Bioinformatics platform of Versailles

The Info Genomics Research Unit (URGI, UR1164) is an INRAE research unit of the Plant Biology and Breeding department.
PlantBioinfoPF, hosted by URGI, supports various research activities on plants of agronomic and forestry interest for INRAE. The platform has joined forces with 3 other INRAE strategic bioinformatics platforms to form the BioinfOmics research infrastructure. It is part of the French Institute of Bioinformatics which is the French node of the European infrastructure: ELIXIR. The platform is part of the Saclay Plant Science network and the Biosphera Graduate School. PlantBioinfoPF is labeled a strategic platform by GIS IBiSA and is ISO-9001 certified.

Expertise

interface development (Java J2EE)
development of pipelines (Python)
databases (PostgreSQL, MySQL)
NoSQL technologies (ElasticSearch, SolR)
data integration (ETL Talend) in fields as diverse as genomics and genetics (genome annotation, RNA-Seq, polymorphism, association genetics, phenotype, genetic resources)
genome analysis (structure and dynamics)
- Analysis of polymorphism (SNP, structural variants)
- RNA-Seq
- gene annotation (structural and functional)
- annotation of repeats

Equipments

a computing cluster: 888 cores
6 dedicated servers (Web, databases: (PostGreSQL, MySQL), development of the GnpIS information system, NFS for disk management, backup management, virtual machines)
a server area with air conditioning and fire safety (UPS), storage units (NAS, DAS), backup robots, connectivity to the Internet network: 1 Gb/sec.

Main achievements

GnpIS : an information system for the genetics and genomics of plants and fungi.
REPET : detection, classification and annotation package for repeats (Transposable element, satellites...) https://urgi.versailles.inra.fr/Tools/REPET
S-MART : Toolbox for handling NGS data, especially RNA-Seq, ChiP-Seq data https://urgi.versailles.inra.fr/Tools/S-Mart
URGI Galaxy Portal : Online tool server, some of which were developed at URGI.
- tools from the S-Mart toolbox - https://urgi.versailles.inra.fr/Tools/Galaxy
- Workflows for differential expression analysis (RNA-seq) or polymorphism analysis (SNP, structural variants)