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WP7

Posted on octobre 7, 2010 by Commentaires fermés

Multiomics metadata infrastructure

Filed Under: Supplemental-material

ReNaBi-Grand-Ouest

Posted on février 2, 2010 by Commentaires fermés

The Grand-Ouest  platform is a federation of different sites of Brittany and Pays de la Loire.

The ReNaBi-GO platform is a bioinformatics platform created in 2002 during the foundation process of Biogenouest. This platform is located in three different cities: Rennes, Nantes and Roscoff. In Rennes, ReNaBi-GO is hosted by the INRIA/IRISA with the GenOuest platform. In Nantes, Inserm hosts ReNaBi-GO with the BiRD platform and in Roscoff it is hosted by the CNRS and UPMC (Université Pierre et Marie Curie) with the ABiMS platform.

20 people are presently working on the platform: 8 persons in Rennes, 4 in Nantes and 8 in Roscoff. These engineers operate the different tasks of a bioinformatics facility: animation, system and database administration, software development, user support, spreading and teaching activities. The Rennes facility is certified according to the ISO 9001: 2000 standard since May 2008, the Nantes facility is certified since October 2008.

Altogether, the 3 sites provide a coherent resource for the community. Each site is characterized by a strong specific technological partnership: Rennes is linked to an INRIA research team focusing on algorithms and bioinformatics applications acceleration, Nantes is linked to a transcriptomic platform and Roscoff is linked to a sequencing facility. On a thematic side, each site possesses its own specificity: Rennes covers many aspects with an emphasis on sequence analysis and specialized architectures for computing, Nantes is focusing mostly on health and transcriptomics, and Roscoff is focusing on Marine sciences. Combining these different expertises ReNaBi-GO covers a large spectrum of scientific fields in Marine Biology, Agronomy, Health and Medicine.

Services provided to the community:

Training

The platform proposes training sessions attended by a broad range of persons ranging from beginners to more accustomed users of bioinformatics tools. The subjects of the training sessions were programming languages, sequence analysis, motif discovery, phylogenetics and transcriptome analysis.

A complete catalog of the training can be seen on this site.

Research area

Projects

  • GRISBI
  • MobyleNet
  • DrMotifs
  • Metadata

Main scientific resources

Databases :

  • AphidBase
  • Germonline
  • CobaltDB
  • Rasta Bacteria
  • MadGene
  • Cyanorak
  • Crispi

Software :

  • BioMAJ
  • Logol
  • Stan
  • Wapam
  • PLAST: parallel local alignment search tool for database comparison
  • GASST :
  • Pygram

Computing resources

ReNaBi-GO provides a complete bioinformatics infrastructure for the community. This includes computing power, storage but also a comprehensive list of software and databanks dedicated to biological data analysis. These resources are accessible anonymously through the different web servers (genouest.org, madtools.org) or after authentication on the cluster. Accounts are free.

Site Cores Storage
GenOuest 256 60 Tb
ABiMS 328 80 Tb
BiRD  60 40 Tb

 

Real time monitoring of GenOuest’s computing resources. Realt time monitoring of ABiMS computing resources.


Filed Under: Platforms

GenOuest

Posted on décembre 6, 2009 by Commentaires fermés

Logo_BioInfoGenouest

GenOuest is a bioinformatics platform hosted by INRIA Rennes Bretagne-Atlantique center and IRISA. This platform acted primarily as a core facility and software tool provider for the analysis of genomic data generated by the different laboratories of Biogenouest (formerly OUEST-genopole®). The plate-forme is IBiSA labelled since 2009.

The platform provides a complete bioinformatics environment: computing power, storage, databanks and also a comprehensive list of software dedicated to sequence analysis. On a national level, the platform is developing an expertise in the field of pattern matching and pattern discovery tool. This activity results from a tight interaction between the GenOuest platform and the Symbiose research team (INRIA).

Among its activities GenOuest is involved in many development projects: user-oriented tools or technological transfer of new algorithms elaborated by Symbiose.
The platform is a member of the GRISBI platform, a joined project between six French bioinformatics platform aiming at the deployment of a bioinformatics grid. GenOuest is also a member of the MobyleNet project.

GenOuest is also providing a complete cursus of bioinformatics training: tools, methodologies, programming languages.

The platform is ISO9001:2000 certified since may 2008.

Outline :

People :

8 persons (2 on a permanent position)

Computer resources

2 clusters (200 cores) / 50 Tb storage

Hosted databases and specific public resources

  • Germonline
  • Mimas
  • Aphidbase
  • Autograph
  • Phymycodb
  • Rasta bacteria

Specific software

  • Stan
  • Wapam
  • Pygram
  • Logol
  • Protomata
  • Plast
  • iThos

Projects

  • GRISBI
  • MobyleNet
  • BioWIC

Training

The whole list of courses is available  here



Web site  : GenOuest

Logo_BioInfoGenouest

GenOuest is a bioinformatics platform hosted by INRIA Rennes Bretagne-Atlantique center and IRISA. This platform acted primarily as a core facility and software tool provider for the analysis of genomic data generated by the different laboratories of Biogenouest (formerly OUEST-genopole®). The plate-forme is IBiSA labelled since 2009.

The platform provides a complete bioinformatics environment: computing power, storage, databanks and also a comprehensive list of software dedicated to sequence analysis. On a national level, the platform is developing an expertise in the field of pattern matching and pattern discovery tool. This activity results from a tight interaction between the GenOuest platform and the Symbiose research team (INRIA).

Among its activities GenOuest is involved in many development projects: user-oriented tools or technological transfer of new algorithms elaborated by Symbiose.
The platform is a member of the GRISBI platform, a joined project between six French bioinformatics platform aiming at the deployment of a bioinformatics grid. GenOuest is also a member of the MobyleNet project.

GenOuest is also providing a complete cursus of bioinformatics training: tools, methodologies, programming languages.

The platform is ISO9001:2000 certified since may 2008.

Outline :

People :

8 persons (2 on a permanent position)

Computer resources

2 clusters (200 cores) / 50 Tb storage

Hosted databases and specific public resources

  • Germonline
  • Mimas
  • Aphidbase
  • Autograph
  • Phymycodb
  • Rasta bacteria

Specific software

  • Stan
  • Wapam
  • Pygram
  • Logol
  • Protomata
  • Plast
  • iThos

Projects

  • GRISBI
  • MobyleNet
  • BioWIC

Training

The whole list of courses is available  here



Web site  : GenOuest