South Green Bioinformatics Platform

Last update: 24 January 2024

This platform is dedicated to bioinformatics applied to genetic and genomic studies on tropical and Mediterranean crops of agronomic interest. It is a network of scientists specialized in bioinformatics that releases new methods and offers resources for computing and data storage. It brings together teams from various research institutes in Montpellier (France), such as Bioversity International, CIRAD, INRAE, L'Institut Agro and IRD.

Objectives

The aims of the South Green platform are to:

  • Promote original tools derived from the methodological research of the network
  • Offer a unique web portal for use of the tools and databases developed by the network
  • Promote collaboration inside the network to develop tools and databases
  • Promote the interoperability of tools developed by the network
  • Propose training for biologists and bioinformaticians
  • Maintain and develop hardware and software by responding to calls for projects to procure funds
  • Promote a quality approach inside the network
  • Provide a link with IFB (Institut Français de Bioinformatique) and RENABI (Réseau national des plateformes bioinformatiques)

Expertise

The platform is in charge of:

  • Developing original methods and tools for the annotation of genomes and transcriptomes, for phylogenetics or for genotyping by sequencing studies developing web-based hubs by species (Banana genome hub, Coffee genome hub,..) where methods used for genome studies are grouped and interoperable
  • Organizing specialized training in bioinformatics (Galaxy, sequences analysis) and informatics (R, Perl, Linux sofwares)

Equipment and installations

Scientific computing

1328 computational cores are divided into:

  • 23 Calculation nodes: Haswell 2680v3: 24 physical cores 48 Logical cores 192 GB RAM
  • 1 node dedicated to R-Studio (and other software with a special function): Xeon E7-4820 32 physical cores, 1 TB RAM
  • 2 BigMem nodes for calculations requiring a lot of bad memory: 1 Xeon E7-4830 v3 node 48 physical cores 96 logical cores, 2.6 To RAM and 1 Xeon Gold 6136 node 48 physical cores 96 logical cores, 3 To RA

All these computational nodes are interconnected by Infiniband at 40 GB/sec.

Connection and computation management

  • 1 Login node: Haswell 2680 v3: 24 physical cores, 48 logical cores, 128 GB of RAM
  • 2 I/O  nodes: Intel E52609 v2,  4/8 cores, 64 GB of RAM

Scientific data storage

  • Temporary space: GPFS scratch: 350 To in RAID 6 without backup for temporary file writing. Beyond a certain time, the files are deleted.
  • Long-term storage: NAS: 815 To in RAID 6 with 11 SSD of 800 GB, with Snapshot security. Each user has 1 To. For larger volumes, a contract must be signed and payment made.
  • Virtualization Platform for website hosting and database management (VM Virtual Machine)
  • 20 virtual machines for web services and database management.

Attention to service reliability and user satisfaction led the ID team to formalize a quality procedure leading to AFNOR certification of the platform in March 2013 (ISO 9001: 2008). If you wish to use these resources, you will find the User’s Charter and necessary information at the SouthGreen site.

Last update: 24 January 2024