Section: Partnerships and Cooperations

National Initiatives

ANR

• ANR Mappi (2010-2013): National funding from the French Agency Research (call Conception and Simulation). This project involves four partners: LIAFA (Université Paris 7), Genescale (Inria Rennes), Genoscope (French National Center for Sequencing) and Bonsai . The topic is Nouvelles approches algorithmiques et bioinformatiques pour l'analyse des grandes masses de données issues des séquenceurs de nouvelle génération.

• PIA France Génomique: National funding from Investissements d'Avenir (call Infrastructures en Biologie-Santé). France Génomique is a shared infrastructure, whose goal is to support sequencing, genotyping and associated computational analysis, and increase French capacities in genome and bioinformatics data analysis. It gathers 9 sequencing platforms and 8 bioinformatics platforms. Within this consortium, we are responsible for the workpackage devoted to the computational analysis of sRNA-seq data, in coordination with the bioinformatics platform of Génopole Toulouse-Midi-Pyrénées

• Mastodons (2012): National funding from CNRS (call Scientific big data ). This call targets the management, analysis and exploitation of massive scientific data sets. We have a collaborative project for Next Generation Sequencing data analysis with LIRMM (Montpellier) and Genscale (Inria Rennes).

• PEPS Bio-Math-Info Silenes (2012-2013): National funding from CNRS. This project involves the GEPV (P. Touzet) and the IBMP (Institut de Biologie Moléculaire des Plantes - UPR2357, Strasbourg) (J. Gualberto, L. Maréchal-Drouard). The topic is Etude comparative de l’architecture du génome mitochondrial chez les Caryophyllacées et les Poacées. It aims to sequence and analyze the genome structure of a number of Silene ecotypes and to compare them to other species.

• PEPS Bio-Math-Info ReSeqVar (2013-2014): National funding from CNRS. This new project aims at designing new read mapping algorithms in the context of human genome resequencing, taking into account known variants. We are two partners: UMR 8199 (Génomique et maladie métabolique, Ph Froguel, O. Sand, part of the LIGAN sequencing platform) and Bonsai .

PEPS

• PEPS Biology-Mathematics-Computer science: “Etude comparative de l’architecture du génome mitochondrial chez les Caryophyllacées et les Poacées”. This project involves three partners: IBMP (Institut de Biologie Moléculaire des Plantes), GEPV (UMR CNRS 8198, Université Lille 1) and Bonsai .

• PEPS Biology-Mathematics-Computer science: “Algorithmes pour l'alignement des lectures et la découverte de variants dans les projets de reséquençage”. This project involves two partners: UMR 8199 Génomique et Maladies Métaboliques and Bonsai .

ADT

• ADT biosciences resources (2011-2013): this ADT aims to build a portal of available applications in bioinformatics at Inria. The projects involves all the 8 teams from theme Bio-A and is more specifically developed by Bonsai and Rennes. An engineer was hired from 2011 to 2013 and worked in Rennes and another one was hired in 2012 and works in Lille.