ARTbio

The Institut de Biologie Paris Seine (IBPS) was created in January 2014 in the Jussieu Campus within the Université Pierre et Marie Curie (UPMC). Its main goal is to bring together all the biology researches developed in the campus so it can become the UPMC's biology flagship.

In May 2015, ARTbio, a bioinformatics platform, was created within IBPS. Aiming for Accessibility, Reproducibility and Transparency in computational biology, the team offers support and analyses services for scientists in the UPMC and elsewhere. For doing so, ARTbio works with the Galaxy system, an open source and web-based platform dedicated to scientific and biomedical research. The Galaxy project proposes a user-friendly interface where everyone would be able to run one's own computational data analyses as well as reproduce and share complete analyses.

Thanks to Galaxy, ARTbio is able to involve biologists in their own computational analyses. Besides accomplishing computational analyses, other types of services are available, as assisting the experimental and computational analyses and providing advanced training in Galaxy usage.

Additionally, ARTbio provides two Galaxy instances: Mississippi (public) and Plastisipi (access restricted to UPMC) which are available for autonomous users for free. These instances are maintained by the team that also develops and adapt tools to the Galaxy environment.

In the Galaxy system, tools can be organized by purpose in suites of tools and be arranged in workflows. ARTbio has made publicly available a suite of tools called Mississipi toolsuite for mining mi, si and pi RNA sequencing datasets. Another suite of tools, suite_metavisitor_1_2 was recently released followed by a BioRxiv preprint. These tools are combined within a set of Galaxy workflows to create the Metavisitor package. Thus, scientists and health professionals can use Metavisitor tools and workflows to detect known viruses and to discover novel viruses fromRNA or DNA sequencing datasets.

During my six months internship at ARTbio, I have been working with the Metavisitor suite. In the pages that follow, I will present my propositions for improving Metavisitor.