South Green

Infrastructure
Propriétaire
Effective storage
370.00 To
Cluster: cores number
1 184 cores
CPU/hours a year
3 000 000 H / an
Bioinformatic tools number
500
Users number (last year)
300
Servers description

Cluster de calcul Dell 24 noeuds

2 noeuds hypermem, un Dell, un Fujitsu

Serveurs bases de données, et serveurs web

Lames de virtualisation

Stockages scratch et NAS

 


Access conditions

Être partenaire d'un projet en lien avec les plantes méditerranéenes et tropicales.

No website documented
Annual visits:
14 293 an
Unique visits:
8 139 an
Quotes:
30
Latest update:
Not documented

GreenPhyl

Description

Base de données de génomique comparative pour l'analyse des familles de gènes chez les plantes et la détection d'ortologie

Access conditions

Publique

No website documented
Annual visits:
14 614 an
Unique visits:
5 177 an
Quotes:
6
Latest update:
Not documented

Banana Genome Hub

Description

base de données de référence sur la génomique et génétique du bananier

Access conditions

Publique

No website documented
Annual visits:
8 106 an
Unique visits:
2 764 an
Quotes:
10
Latest update:
Not documented

OryGenesDB

Description

Base de données pour l'exploration de la génétique inverse du riz

Access conditions

Publique

No website documented
Annual visits:
5 117 an
Unique visits:
3 347 an
Quotes:
42
Latest update:
Not documented

OryzaTagLine

Description

base de données de caractérisation phénotypique d'une collection de lignées d'insertion de T-DNA du riz

Access conditions

Publique et privée

No website documented
Annual visits:
10 688 an
Unique visits:
3 118 an
Quotes:
4
Latest update:
Not documented

TropGene

Description

Base de ressources génétiques et génomiques des plantes tropicales

Access conditions

Publique

Domains of activity
  • Biotechnology
  • Biology
Description of expertise domains

The South Green platform is a local network of scientists gathering Bioinformatics skills based on the Agropolis campus that hosts research institutes such as CIRAD, IRD, INRA, SupAgro, Bioversity international as well as the CGIAR consortium.

Based on this strong local community in the field of agriculture, food, biodiversity and environment, this network of national and international scope, develops bioinformatics applications and resources dedicated to genetics and genomics of tropical and Mediterranean plants. South Green relies on the computer technical platforms of its partner institutes.

The objectives of South Green are:

  • Promote the original tools from methods developed within the network,
  • Propose a single web portal for access to the tools developed by the network,
  • Promote exchange and collaborative developments within the network,
  • Promote interoperability developed within the network applications,
  • Provide training for biologists and bioinformaticians,
  • Ensure the maintenance and development, infrastructure and software applications via requests for funding in partnership,
  • Promote high quality process within the network (e.g. certifications),
  • Promote South Green visibility at the national and international level.
Keywords:
  • NGS data analysis
  • Sequence analysis
  • Structural bioinformatics
  • Evolution and phylogeny
  • Comparative genomics

Formation professionnelle

Trainees:
Not documented
Training time:
Not documented
Upcoming session :
04-10-2018

Analyse de données NGS dédiée à la génomique végétale en Afrique de l'Ouest

Description
Les avancées spectaculaires des technologies de séquençage de 2ème et 3ème génération sont une véritable révolution pour la recherche en science de la vie. Ces techniques permettent le séquençage en quelques semaines de génomes entiers d’organismes complexes, générant une explosion du volume de données génomiques. 
Toutefois l’analyse de telles masses d’informations nécessite des compétences en linux, en bioinformatique ainsi qu’une bonne connaissance et maîtrise de nombreux algorithmes et logiciels. La réalisation de ces analyses nécessite également l’accès à des ressources de calcul telles que des clusters de calcul. 
Le DP IAVAO et le LMI LAPSE en collaboration avec la plateforme bioinformatique South Green organisent, du 4 au 12 Octobre 2018, une formation en bioinformatique dédié à l’analyse de données de séquençage dont les objectifs sont de présenter les technologies de séquençage et les différentes analyses bioinformatiques pour exploiter au mieux cette masse de données afin de pouvoir réaliser des projets génomiques à grande échelle sur leurs modèles (plantes et pathogènes).

