International collaborations

Integrated program ACGT

The project (http://eu-acgt.org/home.html ) aims at delivering the cancer research community an integrated CIT environment enabled by a powerful GRID infrastructure. Our contribution concerns parallelism (Grid development, tumor growth simulation) and data mining (integration of CHAVL in a R environment). It lasted from 2006 to 2010.

Billateral collaborations and visitings

• Argentina. Collaboration with  "Grupo de Procesamiento de Lenguaje Natural ") on grammar learning of sequence structure. Granted by a MinCyT-INRIA program.
• Bulgaria. Collaboration with Sofia university) and South-West University on algorithmics for structural biology. Formely granted by Egide programs.
• Chile. Collaboration with the bioinformatics team of CMM (University of Chile) on systems biology. Granted  Inria-Conycit project 2011-2013.
• Germany. Collaboration with Postdam university on logic programming and boolean constraint solving. Granted by a procope Egide project from 2011 to 2013.
• Netherlands Collaboration wuith CWI Life Sciences and NISB Algorithmic computational biology) on algorithmics for structural biology.

ANR contracts

• BIOWIC 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 Dec. 2011. http://biowic.inria.fr/

• LEPIDOLF 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 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. http://mappi.arthy.org/

• PELICAN 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/

• PROTEUS The PROTEUS project addresses fold recognition and inverse folding problem towards large scale protein structures prediction. It is funded by ANR call Calcul intensif and coordinated by CEA from 2006 to 2010. http://migale.jouy.inra.fr/proteus

Grants from research institutions

• 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 librairy of bioinformatics software 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

• 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

Transfer and service grants

• 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. Eventually the resource will integrate 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 20010 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 .