Deployment of genome databases for insects using Galaxy Genome Annotation

BIPAA is a bioinformatics platform from the French National Institute for Agricultural Research (INRA). It is located in Rennes (France), and it is dedicated to the study of insect genomes. BIPAA is the home of several public reference databases hosting multiple insect genomes: AphidBase (for aphids), LepidoDB (for lepidopterans) and ParWaspDB (for parasitoïd wasps). For each hosted genome, users have access to a collection of web applications allowing to explore reference genome assembly and annotations (e.g. genome browser, gene reports), to analyze this data (e.g. dedicated Galaxy server, specific web applications), and to collect new scientific knowledge (e.g. manual curation of annotations using Apollo). Most of these application are part of the GMOD project. Until recently, the process of making a new genome available online was a long, manual and error-prone process. As the number of hosted genomes is quickly increasing, the need for a new, automatic, flexible, and scalable 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 consitutes a demonstration of GGA for rapid and flexible deployment of information systems for non-model organisms, where Galaxy is used as an orchestrator for data management and loading. 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.