Prérequis

Aucun

Programme

  • Linux et lignes de commandes 
  • Initiation à l’utilisation du cluster du CERAAS 
  • Présentation des technologies de séquençages 
  • Appel de SNP sur des données WGS 
  • Post analyse de données de SNPs
  • Outils Genome Harvest 

Objectifs

Après la formation, les participants seront capables de :

  • se connecter à un cluster Linux
  • lancer des programmes/analyses bioinformatiques
  • définir les étapes pour analyser des données de séquençage
  • analyser des données de séquençage
  • utiliser des gestionnaires de workflow tel que Galaxy ou TOGGLe

Instructors

Access conditions
Not documented
Trainees:
Not documented
Training time:
Not documented
Upcoming session :
01-10-2018

Installing and Managing a High-Performance Computing (HPC) Cluster

Description

This course ran for 5 days covering all the concepts necessary to  install and manage a high-performance computing (HPC) cluster. During this course,  a HPC cluster were installed at CERAAS (Thiès, Sénégal)  by the participants, IT managers from western africa (IRD, ISRA, CERAAS).

Access conditions
Not documented
Trainees:
Not documented
Training time:
Not documented
Upcoming session :
23-04-2018

Metabarcoding analyses (using FROGS in Galaxy and Phyloseq)

Description
This course offers an introduction to metabarcoding analyses at two different levels/steps: bioinformatics with FROGS pipeline in the Galaxy environment, biostatistics with PhyloSeq R package. This includes preprocessing, clustering and OTU picking, taxonomic assignation, estimation of diversity, visualization of statistics results.

Prerequisites

Galaxy, R knowledge

Program

  • Introduction to metagenomics and metabarcoding
  • Pre-processing, Clustering, taxonomic affiliation (FROGS)
  • Handling and visualizing OTU table using PhyloSeq R package (PhyloSeq)

Learning objectives

  • Manipulate tools available for metabarcoding analysis
  • Study sample diversity by using NGS and post-NGS analysis tools
  • Visualize diversity metrics in metabarcoding approach​

Instructors

 

Access conditions
Not documented
Trainees:
Not documented
Training time:
Not documented
Upcoming session :
12-03-2018

Linux For Dummies

Description

 

This course offers an introduction to work with Linux. We will describe the Linux environment, the first linux commands so participants can start to utilize command-line tools and feel comfortable using bioinformatics softwares through a linux terminal.

Prerequisites

No experience required

Program

  • Connecting to a distant HPC
  • Navigating through a Unix file system
  • Creating and deleting files
  • Manipuling and filtering file text
  • Basics searching for text within a file

Learning objectives

After this course, participants should be able to:

  • Connect to a Unix / Linux system
  • Manipulate files and directories within the Linux system
  • Work with text files
  • Run programs from the command-line

Instructors

Access conditions
Not documented
Trainees:
Not documented
Training time:
Not documented
Upcoming session :
13-03-2018

Linux For Jedi

Description

This course offers to develop and enhance advanced Linux shell command line and scripting skills for the processing and analysis of NGS data. We will work on a HPC server and use linux powerful commands to allow to analyze big amount of biological data.

 

Prerequisites

Basic knowledge of Linux (Linux for dummies required)

Program

  • Connecting to a distant HPC
  • Manipuling text files
  • Complex searching for text in a file
  • Combining several commands
  • Writing simple shell scripts

Learning objectives

After this course, participants should be able to:

  • Manipulate and search within text files
  • Chain and combine commands
  • Perform the same actions on many files
  • Write a simple shell script

 

Instructors

Access conditions
Not documented
Trainees:
Not documented
Training time:
Not documented
Upcoming session :
02-10-2017

Survival Guide for Perl applied to Bioinformatics

Description

 

This course provides an introduction to programming using Perl and at the end of the training, participants could write simple Perl programs to handle biological data and to undertstand more complex Perl programs written by others.

Prerequisites

Basic knowledge of Linux (Linux for dummies required)

Program

  • Perl data structures (scalar,arrays, hashes)
  • Structure control ( loops)
  • Basic functions, and operators.
  • Writing and running your own program
  • Passing options and files to his own script.
  • Regular expressions

Learning objectives

  • Writing simple Perl programs to analyze data files
  • Understanding Perl programs written by others
  • Using Perl basic syntax and modules in their own script
  • Run programs from their script, parsing and extracting data from data files

Instructors

Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
Not documented
No upcoming session scheduled

Training courses in bioinformatics applied to Musa Genome

Description

18-22 Novembre 2013

Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
Not documented
No upcoming session scheduled

