Job title: Research Engineer in software development (M/W)
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 SupĂ©rieure (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
Missions:
- Priority mission 1: development of version 2 of Genomicus (http://www.genomicus.fr/) to allow the integration of a large number of genomes and taxonomic groups in line with the needs of ATLASea. The main phases of this development include restructuring of the database and redesign of the visualization and data access interfaces, as well as the potential implementation of a user session system.
- Priority mission 2: development of new features in the front-end of Genomicus (web server/visualization) and integration of Genomicus into the global portal dedicated to the ATLASea project, which brings together other databases and web servers set up by collaborators.
- Other occasional or permanent missions are to be expected. These include automated code deployment (DevOps) and development of data processing automation procedures.
Activities:
To accomplish these missions, the engineer will work primarily in collaboration with members of the research team (a research director, a research engineer, a research assistant, and an associate professor), as well as various other members of ATLASea and collaborators. However, it will be necessary to work independently for a significant portion of the time and demonstrate initiative. The engineer will be required to communicate their work internally and externally, to specialists and non-specialists.
Expected skills:
- Master degree, engineer degree or higher in computer science or bioinformatics
- Good communication skills, attentive listening, proactive approach, enjoy working in a team
- Knowledge in biology and comparative genomics would be a plus but not essential.
Skills and qualities required:
- Good knowledge of SQL database design and querying
- Excellent command of at least one programming and scripting language
- Proficient in PHP, HTML, CSS, and JS programming
- Good knowledge with the git version control tool and continuous integration development cycles
- Understanding of the Linux operating system
- Knowledge of FAIR principles for data analysis and management and software development.
- Ability to provide reports and present results in team meetings.
Personal skills:
- Analytical rigor.
- Excellent organisational skills.
- Autonomy in planning and managing activities.
- Strong interpersonal skills and ability to work in a team.
Work context:
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 supĂ©rieure (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).