About the team/job
The European Molecular Biology Laboratory (EMBL) is a world leader in scientific research and at the forefront in the development of cutting-edge technologies. EMBL scientists generate terabytes of data every day from all fields of modern biology (sequencing, imaging, metabolomics, proteomics…). Secure, traceable, robust, efficient and user-friendly data management solutions are needed to store, share and analyse this data efficiently. The Genome Biology Computational Support (GBCS) group maintains and develops an array of services used EMBL-wide by dozens of scientists daily.
These activities include the development of data management solutions, the maintenance of data analysis platforms (Galaxy, RStudioServer Pro) and associated servers (physical and virtual), the development of NGS analysis workflows as well as supporting both wet and computational biologists in their computational/analysis tasks. In particular, the GBCS team develops STOCKS (https://gbcs.embl.de/STOCKS), a complete web-based solution offering both a modern Electronic Lab Notebook and an advanced dataset management platform allowing you to connect samples, raw and analyzed data to protocols and daily lab notes. With hundreds of users every month, STOCKS usage is growing rapidly and is a key player of the global EMBL data management and open science strategies.
The Genome Biology Computational Support is looking for a highly motivated Senior Django Developer/Bioinformatician to support and develop its different services.
The STOCKS web platform is built around a python Django back-end (exposing a Django-based administration UI, REST API), a modern user facing interface developed in Vue.js and (python) command line clients for our advanced users and automated procedures. You will play a key role in the STOCKS project as the technical lead and main developer of the STOCKS server. You are indeed in charge of specifying and developing the data model, the REST API, integration with other EMBL services and the admin interface. You are also responsible for the deployment and maintenance of the production STOCKS server, including the data backup strategy.
In addition, you are responsible of an EMBL-wide Galaxy installation (https://galaxyproject.org/) maintained by the GBCS. Here, your role covers the maintenance (server configuration, updates, tool installation, deployment of new genomes) of the platform, the wrapping of tools developed internally, the smooth integration with STOCKS and supporting users.
Overall, the position involves:
- the development of the STOCKS back-end. In addition to their developer role, the successful candidate will also be the STOCKS technical lead.
- the maintenance of an EMBL-wide Galaxy installation
- the co-maintenance of EMBL-wide instances of Gitlab and Mattermost (hundreds of users) together with the Bio-IT project
- installation/packaging of tools, workflows and scientific libraries (both on compute servers and within Galaxy using e.g. easybuild), also using container technologies
- maintenance of GBCS servers and virtual machines hosting GBCS services
- supporting users to solve their everyday technical issues
- supporting users of the provided GBCS services (Galaxy, STOCKS, …) on a daily basis and assemble, organize and provide trainings on these services.
- Ideally 5+ years of professional experience with the python Django framework, providing REST endpoints and deploying projects in production.
- Advanced experienced with git and continuous integration techniques (GitHub or GitLab).
- Excellent experience with Unix server administration, database administration, unix user environment set-up including conda and virtualenv technologies, shell scripting.
- Experience with containerization, S3 data storage and deployment of apps in the cloud (Kubernetes, OpenStack).
- Experience maintaining a Galaxy instance and a good understanding of using cluster schedulers (preferrable SLURM).
- Experience in bioinformatics and a good understanding of molecular biology.
- Practical experience with data analysis and workflow management systems like Nextflow, Snakemake or, ideally, the Galaxy platform.
- Very good understanding of the challenges behind large data analysis (e.g. sequencing, bioimage analysis).
- Understanding of LIMS and Laboratory Notebooks.
- Excellent organizational skills.
- Interest in open-source projects.
The successful candidate should be able to work independently, while being an excellent team player, be user/community oriented, open-minded and creative.
Fluency in English is mandatory.
Why join us
You believe in free and open-source initiatives; you like to work on a project with an already established and expanding user base; you want to work in a scientific, international and academic environment; you are creative and like innovative solutions; you want to make the difference.
This is a fantastic opportunity to work in a team at the cutting edge of technology development and work at a world leading institute. EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation with a very collegial and family friendly working environment. The remuneration package comprises a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits.
We encourage personal and professional development and are committed to ensuring our employees feel valued, supported and empowered to reach their potential at work.
Our employees have access to a wide range of benefits including:
- 30 days annual leave per year plus national public holidays
- Flexible work arrangements
- Unique pension scheme
- Annual salary review
- Private medical insurance for you and your immediate family
- Relocation package
- On-site cafeteria and canteen
- Casual dress code
- Social club activities
- On-site childcare facility
- Additional benefits for non-resident staff
More information on Work at EMBL | Jobs | EMBL
What else you need to know
We are Europe’s flagship research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory with more than 1900 employees from many nations, operating across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, Hamburg, Grenoble and Rome.
EMBL is a signatory of DORA. Find out how we implement best practices in research assessment in our recruitment processes here.
Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.
Please apply online through EMBL job site. Please click Apply to access.