Formation galaxy

Description

Octobre 2013

Juin 2012

Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
Not documented
No upcoming session scheduled

Formation bioinformatique LMI LAPSE Dakar

Description

Novembre 2013

Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
Not documented
No upcoming session scheduled

Formation bioinformatique IRD Montpellier

Description

Septembre 2013 (25 personnes) et Octobre 2012 (32 personnes)

Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
Not documented
No upcoming session scheduled

Formation introduction à la bioinformatique, Dassa

Description

Juillet 2013

Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
Not documented
No upcoming session scheduled

Bioinformatics School, Sao Paulo

Description

21-26 novembre 2011

Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
Not documented
No upcoming session scheduled

Bioinformatique appliquée à l'analyse de séquences biologiques, Montpellier

Description

06-10 juin 2011

Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
Not documented
No upcoming session scheduled

Formation ARCAD SP1-SP4, Analyse de données de polymorphisme, Montpellier

Description

09-13 Mai 2011

Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
Not documented
No upcoming session scheduled

Bioinformatique appliquée, Analyse de séquences, Montpellier

Description

21-25 février 2011

Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
Not documented
No upcoming session scheduled

Encontro França-Brasil de BIoinformatica, Universidad Estadual de Santa Cruz (UESC)

Description

08-12 novembre 2010

Access conditions
Not documented
Trainees:
Not documented
Training time:
Not documented
Upcoming session :
16-03-2018

RNASeq analyses (using Galaxy and TOGGLe)

Description
This course offers an introduction to RNASeq analyses using two different workflow management systems: Galaxy and TOGGLe. This includes reference-based mapping, estimates of transcript levels, differential expression (DE) analyses, visualization of statistics results.

Prerequisites

Workflow management system (Galaxy, TOGGLe)

Program

  • Mapping of RNASeq against a transcriptome reference with kallisto (Galaxy)
  • Mapping of RNASeq against an annotated genome reference with TopHat (TOGGLe)
  • Differential expression analysis using EdgeR and DESeq2
  • Plots, clustering, co-expression network: degust, WGCNA

Learning objectives

  • Manipulate packages/tools available for searching DE genes
  • Think about different normalisation methods
  • Detect differentially expressed genes
  • Compare results between two approaches

Instructors

Access conditions
Not documented
Trainees:
Not documented
Training time:
Not documented
Upcoming session :
23-03-2018

Initiation to NGS Workflow Managers developed within the South Green Platform: Galaxy and TOGGLe

Description

This course introduces the 2 commonly used workflow managers in the South Green Bioformatics platform, both in a theoretical and practical way, with hands-on practice sessions. It will help you to quickly develop and run your own pipelines using these tools through an graphical user or command-line interface.

 

Prerequisites

Prior knowledge of workflow managers not necessary Basic knowledge of Linux (Linux for dummies required) - TOGGLe practical

Program

  • Why using a workflow manager to analyse data ?
  • How to perform an analysis ?
  • How to create your own workflow ?
  • How to execute it?
  • Use case

Learning objectives

  • Explaining what Workflow Managers are,
    in which way they differ from each other.
  • How you can use them in your research.
  • Creating your own workflow
  • Analysing your NGS data with Galaxy and TOGGLe

Instructors

Access conditions
Not documented
Trainees:
Not documented
Training time:
Not documented
Upcoming session :
15-03-2018

Introduction to High-performance computing

Description
This course offers an introduction on how to work with HPC Southgreen clusters. It is intended for new users, with the goals of improving user productivity and minimizing the obstacles. The HPC Southgreen cluster are presented, together with the tools to be able to use it. Module load notion, interactive usage and batch jobs submittions will be developped.

Prerequisites

Linux Basics

Program

  • Introduction to HPCs architecture
  • Discover Sun grid Engine (SGE)
  • Data Management on clusters
  • Interactive Usage
  • Submit batch jobs

Learning objectives

After this course, participants should be able to:

  • Use the HPC resources interactively
  • Manage data copies
  • Use module load
  • submit batch jobs

Instructors

Access conditions
Not documented

Formation universitaire

No website documented
Trainees:
Not documented
Training time:
Not documented
No upcoming session scheduled

SUPAGRO

Description

Février 2012, 2013 et 2014

Access conditions
Not documented
Users distribution
International
5 %
National
15 %
Regional
30 %
Local
50%
Explanation about this distribution:
Not documented
Platform's own projects

