Formulaire pour demande d' homologation cati

Base de données génomiques sur les insectes

http://bioweb.ensam.inra.fr/spodobase/, http://www.aphidbase.org, http://www.inra.fr/lepidodb
Centres (Sites) INRA Montpellier, INRA Rennes, plateforme Genouest, INRIA/IRISA

Départements SPE

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).

CycADS annotation database system to support the development and update of enriched BioCyc databases

http://www.cycadsys.org/
Patrice Baa-Puyoulet^1,4, Augusto F. Vellozo^2,4, Jaime Huerta-Cepas³, Gérard Febvay^1,4, Toni Gabaldon³, Marie-France Sagot^2,4, Hubert Charles^1,4 and Stefano Colella1,4
1 Biologie Fonctionnelle Insectes et Interactions, UMR203 INRA INSA Lyon BF2I, bat INSA Pasteur, 20 ave Albert Einstein, 69621, Villeurbanne Cedex, France

2 Laboratoire de Biométrie et Biologie Évolutive, UMR5558 CNRS Université Lyon 1, bat Grégor Mendel, 43 bd du 11 novembre 1918, 69622, Villeurbanne Cedex, France

3 Centre for Genomic Regulation, Barcelona Biomedical Research Park, Barcelona, Spain

4 BAMBOO, INRIA Rhône-Alpes, France

Keywords: metabolism, arthropods, gene annotation, metabolic pathways.
1. The CycADS Software Project
The Cyc Annotation Database System (CycADS) project started in 2008 during the genome annotation for the pea aphid, Acyrthosiphon pisum. Since the early stages of the quest for all metabolism related genes/proteins in the genome, it was clear that an annotation data management system was needed to allow us (and others) to easily create and further update the BioCyc metabolism network reconstruction of the pea aphid. CycADS allows the collection of heterogeneous annotation information to create dedicated files that are processed with the PathwayTools Software (SRI International) to produce BioCyc interfaces.
2. From AcypiCyc to ArthropodaCyc
CycADS has been successfully used to generate AcypiCyc1, the pea aphid BioCyc database, and we decided to build a metabolic network database for other arthropods, for which the genome sequence is available. We kept the same workflow parameters for collecting data from all used annotation methods (Blast2GO, KAAS, PRIAM). The generated ArthropodaCyc2 database includes, at present, metabolic reconstructions for 11 arthropods: Acyrthosiphon pisum, Aedes aegypti, Anopheles gambiae, Apis mellifera, Culex quinquefasciatus, Daphnia pulex, Ixodes scapularis, Nasonia vitripennis, Pediculus humanus corporis, Tribolium castaneum and Drosophila melanogaster (for this last species, both the CycADS version and the FlyCyc database manually curated by the FlyBase team are available). Collecting and organizing information into databases is useful for the researchers studying the metabolism of their newly sequenced model organisms (more arthropod genomes will be sequenced in the near future through the i5K Arthropod Sequencing initiative), and it allows them to better understand different aspects of arthropod biology through comparative studies.

Thanks to the CycADS software, we included, in each database, information on annotation sources and links to genomics databases (including AphidBase, BeetleBase, VectorBase, Hymenoptera Genome Database, FlyBase and wFleaBase). Future plans include adding other sequenced genomes to ArthropodaCyc and the generation of another BioCyc-like database centred on the arthropod endosymbiosis for which both host and symbiont genomes have been sequenced (a beta version of ArtSymbioCyc is already available).