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Platform

Platform

The Plant Bioinformatics facility (PlantBioinfoPF) is hosted by URGI INRAE research unit. The platform belongs to the " Institut Français de Bioinformatique " (IFB) the french node of Elixir , the european network of bioinformatics platforms

This platform was labelled

- by INRAE CNOC commitee as a national strategic platform (  https://doi.org/10.15454/1.5572414581735654E12 )

- by GIS IBISA  (Groupement d'Intérêt Scientifique Infrastrutures en Biologie Sante et Agronomie).


PlantBioinfoPF services cover database design, software engineering, software hosting, data integration and training.

The PlantBioinfoPF activities (Information System and genome analyses) are closely related to URGI research activity (data integration, repeat annotation, genome structure and dynamics). On the one hand, the platform benefits from the research expertise (analysis and tools development) on the other hand it offers a strong support to our research activity with the resources and expertise of its staff (mainly engineers).
 
The platform develops and maintains a modular and interoperable information system ( GnpIS ) for plant and pest genomics to enable scientists to mine genomic and genetic data. GnpIS is accessible through a public web portal allowing to browse each data modules or by searching through all the data simultaneously using a quick search ('google like search') or advanced search (Biomart, Galaxy, Intermine) tools.
 
Some data are under restricted access in the frame of collaborating project before publication.
 
The platform has a strong expertise in developing  pipelines dedicated to genome analyses and particularly to annotate and study the role of transposable elements in genome dynamics and evolution.

The areas of competence and expertise of the platform members are mainly focused on:

  • Interface development (Java J2EE)
  • Development of analysis pipelines (Python)
  • Databases (PostgreSQL, MySQL)
  • NoSQL technologies (ElasticSearch, Solr)
  • Data integration (ETL Talend) of genomics and genetic data (genome annotation, RNA-Seq, polymorphism, Genome wide association studies, phenotype, genetic resources)
  • Genome analysis (structure and dynamics)
    • Repeat annotation (specifically transposable elements)
    • Gene Annotation (structural and functional)
    • RNA-Seq
    • Polymorphism analysis (SNP, structural variants)

The Plant Bioinformatics Facility has a  Data Management Plan (DOI :  10.15454/9HM5UI ).

See the General Terms of Use ( Conditions Générales d'Utilisation en français).

Update: 30 Aug 2021
Creation date: 27 May 2010