South Green bioinformatics platform: Update 2015

Armero A., Baurens Franc-Christophe, Bocs Stéphanie, Breil A., De Lamotte Frédéric, Dereeper Alexis, Droc Gaëtan, Dufayard Jean François, El Hassouni Nordine, Farcy Cédric, Garsmeur Olivier, Guignon Valentin, Hamelin Chantal, Hueber Yann, Kougbeadjo Ayite, Larivière Delphine, Larmande Pierre, Lorenzo Jonathan, Martin Guillaume, Monat Cécile, Ndomassi T., Ortega Abboud Enrique, Pitollat Bertrand, Ravel Sébastien, Ranwez Vincent, Rouard Mathieu, Ruiz E., Sabot François, Sarah Gautier, Sempere Guilhem, Summo Marilyne, This Dominique, Tranchant-Dubreuil Christine, Vallier Félix. 2015. South Green bioinformatics platform: Update 2015. In : Plant Genomics Congress. Global Engage. Londres : Global Engage, p. 51. Plant Genomics Congress. 3, Londres, Royaume-Uni, 11 May 2015/12 May 2015.

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Matériel d'accompagnement : 1 poster

Abstract : In 2015, the South Green Bioinformatics Platform is a network of 35 bioinformaticians from five biology research institutes working with two High - Performance Computing Data Centres to develop and use new tools for NGS/ Omic analytics of tropical and Mediterranean crops under projects studying relationsh ip between genetic diversity, agronomic performance and response to selection. South Green is affiliated to the South regional centre of the French Institute of Bioinformatics (the French node of the European research infrastructure, ELIXIR). This communit y and the HPC data centres are all located in Montpellier, which facilitates close collaboration and significant pooling to best meet the biologists' demands of our research units. Since 2004, we developed web - based applications with both generic and in - ho use components, for databases, analysis workflows and web interfaces, in order to: manage genetic and phenotypic information ( e.g. TropGeneDB), analyse molecular markers and genetic diversity ( e.g. SNiPlay), assemble transcriptomes ( e.g. ESTtik) map RNA - Se q ( e.g. ARCAD), annotate and compare genomes ( e.g. GNPAnnot), reconstruct evolutionary history of gene families by phylogenomics ( e.g. GreenPhyl). We also participate to the analysis of numerous crop species, that requires computing and storage facilities as well as interoperable information systems, such as rice ( e.g. OryGenesDB), wheat, sorghum, sugarcane, banana (Banana Genome Hub), palms, yam, coffee (CGH), rubber, cacao (CocoaGenDB), cotton, apple, grapevine, olive, eucalyptus, cassava. To face the dat a deluge, we must increase our analytics capabilities. We document our operation at both, administrator/ developer and user/ scientist level, to provide high quality services and reproducible research. We pool into working groups on key themes such as GBS, at both, developer (extreme pair programming) and user (interdisciplinary knowledge exchange) level. We provide training sessions each year. Finally, we implemented several instances of the Galaxy workflow manager and encapsulated our tools. These instanc es serve as a catalyst for massive NGS analyses but it remains to increase storage capacity and improve data management plans. (Résumé d'auteur)

Mots-clés libres : Bioinformatique, Plateforme

Classification Agris : F30 - Plant genetics and breeding
C30 - Documentation and information
U30 - Research methods
U10 - Mathematical and statistical methods

Auteurs et affiliations

  • Armero A.
  • Baurens Franc-Christophe, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-5219-8771
  • Bocs Stéphanie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-7850-4426
  • Breil A.
  • De Lamotte Frédéric, INRA (FRA)
  • Dereeper Alexis, INRA (FRA)
  • Droc Gaëtan, CIRAD-BIOS-UMR AGAP (FRA)
  • Dufayard Jean François, CIRAD-BIOS-UMR AGAP (FRA)
  • El Hassouni Nordine, INRA (FRA)
  • Farcy Cédric, CIRAD-BIOS-UMR AGAP (FRA)
  • Garsmeur Olivier, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-8869-3689
  • Guignon Valentin, Bioversity International (FRA)
  • Hamelin Chantal, CIRAD-BIOS-UMR AGAP (FRA)
  • Hueber Yann, Bioversity International (ITA)
  • Kougbeadjo Ayite, Université de Yaoundé (CMR)
  • Larivière Delphine, CIRAD-BIOS-UMR AGAP (FRA)
  • Larmande Pierre, IRD (FRA)
  • Lorenzo Jonathan, Université de Montpellier (FRA)
  • Martin Guillaume, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-1801-7500
  • Monat Cécile, IRD (FRA)
  • Ndomassi T.
  • Ortega Abboud Enrique, CIRAD-BIOS-UMR AGAP (FRA)
  • Pitollat Bertrand, CIRAD-BIOS-UMR AGAP (FRA)
  • Ravel Sébastien, CIRAD-BIOS-UMR BGPI (FRA)
  • Ranwez Vincent, Montpellier SupAgro (FRA)
  • Rouard Mathieu, Bioversity International (FRA)
  • Ruiz E., INRA (FRA)
  • Sabot François, IRD (FRA)
  • Sarah Gautier, CIRAD-BIOS-UMR AGAP (FRA)
  • Summo Marilyne, CIRAD-BIOS-UMR AGAP (FRA)
  • This Dominique, Montpellier SupAgro (FRA)
  • Tranchant-Dubreuil Christine, IRD (FRA)
  • Vallier Félix, Université de Lyon (FRA)

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