Section: Partnerships and Cooperations

National Initiatives

ANR contracts

BIOWIC

Participants : Dominique Lavenier, Olivier Collin, Rumen Andonov, François Moreews, Jonathan Piat, Guillaume Rizk.

The BioWIC project aims to speed up both the design and the execution of bioinformatics workflows. It is funded by ANR call ARPEGE and coordinated by D. Lavenier from Jan. 2009 to June 2012. http://biowic.inria.fr/

LEPIDOLF

Participants : François Coste, Fabrice Legeai, Jacques Nicolas, Andres Burgos, Pavel Senin.

The LEPIDOLF project aims at better understanding olfactory mechanisms in insects. The goal is to establish the antennal transcriptome of the cotton leafworm Spodoptera littoralis, a noctuid representative of crop pest insects. It is funded by ANR call Blanc and coordinated by E. Jacquin-Joly from UMR PISC (INRA) from 2009 to 2012.

MAPPI

Participants : Dominique Lavenier, Pierre Peterlongo, Guillaume Chapuis, Rayan Chikhi, Nicolas Maillet.

The MAPPI project aims to develop new algorithms and Bioinformatics methods for processing high trougthput genomic data. It is funded by ANR call COSINUS and coordinated by M. Raffinot (LIAFA, Paris VII) from Oct 2010 to Dec. 2013.

PELICAN

Participants : Olivier Collin, François Coste, Anthony Bretaudeau, Andres Burgos.

The PELICAN project addresses competition for light in the ocean: An integrative genomic approach of the ecology, diversity and evolution of cyanobacterial pigment types in the marine environment. It is coordinated by F. Partensky (CRNS Roscoff) from 2010 to 2013. http://www.sb-roscoff.fr/anr-pelican/

ECS

Participant : Olivier Collin.

The ECS project explores cooperation in plant symbioses. It provides new insights on how plant-microbe interactions shape the ecological processes and evolutionary trajectories of natural and agricultural ecosystems. This project seeks also to identify new symbiotic partners for plants. It is funded by ANR (Systerra) and coordinated by P. Vandenkoornhuyse from UMR 6553 (CAREN) from 2010 to 2013. http://ecs-project.univ-rennes1.fr/news.php

BIOTEMPO

Participants : Anne Siegel, Jérémie Bourdon, François Coste, Jacques Nicolas, Michel Le Borgne, Geoffroy Andrieux, Sylvain Prigent, Santiago Videla, Andres Aravena.

The BioTempo project aims at developing some original methods for studying biological systems. The goal is to introduce partial quantitative information either on time or on component observations to gain in the analysis and interpretation of biological data. Three biological applications are considered regulation systems used by biomining bacteria, TGF-beta signaling and initiation of sea-urchin translation. It is funded by ANR Blanc (SIMI2) and coordinated by A. Siegel from 2011 to 2014. http://biotempo.genouest.org/wiki.php/Accueil

Programs from research institutions

Participants : Anne Siegel, François Coste, Olivier Collin, Charles Deltel, Dominique Lavenier, Michel Le Borgne, Claire Lemaitre, Pierre Peterlongo, Jérémie Bourdon, Pavlos Antoniou, Andres Burgos, Guillaume Chapuis.

• Alcovna The Alcovna project aims to explore possibilities of extracting information among possibly huge sets of reads without reference genome and avoiding to assemble the data. It is funded by INRIA ARC call and coordinated by P. Peterlongo from oct. 2009 to sept. 2011. http://alcovna.genouest.org

• BioManyCores The BioManyCores project aims to develop a library of bioinformatics softwares implemented on manycore structures such as GPU. It is funded by INRIA ADT call and supervised by J.S. Varré in Sequoia Team in Lille. http://www.biomanycores.org/

• ParaQtlMap The ParaQtlMap project is a join initiative from EPI Symbiose and Genetique Animale. to design high performance software for detecting quantitative trait locus. It is funded by INRIA/INRA call and coordinated by D. Lavenier (EPI Symbiose) and P. Leroy (GA INRA) from oct. 2010 to sept. 2012. https://qgp.jouy.inra.fr/index.php?option=com_content&task=view&id=17&Itemid=28

• Protomata The protomata project aims at developping a software for modeling proteins families with automatas. It is funded by INRIA ADT call (2010-2011) and supervised by F. Coste.

• QuantOursin The QuantOursin project aims at developping modeling tools based on probabilistic framework and average analysis, and apply then to the initiation of urchin translation. It is funded by a PEPS program at CNRS and coordinated by A. Siegel from april. 2010 to december. 2012. http://quantoursin.genouest.org/wiki.php/Accueil

Transfert and service ressources - GenOuest ressource center

Participants : Olivier Collin, Olivier Sallou, Charles Deltel, Anthony Bretaudeau, Delphine Naquin, Aurélien Roult, Romaric Sabas, Claudia Hériveau.

• GRISBI The project intends at developping a production grid dedicated to bioinformatics, by gathering computational ressources of six french ressource centers. It is funded by IBISA and coordinated by C. Blanchet (IPCP Lyon) from 2009 to 2011. http://www.grisbio.fr

• DrMotifs is a project dedicated to develop tools for pattern discovery and research. The resource integrates the tools in a workflow plugged on different databases in order to provide a user friendly tool geared toward motif discovery. It is funded by IBISA and coordinated by O. Collin (Symbiose) from 2010 to 2011. http://drmotifs.genouest.org

• BioMaj The project aims at developing a workflow engine dedicated to data synchronization and processing.The Software automates the update cycle and the supervision of the locally mirrored databank repository. It is funded by Inria ADT program from 2009 to 2011 and coordinated by O. Collin. http://biomaj.genouest.org .

• Inria Biosciences Resources This new project (recruitement of an engineer in november) is focused on the different ways to improve the visibility of Inria's bioinformatics team software production. To achieve this goal, a new web resource will be built. This resource will allow end-users to test and evaluate the new bioinformatics tools created by Inria. It is funded by INRIA ADT program from 2011 to 2013, it involves 8 research teams and is coordinated by Symbiose (Jacques Nicolas and Olivier Collin).