Platform

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

The platform activities (Information System and genome analyses) are closely related to URGI research activity (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).
 
PlantBioinfoPF develops and maintains an information system ( GnpIS ) for plant genomics to enable scientists to mine genomic and genetic data. GnpIS is accessible through a public web portal .
 
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)
• Data integration (ETL Talend) of genomics and genetic data (genome annotation, polymorphism, Genome wide association studies, phenotype, genetic resources)
• Genome analysis (structure and dynamics)
  • Repeat annotation (specifically transposable elements)
  • Gene Annotation (structural and functional)

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).