• Public : UniProt, COG, InterPro, KEGG, MetaCyc, ISFinder,…
• Own : PkGDB (Prokaryotic genome database), MicroCyc (PGDBs built with PathwayTool, P Karp, USA)

Annotation pipeline :
• Integrated tools : tRNA-scan, ReepSeek, Blast, COGnitor, InterProScan, Artemis, CGView, Pathologic (from Pathway Tool)
• Developed tools : AMIGene, MICheck, Syntonizer, RGPFinder, SNIPer,…

MaGe graphical interface :
• Expert annotation : Gene editor, keyword interface, …
• Comparative tools : phyloprofile/synteny, metabolic phyloprofile, LinePlot, …

Organisms :
Bacterial genomes (pathogens, environnemental organisms), ‘simple’ procaryotic metagenomes, archae, plasmid, phages.

Projects:
• 68 MicroScope projects : http://www.cns.fr/agc/mage
• ANR EVOGENO
• ANR SYMPA
• ANR METACOLI
• ANR PFTV MicroScope
• PCRD MICROME

Training:
Information on the MaGe training courses are available at (http://www.genoscope.cns.fr/agc/mage/training)

Web site : MicroScope

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