South Green bioinformatic resources for tropical and Mediterranean crops

Rouard Mathieu, Bocs Stéphanie, Breton Catherine, Comte Aurore, De Lamotte Frédéric, Dereeper Alexis, Droc Gaëtan, Dufayard Jean François, Guignon Valentin, Hamelin Chantal, Larmande Pierre, Lopez David, Mahé Frédéric, Martin Guillaume, Orjuela-Bouniol Julie, Pitollat Bertrand, Ravel Sébastien, Ruiz Manuel, Sabot François, Sarah Gautier, Sempere Guilhem, Summo Marilyne, Tando Ndomassi, Tranchant-Dubreuil Christine. 2020. South Green bioinformatic resources for tropical and Mediterranean crops. . SFBI, IFB, GDR-BIM. Montpellier : SFBI, 1 p. Journées ouvertes de biologie, informatique et mathématique (JOBIM 2020). 20, Montpellier, France, 30 Juin 2020/3 Juillet 2020.

Matériel d'accompagnement : 1 résumé

Note générale : Le congrès s'est tenu en ligne

Résumé : South Green is a bioinformatics platform dedicated to the genetics and genomics of tropical and Mediterranean plants of agronomic interest and their related pathogens. It federates a network of bioinformaticians belonging to different units and institutes of Montpellier (Alliance Bioversity CIAT, CIRAD, INRAE and IRD) with a multidisciplinary expertise ranging from the data integration, bioinformatics software development, sequencing data analyses and high-performance computing. Exchange and collaborative developments are fostered through regular hands-on sessions on synergistic themes (information systems, pangenomic methods, graphical visualizations and workflows managers). The South Green web portal (www.southgreen.fr) gathers all the information systems and tools developed and supported by the platform. Indeed, South Green ensures the development of original information systems such as GreenPhyl, SNiPlay, Gigwa, AgroLD or the Genome Hubs, and offers sequencing data analysis pipelines through two workflow managers: Galaxy and TOGGLe. Overall, South Green's mission is to promote these original tools as well as their interoperability. A significant part of activities also comprises hands-on trainings that are regularly offered in the local community as well as with partners in the Africa and Asia on the following topics: Galaxy, NGS analyses, R, Perl, Linux, HPC administration (southgreenplatform.github.io/trainings/). Besides, South Green provides access to computing facilities for both users and developers engaged in this scientific area. South Green is part of the network of platforms of the French Institute of Bioinformatics (IFB).

Auteurs et affiliations

• Rouard Mathieu, Bioversity International (FRA)
• Bocs Stéphanie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-7850-4426
• Breton Catherine, Bioversity International (FRA)
• Comte Aurore, IRD (FRA)
• De Lamotte Frédéric, INRA (FRA)
• Dereeper Alexis, CIRAD-BIOS-UMR AGAP (GLP)
• Droc Gaëtan, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-1849-1269
• Dufayard Jean François, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-7427-6822
• Guignon Valentin, Bioversity International (FRA)
• Hamelin Chantal, CIRAD-BIOS-UMR AGAP (FRA)
• Larmande Pierre, IRD (FRA)
• Lopez David, CIRAD-BIOS-UMR AGAP (FRA)
• Mahé Frédéric, CIRAD-BIOS-UMR BGPI (FRA) ORCID: 0000-0002-2808-0984
• Martin Guillaume, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-1801-7500
• Orjuela-Bouniol Julie, IRD (FRA)
• Pitollat Bertrand, CIRAD-BIOS-UMR AGAP (FRA)
• Ravel Sébastien, CIRAD-BIOS-UMR BGPI (FRA) ORCID: 0000-0001-6663-782X
• Ruiz Manuel, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-8153-276X
• Sabot François, IRD (FRA)
• Sarah Gautier, INRA (FRA)
• Sempere Guilhem, CIRAD-BIOS-UMR INTERTRYP (FRA) ORCID: 0000-0001-7429-2091
• Summo Marilyne, CIRAD-BIOS-UMR AGAP (FRA)
• Tando Ndomassi, IRD (FRA)
• Tranchant-Dubreuil Christine, IRD (FRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/596098/)

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