This project focuses on the integration between the BioDataRing and CeSGO environments. The purpose is to establish a connection data producing facilities and data analysis facilities.
The BioDataRing infrastructure will be used for data transfer.
Funded by : Région Bretagne
GenOuest is co-leading this project with IFB with INIST as a key partner.
The objective is to make the Data Management Plans (DMPs) produced with OPIDoR readable, not only by humans, but also by machines. This will allow to automate the configuration of computing environments thanks to DMP information. Our aim is to simplify the monitoring of storage and data management, but also to support the production of good quality metadata in order to increase the degree of compliance with FAIR principles.
Funded by : ANR
GenOuest is involved in Elixir-CONVERGE, a project to help standardise life science data management across Europe. To achieve this standardisation, the project will develop a data management toolkit for life scientists. More about CONVERGE.
Funded by : European Commission
CPER CeSGO, 2015-2019
Adopting a vision centered on the scientific project lifecycle and the scientific data lifecycle, CeSGO is developing an e-Science platform associated with a virtual research environment (VRE) dedicated initially to Life Sciences communities. However, due to its generic approach, CeSGO’s VRE is usable by any research community with minor adaptations.
Funded by : Europe, Inria, Région Bretagne
BioMAJ (BIOlogie Mise A Jour) is a workflow engine dedicated to data synchronization and processing. BioMAJ automates the update cycle and the supervision of the locally mirrored databank repository.
The initial purpose of this tool was to ease the work of people managing bioinformatics facilities and helping them to make datasets widely available for every user.
A new development phase has started thanks to the IFB who provides support for 2 years. Chloé Riou is in charge of the developments.
Funded by : Institut Français de Bioinformatique (IFB)
BioDataManager / Genodock , 2017-2019
The increase in the generation of data in biology as well as their heterogeneity are serious problems which, if they are not treated, can threaten the purpose of research projects.
To lay the foundations for effective management of scientific data, it is necessary to associate a dual approach: a technological know-how which allows to manage and manipulate large sets of heterogeneous data , an organization promoting the use of good practices management of such data. The objectives will be to promote effective management of the data on the GenOuest infrastructure in order to provide an environment that will help users managing their data.
In the second part of the project, a tool for genomic data provisioning with Docker containers will be developed.
Funded by : Région Bretagne
BioContainers is an open source and community-driven framework which provides system-agnostic executable environments for bioinformatics software. BioContainers framework allows software to be installed and executed under an isolated and controllable environment. Olivier Sallou and Renaud Jullien are working on Biocontainers.
Funded by : Elixir Excelerate
PIA France bioinformatique – institut français de bioinformatique (IFB)
GenOuest is a member of the Institut Français de Bioinformatique (IFB). GenOuest people are involved in many task forces and groups of IFB.
GenOuest is an active participant of the Biosphere task force.
PIA France Génomique
GenOuest is a bioinformatics platform of France Génomique. Several studies focusing on read assembly and read mapping were carried out by GenOuest.
The MapDeCoDe tool was developped and is hosted by GenOuest.
PIA Rapsodyn, 2012-2019
Optimisation of the RAPeSeed Oil content anD Yield under low Nitrogen input: improving breeding of adapted varieties using genetics and genomics.
RAPSODYN has the ambition to ensure long-term competitiveness of the rapeseed production through improvement of the oil yield and reduction of nitrogen inputs during the crop cycle.
GenOuest is involved in the development of data management services for the project.
More information on Rapsodyn here.
BioDataRing is a data replication project launched by the three bioinformatics platform of the Biogenouest network: ABiMS (Roscoff), BiRD (Nantes) and GenOuest.
Funded by : Région Bretagne, Région Pays de la Loire
PIA BioDataCloud, 2013-2017
Investissements d’Avenir Développement de l’Economie Numerique «Cloud computing» Call, n.3 – Big data