Formulaire pour demande d' homologation cati

BIOS : a BioInformatics Oriented Service architecture for RNA-seq analysis.

http://bios.toulouse.inra.fr

Coordinateurs : Jérôme Gouzy, Sebastien Carrere.
Keywords: web-services, service-oriented architecture (SOA), RNA-Seq.
[e-mail]¹, [e-mail]¹, [e-mail]¹, [e-mail]², [e-mail]¹, [e-mail]³, [e-mail]⁴, [e-mail]⁵, [e-mail]⁶, [e-mail]⁷, [e-mail]⁷, [e-mail]⁸, [e-mail]⁸, [e-mail]⁶, [e-mail]⁹, [e-mail]¹⁰, [e-mail]¹.
¹Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR INRA-CNRS 441/2594, F-31320 Castanet Tolosan, France ; ²Institut Jean-Pierre Bourgin, UMR1318, INRA-AgroParisTech, Versailles, France ; ³Intéractions Biotiques et Santé Végétale (IBSV), INRA UMR/CNRS 1301/6243, F-06903 Sophia-Antipolis, France. ; ⁴Unité de Recherches sur les Espèces Fruitières (UREF), F-33883 Villenave d’Ornon, France ; ⁵Institut de Biologie Intégrative des plantes, UMR 5004-CNRS/0386-INRA/SupAgro/Univ. Montpellier 2, F-34060 Montpellier, France. ; ⁶BIO3P, UMR1099 INRA/Agrocampus Rennes/Univ. Rennes I ; ⁷INRA, UMR 102 Génétique et Ecophysiologie des Légumineuses, F-21065 Dijon, France ; ⁸Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 – Univ. d'Evry Val d'Essonne - ERL CNRS 8196, F-91057 Evry, France ; ⁹Centre de Biologie et de Gestion des Populations (CBGP), UMR INRA-IRD-CIRAD-SupAgro, F-34988 Montferrier/Lez, France ; ¹⁰Biologie du fruit et Pathologie (BFP), UMR1332 INRA-Univ. Bordeaux I&II, F-, Bordeaux, France.
This article presents BIOS, a Service-Oriented Architecture (SOA) for RNA-seq analysis. Through a unified web interface, users build and parameterize their analysis workflow, accessing in a transparent way the data and/or the analytic services proposed by a network of eight servers distributed in eight laboratories. The BIOS network gives access to data of several species of agronomic interest (plants, insects, oomycetes, etc.) as well as permits the identification of differentially expressed transcripts based on data provided by the user in a very simple tabulated format. Five flash tutorials illustrate the proposed analysis programs which are adapted to the various technologies (Sanger, 454, Illumina) used for measurements of expression based on sequence counts with (1) or without replicates (2–4). The data and the analytic services are distributed; the communication between the application and the servers is performed by BioMoby (5) web-services registered in the BIOS central registry (ten web-services for data access, ten analytic web-services, one web-service for network management). In addition, BIOS web-services ensure the interoperability with external systems, allowing for example the integration of expression patterns from “gene report” applications. In order to guarantee a crucial and stable quality of service, the entire network is supervised, both at the hardware and software levels. Thus, functional tests of the web-services are carried out daily. The result of this monitoring is placed at the users' disposal in order to ensure the best possible quality of service and to provide a maximum of transparency.

The service-oriented architecture BIOS, applied to the RNA-seq problem, offers a great flexibility and scalability. Indeed, after being uploaded on one of the servers, data benefits immediately from all the analysis programs available on the network. Conversely, once a new program has been added on a node of the network it can immediately be used to analyze any data.

BIOS is currently used for the data analysis of eighteen species. To date, one publication citing BIOS has been published recently (Biomphalaria glabrata; 454 and illumina data; Deleury et al. Plos One 2012), another one should be submitted in the coming months (Rosa chinensis, Illumina data) and several others are in preparation. This website is free and open to all users and there is no login requirement (login gives access to unpublished data).