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All phases

Genoplante phase I, II, ANR 2005 Bioinformatics

Three main projects were funded sequentially by the Genoplante programme and the "ANR Genoplante":

  • BI0076 (2000-2003)
  • M2 (2004-2005)
  • BIEP (2005-2007)

They were co-coordinated by both private and public Genoplante bioinformatics platforms respectively. Partners in these projects were both public institute (EPST, EPIC) and private companies as Biogemma or Bayer CropSciences.

URGI contact and co-coordinator for Public partners: Delphine Steinbach .

 

Results

These bioinformatics projects leaded to the development of a centralized generic genomic information system composed of different database modules GnpIS and tools, and to the construction of interoperability between the databases.

All the data produced by the projects leaded by biologists in the frame of the Genoplante phase I, phase II were integrated into this information system and are available to query according to the name of projects or via multiples types of queries depending on the type of data requested.

Some partners were dedicated to the submission of curated data to the platform: CIRAD for rice, INRA ASP Clermont-Ferrand for Wheat, INRA Evry/Versailles and INRA URGV Evry for Arabidopsis and rape data,INRA Moulon for maize mapping data.

Some partners were involved in the development of the databases interfaces such as mapping, transcriptomic and polymorphism databases. Working groups were created involving both the platform developers and biologist partners to help the specifications, analysis phases, software conceptions and interfaces tests and deployments.

URGI was also involved as partner in ANR Grape projects (Grape Sequencing project and CoreGrapeGen trilateral project). Our contribution was to manage, link and display genomic and genetic data produced by the projects. For example, the CMap tool was used to show links between the Grape genetic map, physical map and genome (http://urgi.versailles.inra.fr/cmap ). See Projects or Species: Vitis for details.

URGI contact for Vitis: Nathalie Choisne .

 

ANR Bioinformatics 2007

In 2007, a new collaborative project named GnpAnnot was accepted in the frame of the ANR Genoplante call 2007, coordinated by CIRAD and INRA URGI, BIOGER-CPP and BIO3P as main partners. The goal of this project is the development of a transversal structural and functional annotation platform, which allows users:

  • to annotate automatically and manually
  • to browse genome
  • to perform genome comparative analysis

URGI contact for GnpAnnot: Michael Alaux and Joelle Amselem .

This platform will be used for sequencing projects of different species of interest: banana and sugar cane (CIRAD), wheat and grape (INRA URGI), fungal genomes (INRA URGI/BIOGER, management at URGI) and insects (IRISA / INRA-BIO3P).

In 2007, a second ANR Genoplante project GnpInteGr was funded for one year to build a collaborative development environment. It will allow to improve project support through training and web servers.

 

ANR 2005, ANR 2006 generic and targeted projects

A special grant from Genoplante was given for data management and database loading for ANR 2005 and 2006 projects. It started in October 2007. For data submission concerning these projects, please see our Web private site ( Submission part) to have a look at the data submission templates and contact us at urgi-contact[at]versailles.inra.fr.

Daphné verdelet at URGI, was in charge of data integration concerning these projects until 2009.

URGI contact and coordinator : Delphine Steinbach .

 

ANR 2007 bioinformatics project:

A new project was accepted at ANR Call 2007, to continue the development of GnpIS information system and to build an interoperability between the databases modules : ANR GnpInteGR fundings. See Projects/own projects for GnpIS-Interop project detail.

This project leaded to the development of GnpIS quick search and advanced search tools on GnpIS URGI Web portal .

URGI contact and project coordinator: Delphine Steinbach .

Update: 12 Aug 2015
Creation date: 01 Apr 2010
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