Projects

Bioinformatics (Workpackage 2) : 3 partners : UMR Génétique Quantitativ Evolution - Le Moulon - (leader), URGI, BGA)

AMAIZING will produce and manipulate very large bodies of heterogeneous data including million of sequence reads (WP3), genotyping (WP4) and phenotyping data points (WP5).

These data will have to be conveniently stored, pre-processed and made available to the partners of the project and to the international community.

One main goal of WP2 is to provide partners bioinformatics and Information Technology (IT) expertise, hardware services, scientific programming, database management, scientific software and database training.

The project Information System will be based on a set of distributed and existing databases : GnpIS, ThaliaDB and an analysis tool Biomercator, that will be improved to take into account Amaizing User needs.

Outputs :

• A unique breeder and geneticist oriented web portal including interfaces for data access report about data content tools for data analysis
• Databases populated with datasets from the project or other public providers
• Adapted softwar e for high-memory or high-CPU requiring computation

Contacts:

• WP2 Leader: WP2, Johann Joets, from GQE-Le moulon
• 2.4 : Task Leader : Databases access and data analysis tools: Delphine Steinbach, INRA URGI, new position at GQE-Le moulon since 1 rst September 2015
• 2.3 Task Leader and co-leader: Data management : Nathalie Rivière, BGA (Biogemma) and Cyril Pommier INRA URGI since october 2015

News:

• October 2015: 
  • Presentation of the new developments and new data at the general assembly meeting in Pau (WP2: talk)
  • Add new tracks on Jbrowse B73: structural variants (F2) from WP3 (J. Joets & al).
  • Add genetic resources, add phenotyping data from WP4 (B. Gouesnard & al).
• September 2015: 
  • Delphine Steinbach left INRA URGI, to have new position and new missions at INRA GQE-le Moulon. She continues her missions on AmaiZing project on the lead of the 2.4 task (Tools development). Her work at URGI on 2.3 is transferred to Cyril Pommier at URGI. Cyril takes also since the 23 rd october the co-leader ship of task 2.3 (Data management).
• June 2015: 
  • Training session (Webinar using a virtual classroom of INRA e-learning platform) on GnpIS : new functionalities for the Association query form, open to partners. slides and video were made available to partners. Contact Delphine for more details.
• June-July 2014 : 
  • Training session event on GnpIS tool open to partners organized at UMR GQE- Le Moulon, Gif sur Yvette
• October 2014: 
  • Setting of a new tool : Jbrowse containing SNPs and RNASeq data generated by the project (WP6, WP3)
  • Setting of a new functionality in GnpIS: RNAseq meta-data and files are now available in GnpIS portal (module Sequence)
• October 2013 - Second annual meeting in Clermont-Ferrand
• November 2012 - 1st annual meeting in Montpellier
• November 2011 - Kick-off meeting at INRA Versailles

Human ressources: non permanent positions for bioinformatics development or/and data integration tasks

• one CDD 24 months URGI: Mathieu Labernardière in replacement of Sandrine Nsique-Meilo
• one CDD 18 months Biomercator: Lydia Haît-Braham
• one CDD on ThaliaDB: Guy-Ross Assoumou (18 months)

Perspectives: 2015 - 2017

• Continue data integration according to their availability in WPs
  • High throughput genotyping data : 50K, 600K, GBS
  • GWAS data
  • New variants mapped on the genome, pan-genome
  • Genomic selection data
  • Methylation data
• Finish the development of the new query form in GnpIS to query on gene expression : 2015-2016

• For information on the data submission process, please contact WP2 task leaders: 2.3 and 2.4.