Section: Other Grants and Activities
The Symbiose project is involved in the following national collaboration programs (detailed hereafter):
Inra projects Genanimal, Sigenae, BioWorkFlow and BioMAJ .
ANR contracts Proteus, Modulome, PARA, SITCON, DyCoNum.
Inside these collaboration programs or beside, the main teams that we cooperate with are:
Curie Institute, biology, medecine and bioinformatics, Paris (O. Radulescu, A. Siegel, M. Le Borgne)
LiX, INRIA project team AMIB, statistical significance for motif finding algorithms (J. Bourdon)
IML, Marseille and LIRMM, Montpellier: substitutive dynamical systems (A. Siegel).
Helix inria team: biological sequences filtering (P. Peterlongo).
URGI (Unité de Recherche Génomique Info), Versailles: LTR retrotransposons in plant genomes (C. Belleannée).
Laboratoire d'Informatique de Nantes Atlantique, Equipe COD (COnnaissances et Décision), Site Polytech' Nantes, Hiérarchie Implicative Orientée (I.C. Lerman).
Laboratoire d'Informatique, de Modélisation et d Optimisation des Systèmes (LIMOS), Université d'Auvergne, Qualité des Règles d'Association (I.C. Lerman).
Colorado State University, Dept. Computer Science, Fort Collins, USA Key words: parallelism, RNA folfing (D. Lavenier)
GICC UMR CNRS 6239, Tours (Génétique Immunothérapie Chimie et Cancer): logical models and characterization of transposons, RNA folding, GPU (C. Belleannée, D. Lavenier, J. Nicolas)
EPI AMIB (M. Régnier): Average-case analysis and statistical tests (J. Bourdon).
National projects of the GenOuest platform
BioSide is a collaboration with ENSTB-Brest (P. Picouet, S. Bigaret, P. Tanguy) and Station Biologique Roscoff (X. Bailly, E. Corre, G. Le Corguille). It is an environment managing metadata for bioinformatic programs(including the semantics of their parameters and the execution policy) thus providing access to source programs. The intuitive BioSide interface allows the design, execution and storage of workflows (scenarios). Metadata are used both to provide high level help to the final user and to guarantee dynamic extensibility of BioSide. A standalone version is available for phylogenetic programs. A server version will be soon available.
MobyleNet is a joined project between several bioinformatics platforms aiming to develop a bioinformatics web portal. The MobyleNet project involves 8 sites, 5 IBISA platforms, and 3 supporting sites external to this process, either providers of services and/or developers of the core MobyleNet framework. It thus involves seven physical bioinformatics platforms (nodes) distributed over France and having different skills that range from genomics, microarrays, sequence analysis, phylogeny, structural bioinformatics to chemoinformatics and different focuses from microorganism, plants to pharmacology and cancer.
BioMAJ is a joint collaboration between INRA Toulouse (David Allouche), INRA Jouy (Christophe Caron) and IRISA for databanks management. See section 5.3.1 .
GRISBI is an IBISA joined initiative started in oct. 2008 between 6 French bioinformatics platforms: PRABI Lyon, MIGALE Jouy-en-Josas, Genouest Rennes, CBIB Bordeaux, BIPS Strasbourg, CIB Lille. This effort tends to set up a grid infrastructure devoted to Bioinformatics at the national level. The goal is 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 resources of the 6 platforms with grid software components and coordination tools: computing and storage hardware resources, but also database and software resources.
Sigenae and Genanimal
The SIGENAE program (Analysis of Breeding Animals' Genome), coordinated by Inra Toulouse, is the Inra national program of animal genomics. It aims at identifying the expressed part of genomes, developing the map-making of entire genomes and studying genetic diversity of breeding animals (pig, chicken, trout, cow). A privileged international partner is the american ARS (Agricultural Research Service) which develops a comparable project. The transcriptome of trout, chicken and pig are studied in Rennes.
