Team Symbiose

Members
Overall Objectives
Scientific Foundations
Application Domains
Software
New Results
Other Grants and Activities
Dissemination
Bibliography

Section: Software

New activities of the bioinformatics platform in 2009

Participants : Olivier Collin, Hugues Leroy, François Moreews, Aurélien Roult, Romaric Sabas, Olivier Sallou.

National Project BioMAJ (BIOlogie Mise A Jour)

Biological knowledge, in proteomics and genomics context is mainly based on transitive bioinformatics analysis consisting in periodic comparison of data newly produced again corpus of known information. This approach needs on one hand accurate bioinformatics softwares, pipelines, interfaces... and on another hand numerous heterogeneous biological banks, which are distributed around the world.

Data integration represents a major challenge and bottleneck in bioinformatics. Parameters of this complexity include heterogeneity, size (several Tera bytes), number of banks, cross-linked sources, multiplicity of dedicated post treatments with respect to various bioinformatics software (blast, SRS, emboss, gcg, ...), variable banks frequency update, ... A first stake consists in automating the heavy process of updating the data banks for the administrator. Another significant stake to resolve is for the "quality" of service, providing to the users a clear vision of the integrity of data (state, exact origin, ... ) constitutive of their workspaces.

BioMAJ is a joint development between three bioinformatics platforms : INRA Toulouse (David Allouche), INRA Jouy-en-Josas (Christophe Caron) and our platform. BioMAJ is written using state-of-the-art technologies (java, xml, ..) and is based on a parameterizable workflow engine. Post processes are written for the usual formats (gcg, blast, srs, ...) and are easily customisable. BioMAJ has been relased under an opensource licence in April 2008 and has been downloaded more than 100 times and it used in production on 8 french bioinformatics (INRA Jouy, INRA Toulouse, PBIL Lyon, Strasbourg...) platforms. (http://biomaj.genouest.org/ ).

A new development cycle has started in November with a dedicated INRIA ADT (Action for technological development) national project. It will add functionalities like peer-to-peer, real time monitoring, databanks versioning and graphical interface for workflows conception.

National Projects GRISBI and MobyleNet

GRISBI aims to develop a grid dedicated to bioinformatics. This action, funded by IBiSA, involves different actors of the french bioinformatics community : IPCB Lyon (C. Blanchet, C. Eloto, A. Michon), INRA Jouy-en-Josas (J.-F. Gibrat), CNRS Roscoff (C. Caron), CBIB Bordeaux (T. Martin), IGBMC Strasbourg (F. Plewniak), INRIA Lille and GenOuest (O. Collin, A. Roult).

MobyleNet aims to develop a bioinformatics application portal allowing the remote execution of jobs among the different partners computer resources. It gathers different bioinformatics platforms, is managed by P. Tuffery at RPBS, Paris, and is funded by IBiSA. GenOuest provides his technical and development expertise.


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