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ARTbio Flyer

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A summary of the ARTbio facility at the Institut de Biologie Paris Seine

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ARTbio Flyer

  1. 1. Accessible, Reproducible & Transparent bioinformatics at the Institut de Biologie Paris Seine http://artbio.fr • http://mississippi.fr Our Services • ARTbio supports the computational analyses of its users with Galaxy servers. Galaxy users can design and execute computational treatments of data using a friendly web interface. Galaxy ensures transparency and reproducibility of analyses and provides powerful means to share research with collaborators and publishers. • We advise on experimental and statistical designs of Next Generation Sequencing experiments and assist our users in choosing the most appropriate tools and workflow for their analyses. • We ensure advanced training in Galaxy usage. Our Expertise • We conduct research in RNA biology, epigenetics, metagenomics as well as in bioinformatics and publish our results in scientific journals. • We have an in-depth knowledge of the Galaxy software as well as of how it can be used, from raw data acquisition to publication. • We follow advances in software and methods and integrate them in Galaxy. • We ensure quality of projects through continuous integration technologies and AGILE guidelines for interacting with our users. Our Technologies • We use the programming languages R, Python, Perl and Bash, the revision control softwares Git and Mercurial and tools for continuous integration such as Planemo and Jenkins. • We implement virtualization and container technologies (e.g. Docker) that enable reproduction of analyses in different hardware infrastructures and we are connected to cloud infrastructures such as the one provided by the Institut Français de Bioinformatique, allowing us to scale up our computing resources on demand. Contact christophe.antoniewski@upmc.fr & http://artbio.fr
  2. 2. Project support: Over the past year we have provided advanced support to many Next Generation Sequencing (NGS) analysis projects, including projects aimed at understanding epigenetic functions of piRNAs (1), antiviral RNA interference (2) or roles of miRNAs in stem cell differentiation (3). Tools: We developed and made publicly available the mississippi suite of tools for mining small RNA sequencing datasets (4). We are currently releasing a set of Galaxy workflows aimed at detecting viruses or identifying new viral species from small RNA sequencing datasets (5). Another example of development is our DockerToolFactory tool that allows everyone to execute customized R, python, perl or bash scripts without leaving the Galaxy interface (6). Methodology developments: We are closely following progresses in methodologies such as continuous integration (e.g. Planemo, Jenkins CI), environment virtualization (e.g. Virtual machines, Deployment in Clouds and Docker) 1. A. de Vanssay et al., Paramutation in Drosophila linked to emergence of a piRNA- producing locus. Nature. 490, 112–115 (2012). 2. P. Miesen et al., Distinct sets of PIWI proteins produce arbovirus and transposon- derived piRNAs in Aedes aegypti mosquito cells. Nucleic Acids Res. (2015), doi:10.1093/nar/gkv590. 3. A. Jouneau et al., Naive and primed murine pluripotent stem cells have distinct miRNA expression profiles. RNA. 18, 253–264 (2012). 4. https://testtoolshed.g2.bx.psu.edu/view/mvdbeek/mississippi_toolsuite/ 5. https://toolshed.g2.bx.psu.edu/view/drosofff/suite_visitor2/ 6. https://bitbucket.org/mvdbeek/dockertoolfactory

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