Missions

The person recruited will be involved in the development and validation of workflows for the processing and analysis of metagenomic data as part of the ABRomics project (IFB and Institut Pasteur). In this context, the analyses will include the detection of genes and mutations associated with antibiotic resistance by going through the stages of assembly, genome reconstruction (MAGs), and their taxonomic and functional annotation. He/she will also be responsible for developing and implementing innovative algorithms for modelling and predicting the Eco-Evo dynamics of resistance genes. In particular, it is envisaged to implement algorithms to deduce co-occurrence networks resolved at the (pan)genome level in order to detect and predict recent gene flow (ABR). One objective will be to develop a workflow for analysing (pan)genomic networks and predicting the potential spread of ABR in reservoirs/ecosystems. Finally, he/she will also be responsible for interfacing workflows and their interoperability with Galaxy (https://galaxyproject.org/).

Activities

- Developing and improving existing scripts in Python/R
- Implementing tools in Galaxy
- Developing workflows in Galaxy
- Data processing
- Managing and maintaining shared IT tools
- Advising and training on the techniques and tools developed
- Applying and ensuring the application of current rules of deontology, ethics and good clinical and epidemiological practice
- Monitor scientific and technological developments
- Report on the progress of work to the IFB select committee and the ABRomics consortium, and take part in professional networks
- Disseminating and promoting results in the form of technical reports or studies

Skills

Training :
Training in bioinformatics or computer science
Minimum 5 years of higher education (Master's degree) preferred
Technical skills / experience :
- Development of bioinformatics tools
- Integration of Galaxy tools would be a plus
- Linux environments
Knowledge :
- Good knowledge of biology and metagenomics
- Good programming skills (Python strongly preferred, R)
- Knowledge of biostatistics/data analysis
- Knowledge of a cluster computing environment would be a plus
- Knowledge of the Galaxy API
Operational skills:
- Proficiency in the Linux/Unix environment
- Python, virtual environments, Conda
- Use of Git
- Working in a team
- Finding technical solutions to a given problem
- English language skills
Behavioural skills :
- Being able to make proposals
- Ability to listen and summarise with technical and non-technical contacts
- Technical autonomy and management of priorities
- Organisational skills
- Public speaking skills

Work Context

The IFB is involved in a number of large-scale national application projects in various areas of Life Sciences and Health, including the ABRomics project, which aims to develop a secure cross-sector One Health digital platform to make (meta)genomic data on bacterial infectious diseases and their associated clinical and epidemiological metadata accessible to a meta-network of researchers from 44 teams including epidemiologists, clinical microbiologists, bioinformaticians and mathematicians and the wider research community (https: https), clinical microbiologists, bioinformaticians and mathematicians and the wider research community (https: //www. france-bioinformatique.fr/actualites/abromics-a-digital-platform-on-antimicrobial-resistance-to-store-integrate-analyse-and-share-multi-omics-data/). The platform will meet two main objectives:
- To establish a repository of structured, interoperable, standardised and well-annotated multi-omics microbiological data of human, animal and environmental origin, with appropriate mathematical and bioinformatics tools to answer research questions related to antibiotic resistance that could not be addressed without such a platform.
- To set up a shared platform to facilitate the monitoring of antibiotic resistance in human and veterinary medicine, including environmental and food isolates, in order to monitor the transmission and epidemics of pathogens in your country.

Constraints and risks

Constraints and risks associated with working at a computer workstation.