Mots-Clés

R package Docker Markdown

Description

TITLE

Packaging and dockerization of R tools for the analysis of biological data.

KEYWORDS

R, package, Docker, markdown, bash

CONTEXT

The Hub of Bioinformatics and Biostatistics (henceforth, the Hub) was created in early 2015 as a platform of the Institut Pasteur. The driving idea behind the Hub's creation was to 1) bring together all bioinformaticians and statisticians, previously working in different experimental research Units within the campus, to promote a synergy among research engineers, stimulate their creativity and the development of novel ideas and 2) strengthen the bioinformatics and biostatistics support to Pasteur units through the recruitment of 45 new highly skilled and experienced research engineers during the last six years. Currently, the Hub is the biggest facility dedicated to computational biology in France. Support of the Hub to Pasteur units may take different forms depending on the needs of scientists. Our activities stretch from simple advice given on data analysis or experimental planning, up to long-term collaborative projects. Another mission of the Hub engineers is to contribute to the research effort in computational biology, for instance by the development or improvement of tools for the worldwide scientific community.

INTERNSHIP PROPOSAL

We are seeking a bright and highly motivated master student, who is interested in the development of highly trustable bioinformatical tools for the worldwide scientific community. The aim of the the internship is to take in charge and finish two projects.

The first project, "cute", aims to make available more than 40 R homemade functions.

See https://gitlab.pasteur.fr/gmillot/cute_little_R_functions

Steps are as follow:

- Challenge the functions.

- Package these functions for the different R package distributions (CRAN and Bioconductor).

- Creation of R Docker images that include the packages.

- Creation of a web page tutorial.

The second project, "slitherine", is a R wrapper of serpentine, a python tool to compare HiC matrix contacts (https://pubmed.ncbi.nlm.nih.gov/32311033/).

See https://gitlab.pasteur.fr/gmillot/slitherine

Steps are as follow:

- Creation of a Docker image.

- Creation of a web page tutorial.

- Implementation of the tool for a new way to compare to matrix contacts (collaboration with Vittore Scolari, Institut Curie and Romain Koszul, Institut Pasteur).

Each of these projects will lead to a publication.

ELIGIBILITY CRITERIA

M2 Master student or 5th year of an engineering school.

Strong experience in R. Strong motivation in informatics (Linux, bash, coding, etc.).

Strong analytical, verbal, and scientific writing skills in French. English is appreciated.

Knowledge of Markdown, Docker, GitHub and Nextflow would be a plus but is not a prerequisite, as it can be learned during the internship.

DURATION

Internship duration will be 6 months from 1 February 2022.

LOCATION

François Jacob Building, Institut Pasteur, 28 rue du Docteur Roux 75015 Paris.

APPLICATION

Please send your CV + short motivation letter or introductive email + recommendation letters (if any) to gael.millot@pasteur.fr.