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The 2017 Galaxy Community Conference (GCC2017) is being held in Montpellier, France, 26-30 June.  GCC2017 will include keynotes and accepted talks, poster sessions, demos, birds-of-a-feather meetups, exhibitors, and plenty of networking opportunities. There will also be three days of pre-conference activities, including hackathons and training. If you work in data-intensive biomedical research, there is no better place than GCC2017 to present your work and to learn from others.
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Thursday, June 29 • 15:40 - 17:00
P21: Deployment of genome databases for insects using Galaxy Genome Annotation

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Anthony Bretaudeau 1*
1 : Institut de Génétique, Environnement et Protection des Plantes  (IGEPP), Institut National de la Recherche Agronomique : UMR1349, Universite de Rennes 1 : UMR1349, Agrocampus Ouest : UMR1349Domaine de la Motte au Vicomte BP 3532735653 Le Rheu -  France
* : Corresponding author

BIPAA is an INRA bioinformatics platform located in Rennes (France). It is dedicated to insect genomics.

BIPAA is the home of several reference genome databases: AphidBase (aphids), LepidoDB (lepidopterans) and ParWaspDB (parasitoïd wasps).

For each genome, a collection of web applications (including JBrowse, Tripal or Apollo from GMOD project) allows users to explore reference assemblies and annotations (e.g. genome browser, gene reports), to analyze them (e.g. dedicated Galaxy server), and to collect new scientific knowledge (e.g. manual curation using Apollo).

As the number of hosted genomes is quickly increasing, the need for an automatic, flexible, and scalable hosting architecture imposed itself. As a result, we set up a new system, based on the developments from the Galaxy Genome Annotation project (GGA, https://github.com/galaxy-genome-annotation).
Making a new genome available is now as easy as launching a collection of pre-configured dockerized web applications, and loading the reference data (genome, annotation) using a dedicated GGA Galaxy flavor instance.

This constitutes a demonstration of GGA for rapid, flexible and reproducible deployment of information systems for non-model organisms, where Galaxy is used as an orchestrator for data management.

In this poster we will expose the architecture of this new system as used on BIPAA (10 genomes already online). We will also highlight the specific developments that were done, and present the planned features for the coming months.

All developments are available under a free license (MIT or AGPL) and were contributed to the GGA or GMOD GitHub repositories.

avatar for Anthony Bretaudeau

Anthony Bretaudeau

INRA, BIPAA and GenOuest platforms
I work on insect genomics: analysis tools in galaxy and the galaxy genome annotation project | I also like to talk about bunnies and other fun animals.

Thursday June 29, 2017 15:40 - 17:00
Le Corum Le Corum

Attendees (5)