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Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientiﬁc software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting… (More)
Research processes in Life sciences are evolving at a rapid pace. This evolution, mainly due to technological advances, offers more powerful equipment and generalizes the digital format of research data. In the data deluge context, we need to overcome the current "datanami" and prepare for the future. In Life Sciences, we are noting a sharp increase of… (More)
BACKGROUND Many bioinformatics tools use reference data, such as genome assemblies or sequence databanks. Galaxy offers multiple ways to give access to this data through its web interface. However, the process of adding new reference data was customarily manual and time consuming, even more so when this data needed to be indexed in a variety of formats… (More)
Multi user open source batch scheduling software based on Docker containers with custom scheduler and executor plugin mechanisms.
BACKGROUND With next-generation sequencing (NGS) technologies, the life sciences face a deluge of raw data. Classical analysis processes for such data often begin with an assembly step, needing large amounts of computing resources, and potentially removing or modifying parts of the biological information contained in the data. Our approach proposes to focus… (More)
We report the development of the ReproGenomics Viewer (RGV), a multi- and cross-species working environment for the visualization, mining and comparison of published omics data sets for the reproductive science community. The system currently embeds 15 published data sets related to gametogenesis from nine model organisms. Data sets have been curated and… (More)