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Plateforme Bioinformatique

Introduction

The Plateforme Bioinformatique (PB-IBENS) is a facility of the Institut de Biologie de l’ENS (IBENS). It defines, develops and deploys the hardware and software resources that meet the specific bioinformatics needs of researchers. It is responsible for the maintenance and deployment of the computing cluster “BioClust” accessible to all partners of the LABEX Memolife (IBENS, ESPCI, Collège de France). PB-IBENS also maintains and supports online tools (web and database servers) developed by the IBENS teams, some of which are labeled by the European Infrastructure Elixir. It is involved in bioinformatics training at the ENS, organises seminars and participates to external courses. PB-IBENS benefits from the CBC scientific environment in order to direct users towards specialists who can answer their technical questions related to their specific analyses (Single-Cell, RNASeq, Bioimaging, evolution, etc.).

Services

Computing cluster: BioClust

Bioclust is the computing cluster of PB-IBENS, accessible to all LABEX MEMOLIFE members. Currently, it comprises 74 nodes for 2138 virtual cores and 7.2Tb of memory. Users execute jobs through the HT-Condor scheduler, to run tools from the large range of available software already available (more than 200 packages and tools dedicated to bioinformatics).

If you are member of IBENS or Memolife Lab partners, you can ask for an account to admin-bioclust chez bio.ens.psl.eu to access this computing facility.

Web and database servers

The PB-IBENS hosts web servers and tools freely accessible to the international community. Two are labeled by Elixir and are part of the ELIXIR-FR node (Institut Français de Bioinformatique):

  • RSAT: Regulatory Sequence Analysis Tools (RSAT) is a software suite combining specialized tools for the detection of regulatory signals in non-coding sequences. It includes tools for sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. The RSAT code is maintained and further developed by PB-IBENS. For information on downloading the code, please contact rsat-contact. The specific Rsat Protist instance is hosted and maintained by the PB-IBENS.
  • GENOMICUS: Genomicus is a database and a web server that integrates comparative genome data and ancestral genome reconstruction in a fast and intuitive way. It enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversally across different species, and chronologically along evolutionary time. A user-friendly graphical interface allows syntenic comparisons and gene order alignments between pairs of genomes or multiple genomes at different scales: local gene order, karyotypes, matrix plots, etc. Different phylums such as Vertebrates, Plants, Fungi, Metazoa (as per Ensembl Genomes) are represented and regularly updated, as well as specific versions on Tunicates, Fish and Amphioxus.


Training

The PB-IBENS is involved in all the bioinformatic training hosted by the Ecole normale supérieure. From Licence to Master2, bioinformatic courses are opened to PSL students and accessible to PSL staff members (PhD student, PostDoc, researcher or engineers) according to availability.