Mots-Clés

antiobioresistance, bacterial taxonomy, resistome, virulome, Galaxy workflow

Description

CONTEXT:

The Institut Français de Bioinformatique (IFB; france-bioinformatique.fr) is a national biology-health infrastructure (INBS) that federates 36 regional bioinformatics platforms and teams, and a coordinating unit, IFB-core (UAR CNRS 3601). The IFB is also the French node of the European Bioinformatics Research Infrastructure ELIXIR (ESFRI). The main mission of IFB is to support life science research by deploying a digital infrastructure, software resources, bioinformatics services and training, anticipating future developments in the field and participating in methodological innovations. IFB activities cover the diversity of the thematic fields of all its supervisory bodies: fundamental research, health, environment and agronomy.

The IFB is involved in several large-scale national projects in different areas of Life Sciences and Health, including the ABRomics project, which aims to develop a digital platform for collecting, analyzing, organizing and making accessible bacterial (meta)genomic data and their metadata for clinical and epidemiological antibiotic resistance research and surveillance (www.abromics.fr). ABRomics relies on a network of researchers from 44 teams including epidemiologists, clinical microbiologists, bioinformaticians and mathematicians, and the wider research community. ABRomics will provide a unique data storage and analysis infrastructure, developed by a team with expertise in DevOps, database and software development, data management and data analysis.

In this context, we are recruiting an engineer whose main mission will be to ensure the deployment of analysis workflows based on genomic and metagenomic sequencing data (Illumina, nanopore), from data quality control and assembly to the typing of analyzed bacteria and the detection and classification of resistance genes.

WORKING ENVIRONMENT:

The position is located on the AuBI bioinformatics platform (https://mesocentre.uca.fr/projets-associes/plateforme-aubi), which is hosted at the Mésocentre Clermont Auvergne (UCA, Site des Cézeaux). The candidate will be directly supervised by a platform engineer involved in the ABRomics project, in close collaboration with several other IFB engineers involved in the development of the digital platform. The candidate will also work closely with UMR Inserm 1071 M2ISH/ Centre National de la Référence de la résistance aux antibiotiques (Site Dunant). The development team is located at different sites in France, and regular remote work is essential.
The successful candidate will be integrated into the host team, and will participate in IFB and ABRomics project working groups relevant to his/her mission, both on-site and via visioconferences. The job will require occasional travel in France and abroad to take part in meetings, training courses and/or scientific events.

MISSIONS AND ACTIVITIES:

The recruited engineer will be involved in the development and validation of workflows from the collection of "-omics" data, to the detection of genes and mutations associated with antibiotic resistance. The first workflows will focus on genomics and metagenomics, and should handle different types of input data (short and long-reads) and integrate all the key steps of assembly-based analyses (cleaning, taxonomy, quality, assembly, typing, functional annotation). The person recruited will also be responsible for interfacing workflows and their interoperability with Galaxy (https://galaxyproject.org/).
In addition, 20% of working time will be allocated to activities linked to the host site.

The recruited engineer will be responsible for the following activities:

- Develop and improve existing scripts in Python/R
- Code tools and build workflows in Galaxy
- Perform data processing
- Benchmark tools on the IFB computing cluster
- Adapt IT applications to the needs of the multi-sites of the project
- Manage and maintain the developed and shared tools
- Provide advice and training on the techniques and tools developed
- Apply and enforce current rules of deontology, ethics, good clinical and epidemiological practice
- Maintain a scientific and technological watch
- Report on work progress to the IFB scientific committee and the ABRomics consortium, and participate in professional networks
- Disseminate and promote results in the form of technical reports or studies

COMPETENCES:

Training:

Training in bioinformatics or computer science
Minimum level Bac+5 (Master) preferred

Knowledge:
- Good knowledge of biology and genomics
- Good knowledge of Python programming (strongly preferred), and of R
- Knowledge of data analysis
- Knowledge of how APIs and webservices work
- Knowledge of a computing cluster environment would be a plus
- Knowledge of environment managers (conda)
- Knowledge of docker would also be a plus

Technical skills / experience:
- First experience in developing Galaxy tools would be a plus
- Linux environments
- Free Software and Open Data culture

Operational skills:
- Proficiency in the Linux/Unix environment
- Practice of Python, virtual environments, Conda
- Use of Git
- Teamwork skills
- Find technical solutions to a given problem
- English language skills

Behavioral skills:
- Ability to make proposals
- Ability to listen and summarize to technical and non-technical contacts
- Technical autonomy and management of priorities
- Organizational skills
- Ability to work in a multi-site team