The Institut de Biologie Paris Seine provides bioinformatics support and expertise using the Galaxy platform. They assist users in computational analyses of sequencing data, ensure transparency and reproducibility. They also provide training in Galaxy usage, conduct research in RNA biology and epigenetics, and follow advances in software and methods. The institute has expertise in programming languages, version control systems, and virtualization/container technologies. They have supported many Next Generation Sequencing analysis projects and developed publicly available tools.

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. 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