Not Documented

Collaborations
National projets

ANR MSD-MIND

ANR GNPAnnot: a community annotation system

ANR MusaTract: sequencing project of the banana genome

ANR CoffeaSeq: sequencing project of the coffee tree genome

International and European projects

CGIAR Research: Programmes TRB et GRISP

GLASS

IRIGIN

EURIGEN: Genotyping for the Conservation and Valorization of European Rice Germplasm

EURoot: Enhancing resource Uptake from Roots under stress in cereal crops

Projects with industry

GreenPhyl: Biodiversity, CIRAD, Syngenta

Collaboration projects not founded through an external organism
Not documented
Provision of services not founded through an external organism
Not documented
Animations (Workshops, Work-groups, seminars, conferences ... )

Contribution aux séminaires de l'IBC: http://www.ibc-montpellier.fr/events/seminars/plenary-sessions

Groupe de travail Galaxy-IFB: http://www.ifb-galaxy.org/index.html

Workshop on Crop Ontology and Phenotyping Data Interoperability (CIRAD Montpelllier, Avril 2014)

Workshop Semantic for Biodiversity dans le cadre de ECCB2013 (Montpellier, Mars 2013)

Internal publications

Droc, G., Lariviere, D., Guignon, V., Yahiaoui, N., This, D., Garsmeur, O., Dereeper, A., Hamelin, C., Argout, X., Dufayard, J.-F., Lengelle, J., Baurens, F.-C., Cenci, A., Pitollat, B., D'Hont, A., Ruiz, M., Rouard, M., Bocs, S. The Banana Genome Hub. Database (2013) doi:10.1093/database/bat035


Guignon V, Droc G, Alaux M, Baurens FC, Garsmeur O, Poiron C, Carver T, Rouard M, Bocs S (2012) Chado Controller: advanced annotation management with a community annotation system. Bioinformatics. doi:10.1093/bioinformatics/bts046


Hamelin C, Sempéré G, Jouffe V, Ruiz M. TropGeneDB, the multi-tropical crop information system updated and extended. Nucleic Acids Res. 2013;41(Database issue):D1172-5


Peralta M, Combes M-, Cenci A, Lashermes P, Dereeper A. SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species. International Journal of Plant Genomics. 2013;2013.


Wollbrett J, Larmande P, de Lamotte F, Ruiz M. Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases. BMC Bioinformatics. 2013;14:126.


Droc, G., Lariviere, D., Guignon, V., Yahiaoui, N., This, D., Garsmeur, O., Dereeper, A., Hamelin, C., Argout, X., Dufayard, J.-F., Lengelle, J., Baurens, F.-C., Cenci, A., Pitollat, B., D'Hont, A., Ruiz, M., Rouard, M., Bocs, S. The Banana Genome Hub. PAG XXII. San Diego; 2014.


Dereeper, A. et al. The Coffee Genome Hub. PAG XXII. San Diego; 2014.


Garsmeur O, Droc G, Woltinge D, Van-Oeveren J, Martin G, Harrison B, et al. Whole Genome Profiling to Generate a Core Physical Map of the Gene Rich Part of the Sugarcane Genome. San Diego; 2014.


Maillol V, Bacilieri R, Bocs S, Boursiquot J-, Carrier G, Dereeper A, et al. Role of Galaxy in a bioinformatic plant breeding platform. In: Galaxy Community Conference. Chicago; 2012.


Guignon V, Cenci A, Rouard M. Exchange your knowledge en plant gene families. International Biocuration Conference (ISB2014) 2014.


Lariviere D, Dufayard JF, Bocs S, This D. Integrative System For Gene Family Gathering and Analysis In A Context of Crops’ Stress Response Study. PAG XXII. San Diego; 2014.


Monat C, Tranchant-Dubreuil C, Lorieux M, Ghesquière A, Ruiz M, Sabot F. African Rices Genome Projects : GLASS and Irigin. PAG XXII. San Diego; 2014


Network, South Green The South Green Bioinformatics platform. PAG XXII. San Diego, 2014.


Dereeper, A., Bocs, S., Rouard, M., Guignon, V., Ravel, S., Tranchant-Dubreuil, C., ... & Droc, G. (2015). The coffee genome hub: a resource for coffee genomes. Nucleic acids research43(D1), D1028-D1035.

External publications

Carrier G, Le Cunff L, Dereeper A, Legrand D, Sabot F, Bouchez O, et al. Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L. PLoS ONE. 2012;7(3):e32973.


