ATLASea is a program focused on the genomics of marine biodiversity along the French coast. Led by the CNRS and the CEA, it includes numerous partner institutions in France and is part of a broader international context. ATLASea will sequence the genomes of 4,500 species along the French coastline in mainland France and overseas. The 8-year program will sample marine biodiversity under the coordination of the MNHN through expeditions and with the help of marine stations. Sequencing and genome assembly will be performed at Genoscope under the coordination of France GĂ©nomique, and data will be managed and analyzed under the coordination of the French Institute of Bioinformatics (as part of the BYTE-SEA project). Pilot projects coordinated by the ANR will offer the French scientific community the opportunity to exploit this massive data in the context of the analysis and synthesis of marine molecules, the ecology of invasive species, and innovation.
Job Description
As a partner of the BYTE-SEA project, dedicated to setting up the IT infrastructure for the PEPR ATLASEA, the GenOuest platform is recruiting a software developer (M/F) to contribute to the development of an automated system for creating web portals dedicated to exploring the genomic data produced by the project.
The software developer will work on continuous integration pipelines, data processing and validation workflows, and the integration of existing or to-be-created web applications. He/she will be responsible for ensuring the scalability of the solutions chosen for the integration of several thousand genomes. Finally, he/she will take an active part in national and international collaborations within the framework of the project by actively participating in meetings and workshops.
Main activities
- Contribute to the development of the BEAURIS software (https://gitlab.com/beaur1s)
- Ensure the maintenance and evolution of existing modules
- Integrate new data pre-processing modules
- Integrate new web components for data visualization
- Ensure the dissemination of generated data in accordance with FAIR principles and those of open science
- Ensure interconnection with external databases
- Ensure the scalability (calculation, web interfacing) of the existing solution for several thousand genomes
- Disseminate and promote results and technological achievements in the form of reports, publications, and oral presentations
- Ensure technological watch
- Participate in European and international initiatives around the ATLASea project and international partner projects (Earth BioGenome Project)
Related activities
- Present your activities: webinars, work meetings by videoconference and in person.
- Participate in user support and assistance.
- Participate in the organization and delivery of training courses on the use of the solutions implemented
Skills
- Proficiency in Python language in Linux environment
- Proficiency in web technologies (JavaScript, REST API)
- Knowledge and practice of continuous integration, continuous delivery and continuous deployment
- Knowledge of associated tools and technologies (GitLab CI, Docker, Ansible).
- Basic knowledge of HPC computing systems (Slurm, …)
- Background in the field (bioinformatics, genomics)
- English language: B2 to C1 (Common European Framework of Reference for Languages)
- Ability to write documentation
- Ability to work in project mode and as part of a team.
- Ability to work remotely.
- Responsiveness, autonomy, initiative, thoroughness.
- Managing emergency situations and prioritizing.
- Team spirit and sense of collaboration.
- Listening skills and interpersonal skills.
- Ability to learn and train continuously in a rapidly changing scientific context.
- Skills in development and continuous integration methods
- Guarantee the quality and relevance of analysis tools and results
- Scientific rigor, organizational skills.
- Interpersonal skills and a taste for teamwork
Working environment
The position is attached to the GenOuest platform, within the IRISA computer science research laboratory in Rennes. The GenOuest platform is a member of the French Institute of Bioinformatics. Established in the bioinformatics community for more than 20 years, GenOuest offers its services to a large community of more than 800 scientists and carries out numerous development projects focusing on computation, reproducibility of treatments and management of scientific data.
The software developer will work in close collaboration with the platform engineers and the program partners (IFREMER-SeBiMer (Plouzané), ABiMS (Roscoff), IFBcore (Paris), ENS Ulm (Paris), MNHN (Paris) and Genoscope (Evry).
The position offered is located on the Beaulieu campus in Rennes, with travel to the host teams’ sites to be expected.
Full-time position, 38.5 hours per week with RTT.
Contract duration: 12 months renewable
Possibility of teleworking after 6 months of seniority.
About the laboratory