EMBnet.journal 16.1.23-24

The French EMBnet node: AGM 2010 report

Guy Perriere.png

Guy Perrière

Laboratoire de Biométrie et Biologie Évolutive, Université Claude Bernard, Lyon, Villeurbanne Cedex - France

The ReNaBi (Réseau National des plates-formes en Bioinformatique) is the French EMBnet node since 2008. Present head of ReNaBi is Claudine Médigue (Génoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex) and its delegate for EMBnet is Guy Perrière. This structure is a national network of 13 bioinformatics platforms officially commissioned by IBiSA a national French agency. IBiSA individually evaluates each platform every four years in order to determine if it still can be labelled as such. Among the requirements for a labelling are:

  • self-funding of the platform
  • dedicated personnel
  • regular formation and teaching activities
  • public on-line services offered

At this date, all the ReNaBi platforms met those requirements. Those platforms are also affiliated

with many research laboratories and universities all around France (in Bordeaux, Lyon, Marseille, Montpellier, Paris, etc.) and are routinely used to assist research, mainly at academic level.

Due to the fact ReNaBi gathers many sites having a broad range of activities, the computing services offered cover the whole spectrum of bioinformatics:

  • access to general or specialized sequence databases
  • alignment and similarity search programs
  • general sequence analysis package
  • biostatistics packages
  • molecular phylogeny programs
  • tools for proteomics and transcriptomics data analysis
  • tools for protein structure prediction and modelling
  • Next Generation Sequencing (NGS) specific programs and pipelines

As all the platforms are independent, it is not possible to give a global financial assessment. The ReNaBi itself receives a recurring funding of 50,000€ from IBiSA in order to support scientific animations such as workshops, conferences or thematic networks. As for the conferences supported, the main one is the French national conference in bioinformatics: JOBIM (Journées Ouvertes en Biologie Informatique et Mathématique). Among the different thematic networks, one is devoted to the use of grid computing and one to NGS users.

Again, due to its very own structure, it is difficult to give the complete list of machines available through ReNaBi. Standard equipment for a ReNaBi platform consist usually in a small computing cluster with about 100-500 cores, a mail server, one or two databases server(s), and a set (of variable size) of micro-computers. If we take the example of the PRABI (Pôle Rhône- Alpes de Bioinformatique), we have:

  • one Dell PowerEdge 2950 (2×quadcore CPU@2.66 GHz, 8 Gb RAM, 146 Gb disk)
  • one Dell PowerEdge 2950 (2×quadcore CPU@2.66 GHz, 8 Gb RAM, 600 Gb disk)
  • one Dell PowerEdge 2950 (2×quadcore CPU@2.66 GHz, 32 Gb RAM, 900 Gb disk)
  • three Sun Fire X4500 M2 (8×quadcore CPU@2.3 GHz, 64 Gb RAM, 3×145 Gb disk)
  • two Sun Fire X4500 M2 (8×bicore CPU@2.8 GHz, 64 Gb RAM, 3×145 Gb disk)
  • one Sun Fire V490 (4×bicore CPU@1.5 GHz, 16 Gb RAM, 2×146 Gb disk)
  • one Sun Fire 880 (8 CPU@900 MHz, 28 Gb RAM, 6×36 Gb disk)

This, for the sole genomic aspects covered by this platform. Indeed, all aspects related to protein structure prediction and biostatistics have also their own sets of dedicated computers.

Lastly, the ReNaBi is involved in the Elixir European initiative. Particularly, we plan to modify its legal status in order to apply for being a node in the forthcoming Elixir infrastructure.

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