Activities and projects

 

I am currently involved in the following projects: 

ANR BioWIC : The BioWIC workflow environment provides an efficient way to easily connect standard bioinformatics programs with user data or common genomic banks. In addition, time-consuming programs can be substituted by their parallel version running on different parallel hardware accelerators according to the resources available on the platform.Both activities are matched by the design of a dedicated workflow environment targeting heterogeneous hardware such as parallel computers (clusters), reconfigurable accelerators (FPGA) or graphic processing units (GPU).

link : http://biowic.inria.fr 

ANR PELICAN : Competing for light in the ocean: An integrative genomic approach of the ecology, diversity and evolution of cyanobacterial pigment types in the marine environment

link : http://www.sb-roscoff.fr/anr-pelican/ 

ANR ECS : ECS project will explore cooperation in plant symbioses, specifically exploring how plant mi crobe interactions shape the ecological processes and evolutionary trajectories of natural and agricultural ecosystems. 

GRISBI : it is a joined initiative between six French bioinformatics platforms: PRABI Lyon, MIGALE Jouy-en-Josas, GenOuest Rennes et Roscoff, CBIB Bordeaux, BIPS Strasbourg, CIB Lille. This effort tends to set up a grid infrastructure devoted to Bioinformatics at the national level. The goals of this bioinformatics grid is to be able to address challenging bioinformatics applications dealing with large scale systems : comparative genomics and genome annotation, protein function prediction, molecular interaction like protein-protein or DNA-protein, … This will be reached by sharing and by mutualizing the existing resources of the six platforms with grid software components and tools to coordinate and mutualize these resources : computing and storage hardware resources, but also database and software resources. For the first times the grid connection will concern the current six platforms. For the following steps, this model may be extend, according to the possibilities, to other bioinformatics, biological and computing platforms from interested research agency, such as for example national supercomputing centres or local and generic computing mesocentres. 

link : www.grisbio.fr

BioMAJ :
link : http://biomaj.genouest.org

DrMotifs : DrMotifs is a resource dedicated to motifs discovery and research. Many different tools have already been integrated in a single execution environment. All software are interfaced and usable through a web interface based on Mobyle or through web services. The project is still in its development phase and the mainstream tools (Interproscan, hmmer, MEME, Emboss tools) have already been integrated. In the next weeks, new tools as Protomata or Logol elaborated by INRIA's research team Symbiose will be incorporated in the environment. In its final phases, the project will integrate the tools in a workflow plugged on different databases in order to provide a user friendly tool geared toward motif discovery. This resource will support the data analysis steps performed after many proteomics experiments. The programmatic interface allows the use of the different tools in a workflow environment. 

link : http://drmotifs.genouest.org 

To be named (funded by IBiSA 2010) : metadata infrastructure This project has been recently funded by IBiSA (november 2010) and it will allow us to launch an initiative geared towards the setup of a metadata infrastructure for Life Science and Bioinformatics. Among our partners: INIST with the SIDR project. 

Coordination

 

• Member of ReNaBi steering committee 
• Coordinator for ReNaBi-GO (Grand Ouest). This regional centre includes the bioinformatics platforms of Nantes, Rennes and Roscoff. 
• Member of Biogenouest scientific committee In charge of Biogenouest bioinformatics action
• Member of the organisation committee of JOBIM 2009 (Nantes), Biograle 2008 and 2009, ISyIP 2009.
• Webmaster for ReNaBi's web site

Former work experience

 

For 14 years I was head of the "Service Informatique et Génomique" in Roscoff (Station Biologique CNRS). Earlier I worked in Nancy at INIST. 

Publications and communications 

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Articles 

• GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle Aurélie Lardenois, Alexandre Gattiker, Olivier Collin, Frédéric Chalmel and Michael Primig Database (2010)  (article) 
• AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome. F Legeai, S Shigenobu, J-P Gauthier, J Colbourne, C Rispe, O Collin, S Richards, A C C Wilson, T Murphy, D Tagu. - Insect Mol Biol (2010) vol. 19 Suppl 2 pp. 5-12  (article) 
• MIMAS 3.0 is a Multiomics Information Management and Annotation System. Alexandre Gattiker, Leandro Hermida, Robin Liechti, Ioannis Xenarios, Olivier Collin, Jacques Rougemont, Michael Primig. - BMC Bioinformatics (2009) vol. 10 pp. 151 (article) 
• BioMAJ: a flexible framework for databanks synchronization and processing. Olivier Filangi, Yoann Beausse, Anthony Assi, Ludovic Legrand, Jean-Marc Larré, Véronique Martin, Olivier Collin, Christophe Caron, Hugues Leroy, David Allouche. - Bioinformatics (2008) vol. 24 (16) pp. 1823-5 (article) 
• The loss of the hemoglobin H2S-binding function in annelids from sulfide-free habitats reveals molecular adaptation driven by Darwinian positive selection. Xavier Bailly, Riwanon Leroy, Susan Carney, Olivier Collin, Franck Zal, Andre Toulmond, Didier Jollivet.- Proc Natl Acad Sci USA (2003) vol. 100 (10) pp. 5885-90 (article)
• KID, a Kinase Inhibitor Database project. Olivier Collin, L Meijer. - Pharmacol Ther (1999) vol. 82 (2-3) pp. 165-8 
• Arylsulphatase from Alteromonas carrageenovora. T Barbeyron, P Potin, C Richard, Olivier Collin, B Kloareg. - Microbiology (Reading, Engl) (1995) vol. 141 ( Pt 11) pp. 2897-904 
• Increased resolution of large DNA fragments by a two dimensional pulse field gel electrophoresis. P Sanséau, C Tiffoche, A Kahloun, Olivier Collin, J P Rolland, J P Le Pennec. - Anal Biochem (1990) vol. 189 (1) pp. 142-8 
• Characterization of a ferritin isolated from the midgut epithelial cells of a homopteran insect, Philaenus spumarius L. Olivier Collin, D Thomas, M Flifla, C Quintana, J Gouranton. - Biol Cell (1988) vol. 63 (3) pp. 297-30 (article)

Posters and Communications 

• Renabi grisbi - Grande Infrastructure pour la Bioinformatique C. Blanchet, C. Gauthey, O. Collin, T. Martin, N. Melab, F. Plewniak, F. Samson, B. Spataro et C. Caron JOBIM 2010 
• BioDesc : gestion d’un entrepôt multiformat de descriptions de ressources bioinformatiques P. Picouet, Z. Doughi, L. Brillet, E. Corre, C. Caron, O. Collin, F. Moreews et X. Bailly JOBIM 2010 
• « BioWorkFlow: Web Services toolkit and workflow applications evaluation to deploy a confidence network » Marc Wessner, Martin Senger, Franck Samson, Philippe Picouet, François Moreews, Hervé Ménager, Véronique Martin, Sébastien Letort, Catherine Letondal, Mark Hoebeke, Jérome Gouzy, Jean-françois Gibrat, Erwan Corre, Olivier Collin, Sébastien Carrere, Christophe Caron, Pierre Tufféry and Bertrand Néron. JOBIM 2008 Lille