Biogenouest Integrative Biology Project

Owner: Yvan Le Bras

Group members: 2

Description:

The main task of the Integrative Biology project of Biogenouest is to promote a systems approachn biology by (1) facilitating the acquisition and analysis of heterogeneous data, (2) defining the existing methods, and (3) providing integration tools.

Todaybecause many technology platforms in the life sciences providing a substrate of interest in the integration of data are in these themes, we focus on the integration of genomic data, from genome to metabolome through the transcriptome and proteome. Our role is (1) to inform the relevant laboratories (laboratory science of living in the West of France) about the existence of the project and the actions implemented and (2) to organize these approaches by the existence of working groups and training.

 

 

 

Context

            More and more data are generated in Life sciences, notably with the development of high throughput approaches and of next generation sequencing, while the information which is extracted from it remains limited. Increasing difficulties appear in laboratories as regards the treatment and the analysis of data. How to transform data into knowledge? Reductionist approaches led until now on biological processes allowed to deposit an essential substrate in determination of the "How". These bases seem today sufficient in some domains to lead investigations in the sense of the "Why " by holistic approaches. Integrative Biology (Aderem, on 2005; Brazma and al., on 2006; Friboulet and Thomas, on 2005; Liu, on 2005), via an integration of the data of different organization levels (from metabolite to population through organ, organism and population), of different species or different genomic approaches (from positional genomics to metabolomic through transcriptomic, proteomic and interactomic), represents the approach that will allowed to take out information of data and signification of noticed processes.

Problems and Methodology

            The main mission of the Biogenouest federal plan in Integrative Biology is to promote a systemic approach of biology, (1) by making easier the acquisition and the analysis of heterogeneous data, (2) by defining existent methods, and (3) by offering integration tools. Project articulates around 2 main questions.

             (I) How to produce integrable data? After inquiries performed to the different Breton and ligeriens actors in biological Sciences (platforms and research units), we see an important heterogeneity of treated and produced data, as studied organisms. To make easier the production of integrable data, different tracks are offered treating the management of data. Different needs in training having come out from this first inquiries, federal plan will constitute a thinking basis to the organization of trainings in the West France regions.

            (Ii) How to analyze data in an integration scope? Once raw data transformed (for example from data coming from private software), we have to analyze them. Different problems exist then in the exploration of data (visualization, normalization, first statistical approaches, etc.), as with the semantics (annotation and ontology), biostatistics and modeling approaches.

Preliminary results

Until now, because many technological platforms in living sciences being offering an interest substrate for the integration of data are in these topic, we are mainly focused on the integration of genomic data. My role is (1) to inform laboratories (laboratory in life science of west France regions) of the existence of the project and of actions set up as well as (2) to federate their approaches by the existence of working groups and of trainings.

To make the treatment and the analysis of data easier, Olivier Collin (Symbiosis project, INRIA Rennes), of the GenOuest platform, works on a web platform dedicated to manipulation of files and statistical analyses. This platform will allow to save and to manipulate big data with speed and made easier collaboration and workflow save. This will used existent web platform such as GALAXY, MOBYLE, GenePattern or Babelomics.

Another data management problem concerns the homogenization of file formats, metadata recording as well as services interoperability. Here, we propose to use ISA INFRASTRUCTURE and to work in partnership with Olivier Dameron (U936 Conceptual Modeling of Biomedical Knowledge, INSERM Rennes 1 University) on ontology side.

Semantic approaches developed by Olivier Dameron with Christian Diot (UMR GAREN, INRA Agrocampus-Ouest) and Frederic Herault (UMR GAREN, INRA Agrocampus-Ouest) for multi-species approaches and characterization of genes clusters by their annotations will allow to enhance the resolution of problems linked to the analysis of data in an integration aim. It's the same for biostatistical approaches developed by David Causeur (Applied Mathematics, Agrocampus-Ouest) and its team on the analysis of high-throughput data, in factors analysis (FAMT method) and the networks inference. Finally, an important place is give to modeling approach. Works developed within INRIA notably by Ann Siegel, Jérémie Bourdon, Irena Rusu, Guillaume Fertin and Michel LeBorgne but also in Nantes by Damien Eveillard (LINA UMR 6241 CNRS / Nantes University) in collaboration with different teams of the Roscoff biological station or UMR GAren INRA Agrocampus-Ouest will allow to realize big strides in large scale modeling (building of networks, processes overview, etc.) and dynamic modeling (prediction, kinetics, fine approach, etc.).

 

Brief description: Promote Integrative Biology in the west of France

Category: Research institute

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Website: http://int-gen.genouest.org/

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