D’Hont A, Denoeud F, Aury JM., Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, et al. (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature, 10.1038/nature11241


Dussert S, Guerin C, Andersson M, Joët T, Tranbarger TJ, Pizot M, et al. Comparative transcriptome analysis of three oil palm fruit and seed tissues that differ in oil content and fatty acid composition. Plant Physiol. 2013;162(3):1337-58.


Frouin J, Filloux D, Taillebois J, Grenier C, Montes F, de Lamotte F, et al. Positional cloning of the rice male sterility gene ms-IR36, widely used in the inter-crossing phase of recurrent selection schemes. Molecular Breeding. 2013:1-13


Gébelin V, Leclercq J, Leclercq J, Argout X, Chaidamsari T, Hu S, et al. The small RNA profile in latex from Hevea brasiliensis trees is affected by tapping panel dryness. Tree Physiol. 2013;33(10):1084-98.


Hippolyte I, Jenny C, Gardes L, Bakry F, Rivallan R, Pomies V, et al. Foundation characteristics of edible Musa triploids revealed from allelic distribution of SSR markers. Ann Bot. 2012


Nabholz B, Sarah G, Sabot F, Ruiz M, Adam H, Nidelet S, et al. Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (O. glaberrima). Molecular Ecology. 2014


Pérez-Quintero AL, Rodriguez-R LM, Dereeper A, López C, Koebnik R, Szurek B, et al. An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains. PLoS ONE. 2013;8(7):e68464.


Ranwez V, Holtz Y, Sarah G, Ardisson M, Santoni S, Glémin S, et al. Disentangling homeologous contigs in allo-tetraploid assembly: application to durum wheat. BMC Bioinformatics. 2013;14(Suppl 15):S15


Wei F-, Droc G, Guiderdoni E, Hsing Y-. International Consortium of Rice Mutagenesis: resources and beyond. Rice (N Y). 2013;6(1):39.

Publications with the hosting laboratory
Cenci A, Guignon V, Roux N, Rouard M (2014) Genomic analysis of NAC transcription factors in banana (Musa acuminata) and definition of NAC orthologous groups for monocots and dicots. Plant Mol Biol. doi:10.1007/s11103-013-0169-2.

Combes M-, Dereeper A, Severac D, Bertrand B, Lashermes P. Contribution of subgenomes to the transcriptome and their intertwined regulation in the allopolyploid Coffea arabica grown at contrasted temperatures. New Phytol. 2013;200(1):251-60.


Coudert Y, Dievart A, Droc G, Gantet P. ASL/LBD phylogeny suggests that genetic mechanisms of root initiation downstream of auxin are distinct in lycophytes and euphyllophytes. Mol Biol Evol. 2013;30(3):569-72.


Courtois B, Audebert A, Dardou A, Roques S, Ghneim-Herrera T, Droc G, et al. Genome-wide association mapping of root traits in a japonica rice panel. PLoS ONE. 2013;8(11):e78037


Courtois B, Frouin J, Greco R, Bruschi G, Droc G, Hamelin C, et al. Genetic Diversity and Population Structure in a European Collection of Rice. Crop Sci.. 2012;52(4):1663-75.


Dereeper A, Guyot R, Tranchant-Dubreuil C, Anthony F, Argout X, de Bellis F, et al. BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution. Plant Mol Biol. 2013;83(3):177-89.


Duan C, Argout X, Gébelin V, Summo M, Dufayard JF, Leclercq J, et al. Identification of the Hevea brasiliensis AP2/ERF superfamily by RNA sequencing. BMC Genomics. 2013;14:30


Lacape J-, Claverie M, Vidal RO, Carazzolle MF, Guimarães Pereira GA, Ruiz M, et al. Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton. PLoS ONE. 2012;7(11):e48855


Lorieux M, Blein M, Lozano J, Bouniol M, Droc G, Dievart A, et al. In-depth molecular and phenotypic characterization in a rice insertion line library facilitates gene identification through reverse and forward genetics approaches. Plant Biotechnol J. 2012;10(5):555-68.


Mieulet D, Diévart A, Droc G, Lanau N, Guiderdoni E. Reverse genetics in rice using Tos17. Methods Mol Biol. 2013;1057:205-21


Sabot F. Tos17 rice element: incomplete but effective. Mob DNA. 2014;5(1):10.

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