ARCAD Bioinformatics – SP4

Journées ARCAD 2010

17 & 18 novembre 2010 –Amphithéâtre Agropolis International

WP1. Development of a collaborative

bioinformatics network

WP2. Module for data management

WP3. Module for diversity analyses

WP4. Module for sequence annotation

and orthologue gene prediction

ARCAD Bioinformatics – SP4

Development of a collaborative bioinformatics network

Data Integration team part of the Research Unit Plant Development and Genetic Improvement

Development of a collaborative bioinformatics network

Data Integration team part of the Research Unit Plant Development and Genetic Improvement ISEM

N GaltierE DouzeryV Ranwez

INRA AvignonJP Bouchet

IRDF Sabot

Etc.

Arcad Bioinformatics Partnership

UMR DAP

team ID

Arcad Bioinformatics

Regional

LIRMM

CINES

ISEM

UMR DIA-PC

UMR LGDP

SySDiag/ CNRS

IGH

ATGCMontpellierBioinformaticsPlatform

IRD

South GreenBioinformaticsPlatform

• Label IBISA – 25 keuros 2010 pour cluster• Renabi-Sud• Projet Grand Emprunt Infrastructures

Arcad Bioinformatics Partnership

UMR DAP

team ID

Arcad Bioinformatics

InternationalFrance

Regional

GCP program

Bioversity, IRRI, CIMMYT,ICRISAT,CIP, EBI, Embrapa

GMOD consortiumSanger Institute, UKBiotec, Thailand

URGI, UMR LIPM, Genoscope,CNG,GenoToul, LABRI

LIRMM

CINES

ISEM

UMR DIA-PC

UMR LGDP

SySDiag/ CNRS

IGH

ATGCMontpellierBioinformaticsPlatform

IRD

South GreenBioinformaticsPlatform

Resources

208 Nehalem cores computer cluster, a low latency Infiniband network, and a 16 To storage capacity.

http://southgreen.cirad.fr/

TropGENE Version 2.0

http://tropgenedb.cirad.fr/

TropGENE-DB, a multi-tropical crop information system.Ruiz M, Rouard M, Raboin LM, Lartaud M, Lagoda P, Courtois B.Nucleic Acids Res. 2004 Jan

Chantal Hamelin

Manuel Ruiz

http://tropgenedb.cirad.fr/

http://orygenesdb.cirad.fr/tools.html/

Gaëtan Droc

OryGenesDB: a database for rice reverse genetics.Droc G, Ruiz M, Larmande P, Pereira A, Piffanelli P, Morel JB, Dievart A, Courtois B, Guiderdoni E, Périn C.Nucleic Acids Res. 2006 Jan

http://orygenesdb.cirad.fr/tools.htmlhttp://gohelle.cirad.fr:8080/tropgene/JSP/index.jsp

Orylink

OryGenesDB 2008 update: database interoperability for functional genomics of rice.Droc G, Périn C, Fromentin S, Larmande P.Nucleic Acids Res. 2009 Jan

Gaëtan Droc

Pierre Larmande

• Funded by the French National Research Agency ANR (2008-2010)

• CIRAD, Bioversity & INRA

• Community annotation system (CAS) of structural and functional annotation

• Automatic predictions and manual curations of genes and transposable elements

• Based on GMOD components

Stéphanie Sidibe Bocs

v2.0

•16 plant species

•13.000 gene families•587.000 genes

Phylogenomics of plant genomes:a methodology for genome-wide searches for orthologs in plants.Conte MG, Gaillard S, Droc G, Perin C.BMC Genomics. 2008

GreenPhylDB: a database for plant comparative genomics.Conte MG, Gaillard S, Lanau N, Rouard M, Périn C.Nucleic Acids Res. 2008

Matthieu Conte

Mathieu Rouard

Xavier Argout

SNIPlay

Alexis Dereeper

A web-based tool for SNP and polymorphism analysis. From sequencing traces, alignment or allelic data given as input, it detects SNP and insertion/deletion events, and sends sequences and allelic data to an integrative pipeline (haplotype reconstruction, haplotype network, LD, diversity)

http://gendiversity.cirad.fr/Home

Cartes génétiquesCartes physiques

Études génotypiques

Marqueurs Individus

Marqueurs

Annotations génomiques

A

E

C

D

B

Données passeportDonnées de germplasm

Données géographiques

Individus

…

(CMap, TropGENE,Gramene)

(DIVAGIS)(OrygenesDB, Chado, GNPAnnot)

(SINGER, TAIR, ICIS,GCP Central Registry)

Études de diversité génétique

(TropGENE, Gramene)

Web Portal

Private and public access

Data accessWeb Portal

Genomics annotation

Markers, maps, phenotypes, QTL

External data : passport, GIS, diversity studies

Phylogenomics annotation

Transcriptomics annotation

SNPannotation

Galaxy

Data analyses

Generic workflows

High power computing

Transcriptomics NGS data

New tools

High power computing

GenTic2

GenDiversity

Web connexion

to HPC

CPU

Web Queries

Databases

Web Services

Toolbox

NGS analyses

Phylogenomic analyses

From the workplan to the real world

• Three bioinformatics engineers were recruited

• Regular meeting with biologists, writing documents (User

Story) in order to precisely define the user’s needs

• Test of several softwares, parameters and analysis

methods for the treatment of Next Generation

Sequencing data. These technologies are evolving

rapidly. Consequently, this part is a long and difficult task

which needs many interactions with collaborators

• Development of informatics components for Web

connection to High Power Computing facilities, for

automatic Web Interfaces generation, and for connection

to external databases.

Communications

• Sarah, G et al., 2nd International Workshop on Next Generation

Sequencing (NGS) Data Analysis,1 – 3 November 2010, ICRISAT,

Hyderabad, AP, India

• Ruiz, M et al., Encontro Brasil/França de Bioinformática, 08 - 12

november 2010, Ilheus, Brazil

Main achievements / Perpectives

for 2011

• Achievements

• South Green Bioinformatics platform is a component of

the national Renabi network (GIS IBISA)• First analyses of SP1 data (Medicago sativa, tomato,

rice) : assembling of 454 and Solexa data, cleaning,

SNP detection.

• Perspectives

• Working integrated modules for diversity analyses and

comparative genomics

• Web private access to the first ArCad data

• PlantNet

Thank you for your attention