Bioinformatics Jobs at EMBL Germany
Are you searching for cutting-edge Bioinformatics Jobs that combine software engineering, spatial omics, and real-world biomedical impact? This exciting opportunity at EMBL Hiring in Heidelberg offers one of the most competitive Life Science Jobs in Europe. Designed for professionals and fresh talent alike, this role represents a premium Jobs Opportunity for life science graduates seeking meaningful jobs in Germany within a world-class research ecosystem.
About the Company
The European Molecular Biology Laboratory (EMBL) is one of the world’s leading research institutions driving innovation across molecular biology and bioinformatics. Through EMBL Hiring, scientists and engineers from across the globe access elite Life Science Jobs in Germany and beyond. EMBL is known for its collaborative culture, open science philosophy, and commitment to scientific excellence and diversity.
Job Details:
- Job Title: Research Software Engineer – Spatial Omics
- Organization: European Molecular Biology Laboratory (EMBL)
- Funding Partner: GlaxoSmithKline (GSK) – Cellzome
- Location: Heidelberg, Germany
- Work Model: Hybrid
- Employment Type: Full-time
- Job Requisition ID: JR2757
- Contract Length: 2 years (with possibility of 1-year extension)
- Closing Date: 15 February 2026
Bioinformatics Job Role Overview
The Oliver Stegle Team and the Bioimage Analysis Support Team at EMBL Heidelberg are seeking a Research Software Engineer to contribute to the development and maintenance of highly-used open-source software for spatial omics data analysis.
This role is funded by GSK as part of a collaboration between Cellzome (a GSK company) and EMBL. The successful candidate will work closely with computational bioimage analysis teams at GSK, as well as with the scverse open-source ecosystem.
The position focuses on expanding and maintaining SpatialData, a geospatial Python–based data infrastructure for spatial omics developed at EMBL.
Key Responsibilities
-
Software Development & Infrastructure
- Develop software to improve the robustness, scalability, and functionality of the SpatialData framework
- Refactor existing codebase components to enhance long-term stability and maintainability
- Support development of data analysis pipelines for spatial omics workflows within GSK
-
Open-Source & Standards Development
- Contribute to Next Generation File Format (NGFF) and OME-Zarr
- Advance open standards for bioimaging and spatial omics data
- Collaborate with EMBL, GSK, and scverse contributors
-
Automation & CI/CD
- Set up, test, and maintain continuous integration (CI) pipelines
- Ensure automation systems run smoothly to support software reliability
-
Documentation & Training
- Improve technical documentation and example notebooks
- Develop training materials to support adoption by external developers and users
Required Qualifications for Bioinformatics Jobs
- Master’s degree in Life Sciences or equivalent professional experience
Preferred Qualifications
- Experience contributing to open-source projects
- Proficiency with Git and GitHub workflows
- Background in:
- Bioinformatics
- Single-cell analysis
- Spatial biology
- Experience in:
- Scientific or software user support
- Organising and delivering scientific workshops
Technical Skills (Python)
- Experience with or willingness to learn:
- Geospatial: dask, xarray, geopandas
- Bioimaging: zarr, ome-zarr, napari
- Single-cell / Spatial Omics: AnnData, Scanpy, SpatialData, scverse tools
Core Competencies
- Strong curiosity-driven and research-oriented mindset
- Passion for open-source software and community development
- Excellent communication and organisational skills
- Ability to collaborate across multidisciplinary, international teams
- Fluency in English
Professional Development Opportunities
- Collaboration with multidisciplinary teams across EMBL, GSK, and scverse
- Support to attend leading conferences and workshops:
- Single-cell & spatial omics (e.g. SCG)
- Python & data science (e.g. PyCon, PyData)
- Deep exposure to the open-source geospatial and bioimaging software stack
Salary & Benefits
Compensation
- Grade 5 salary: from €4,031.02/month (net, before 12.05% social security deduction)
- Annual salary review
Benefits
- Salary exempt from income tax
- Pension scheme and social insurances
- Private medical insurance (family included)
- 30 days annual leave + public holidays
- Flexible working arrangements
- Relocation package (if applicable)
- Family benefits (child allowances, parental leave, kindergarten access)
- International newcomer support (visa exemption, education grants, travel support)
- Campus amenities (gym, cafeteria, shuttle bus, social clubs)
Application Process for Bioinformatics Jobs
Applicants must submit via the online system:
- CV
- Cover letter (detailing open-source experience or interest)
- Contact details for 3 referees
- Optional: Links to GitHub or repositories demonstrating contributions
