Job title: Research Engineer – Comparative Genomics workflow development (M/F)
Number of positions proposed: 1
Type of contract: Fixed-term contract – 24 months renewable or permanent project contract
Workplace: DYOGEN Team, led by Hugues Roest Crollius at Institut de Biologie de l’École Normale Supérieure (IBENS) in Paris, France
Expected date of employment: 1 March 2024
Proportion of work: Full time
Remuneration: Between €2900 and €3500 gross salary per month depending on experience
Desired level of education: Master, engineer or higher degree
Application deadline: February 1st, 2024
The recruited engineer will have the responsibility of developing novel computing solutions for building gene families and reconstructing their evolutionary history, using data from synteny and molecular evolution. The person recruited will carry out the computation required to keep the ATLASea portal up to date with comparative genomics data from existing tools and the new tools developed
The recruited engineer will have the responsibility of developing novel computing solutions for building gene families and reconstructing their evolutionary history, using data from synteny and molecular evolution. The person recruited will carry out the computation required to keep the ATLASea portal up to date with comparative genomics data from existing tools and the new tools developed:
- Implementing innovative solutions (data model, algorithms) to address the technological complexities associated with comparing thousands of annotated eukaryotic genomes.
- Collaborating with the team’s researchers to develop innovative bioinformatics methods.
- Creating analysis pipelines with parallel computing capabilities on a high-performance computing cluster (HPC).
- Work closely with all engineers of the ATLASea project to guarantee data accuracy and reproducibility while also facilitating global accessibility for the scientific community.
- Develop and manage bioinformatics data analysis pipelines adhering to the FAIR principles (Findable, Accessible, Interoperable, Reusable) for increased efficiency and ease of use.
- Collaborate with BYTE-Sea project partners to organize and maintain long-term storage of comparative genomics data.
- Stay updated on advances in genomics, bioinformatics, and computational biology.
- Share findings, including biological results and analysis tool development, through presentations and publications.
- Master, or engineer degree or higher degree in computer science or bioinformatics, with a focus on workflow and production system development.
- Fluent in French and English, with excellent communication and listening skills, and a collaborative mindset.
- Knowledge in genome evolution and comparative genomics is a desirable asset.
Skills and qualities required:
- Knowledge on implementing parallel computing on HPC systems.
- Strong programming skills.
- Familiarity with Linux/Unix operating systems.
- Ability to develop data analysis pipelines using tools (such as snakemake or nextflow).
- Understanding of FAIR principles for data analysis, management, and software development.
- Fluent in written and spoken English.
- Strong analytical skills.
- Very good organizational abilities.
- Self-driven and capable of independently managing tasks.
- Excellent interpersonal skills and capability to work effectively in a team.
The research engineer will work on the PEPR ATLASea programme, the aims of which are to sample, sequence and analyse the genomes of 4,500 marine species from the coasts of France, with a high coverage of species from mainland France and including species from French overseas territories.
Led by the CNRS and the CEA and funded for 8 years, ATLASea is a consortium of 7 institutions and 5 research federations and infrastructures bringing together around 50 engineers and researchers. The position is part of the targeted BYTE-Sea project, which will develop all the IT infrastructure and tools for processing and analysing the data and make it available to the international community. The engineer will work as part of the DYOGEN (Dynamics and Organisation of Genomes) team at the Institut de Biologie de l’École normale supérieure (IBENS). The engineer will interact regularly with the other bioinformatics engineers involved in the partner laboratories of the ATLASea PEPR. IBENS is a multidisciplinary fundamental research institute in the 5th arrondissement of Paris. It has first-rate platforms, including a 4000-core computing cluster.
Risks and constraints:
The job is located in a sector covered by the protection of scientific and technical potential (PPST), and therefore requires, in accordance with the regulations, that the person recruited be authorised by the competent authority (FSD).