Symbiose collaborates to this program via an Inra engineer, F. Moreews, contributing to the Sigenae information system. We are studying with UMR Inra 598 the modeling of fatty acids metabolism (see Sec. 6.3 ). We have also developed sigReannot, an oligo-set re-annotation pipeline based on similarities with the Ensembl transcripts and Unigene clusters  .
Proteus (Fold recognition and inverse folding problem)
The project PROTEUS (ANR-06-CIS6-008) started in January 2007 and involves also BIOS at Ecole Polytechnique (coordinator T. Simonson), MIG at INRA Jouy-en-Josas, the Physics Lab. at Ecole Normale Supérieure of Lyon and ABI at UPMC, Paris 6. The standard but difficult «fold recognition» problem requires identifying the 3D structure among a library of possible structures. A complementary approach turns the problem around, and poses the «inverse folding problem»: to enumerate all the amino acid sequences compatible with a given 3D structure. On the one hand, we will predict the fold of all bacterial proteins of unknown structure (300.000 proteins). On the other hand, we will solve the inverse folding problem for 1300 folds, out of 2300 known today (SCOP database), using the emerging technique of directed evolution, which mimics the natural evolutionary process. Reports of the project are available on its web site (http://migale.jouy.inra.fr/proteus ).
BioWIC: Bioinformatics Workflows for Intensive Computation
The increasing flow of genomic data provided by the steadily improvement of new biotechnologies cannot be now efficiently exploited without a systematic in silico analysis. Data need to be filtered, curated, classified, annotated, validated, etc., to be actively used in a discovery process.
Such treatments can be very critical, especially in terms of time. The design of complex pipelines is a tedious and error-prone activity which requires consequent human resources. The execution time of several bioinformatics program can also be a major bottleneck when huge amount of data need to be processed. The BioWIC environment aims to save time in both directions.
Partnaires of the BioWIC project are the CAIRN INRIA group (Rennes), the MIG INRA group (Jouy-en-Josas) and the ELIAUS group (University of Perpignan).
Modulome: Identifying and displaying modules in genomic sequences
This ANR project, Modulome (http://www.irisa.fr/symbiose/projets/Modulome/ ), aims at providing methods for the identification, visualization and formal modeling of the structure of genomes in terms of an assembly of nucleotides "modules" that are repeated along a genome or between several genomes. Three other teams of Biologists and bioinformaticians are involved in this project: URGI/Inra Versailles, LME/Ifremer Brest and GICC/CNRS Tours. See details in section 6.2.1 .
This ANR project is funded by the “blanc” program of the ANR. It started on october 2009. It is leaded by E. Jacquin-Joly from UMR PISC 1272 and implies INRIA Rennes Bretagne Atlantique (F. Coste) and UMR GABI INRA (P. Martin). LepidOLF ANR 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. This antennal gene repertoire will then be used to identify for the first time the complete repertoire of olfactory genes (among them olfactory receptors) in a Lepidoptera crop pest. This repertoire will be used to design the first available 'antennal' microarray. This array will be used to establish the molecular signature of different functional types of sensilla and will also offer us the possibility to investigate the mechanisms of olfactory plasticity at the peripheral level.
Sitcon: Modeling signal transduction induced by a chimeric oncogene
This ANR project belongs to the "Biologie Systémique" program. The Ewing inducible cellular model, developed by one of the biologist partners of the project, is characterized by a malignant genomic translocation and appearance of a chimeric gene EWS/FLI-1 whose activity leads to the uncontrolled cell growth. The goals of the projects are to reconstruct the corresponding interaction network, including signal transduction pathways and from a detailed model of functioning, to propose new validation experiments. See details in section 6.3.1
DyCoNum: Dynamical and Combinatorial studies of Numeration systems
Participant : Anne Siegel.
The "Jeunes chercheurs" program funded a project named DyCoNum aiming to consider by a transversal approach digital expansions in several number systems. This project focuses on integer base expansions, non-standard systems with integer base (signed digit expansions), beta-expansions and substitutive numeration systems, (generalized) continued fractions. This program involves W. Steiner and C. Frougny (LIAFA, Paris 7) and B. Adamczewski (Institut Camille Jordan, Lyon 1).