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1.Caractérisation de la mission du Cati : 3

2. Organisation du Cati 6

Projets Phares 15

Axe 1: Organisation et régulation des génomes 16

ANAIS: Analysis of NimbleGen Arrays Interface 17

BIOS : a BioInformatics Oriented Service architecture for RNA-seq analysis. 18

CycADS annotation database system to support the development and update of enriched BioCyc databases 20

FrameDP: sensitive peptide detection on noisy matured sequences 21

iANT : integrated ANnotation Tool 22

Portail Meloidogyne incognita 24

Legoo : a bioinformatics gateway towards integrative legume biology 26

REMORA : un poisson pilote dans l'océan des web-services BioMOBY 28

ISYIP: Plate-forme bio-informatique pour la génomiques sur les insectes 30

Axe 2 : Génomique comparative et caractérisation de la biodiversité 31

ANATool : The Arabidopsis Natural Accession Tool 32

CFBP : Collection Française de Bactéries associées aux Plantes 33

E-phytia et Di@gnoPlant® : un continuum de services du Web au terrain en protection des plantes 34

Florapis : base de données photographiques et bibliographiques sur le butinage des abeilles domestiques 36

Site web Insectes du patrimoine 38

La base R-SYST : identification des espèces de groupes d'organismes d'intérêt 39

Narcisse : navigateur de génomes comparés 41

SESAME: genotyping based on high-throughput multiplex amplicon sequencing 43

Axe 3: Intégration et Représentation des Connaissances 44

MetExplore: Collaborative platform for building, analyzing, simulating and improving metabolic networks 45

AgroBI-VTC 47

Exemple de Projet Structurant du futur CATI 49

BBRIC WORKSPACE 50

Projets Phares

Axe 1: Organisation et régulation des génomes

ANAIS: Analysis of NimbleGen Arrays Interface

http://anais.versailles.inra.fr

Adeline Simon¹, Eric Biot²

¹UR1290 BIOGER−CPP, INRA, Grignon

²Institut Jean-Pierre Bourgin, UMR1318, INRA-AgroParisTech, Versailles, France

Contact: [e-mail]

Publication : Simon A, Biot E. (2010). ANAIS: Analysis of NimbleGen Arrays Interface. Bioinformatics 2010 Oct; 26(19):2468-9.
Summary: ANAIS is a user-friendly web-based tool for the processing of NimbleGen expression data. The interface reads single-channel microarray files generated by NimbleGen platforms and produces easily interpretable graphical and numerical results. It provides biologists six turnkey analysis modules—normalization, probe to gene, quality controls, differential expression, detection, queries and clustering—to explore quickly, freely and without the need for computer programming, NimbleGen transcriptome data.
May 2012 inventory :

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  206 users since july 2010
  
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  442 projects currently on the server
  
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  3 citing articles :
  

Title : Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations.

Author(s): Rouxel T. et al.

Source : Nat Commun. 2011 Feb;2:202.

Title : Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Author(s): Amselem A. et al.

Source: PLoS Genetics. 2011 Aug;7(8):e1002230
Title : HdfR is a regulator in Photorhabdus luminescens that modulates metabolism and symbiosis with the nematode Heterorhabditis

Author(s) : Easom CA. and Clarke DJ.

Source : Environmental Microbiology (2012) 14: 953

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).