Research Software Engineer

Spatial Transcriptomics is a rapidly emerging field that combines the "what" of genomics with the "where" of imaging. To support this, the Functional Genomics team is partnering with the BioImage Archive to create a unified resource for this data. You will join a unique, interdisciplinary project bridging these two world-leading teams. We are looking for a talented developer to build the "Spatial Transcriptomics Portal," a greenfield resource that will support scientists worldwide to submit, find, explore, and reuse this complex multi-modal data.

Your role will work across the full technical stack to architect and build a new platform from the ground up. You will act as the technical bridge between the genomic and imaging domains, designing systems that allow these distinct data types to be harmonised, validated, and visualised together.

• Portal Development: Design and implement the new Spatial Transcriptomics portal, including backend API services, frontend user interfaces, and supporting infrastructure.
• Search & Discovery: Develop a shared and powerful search interface that allows researchers to discover datasets based on the rich biological metadata facets that accompany these experiments.
• Data Flow & Validation: Design automated pipelines to validate incoming data against agreed standards (FAIR principles) and route submissions to the correct archival resources.
• Data Conversion: Support the development of conversion pipelines to transform raw data files into cloud-native formats (e.g., OME-Zarr) optimised for visualisation in the portal.
• Visualisation Integration: Embed and integrate advanced spatial visualisation tools into the portal, ensuring users can seamlessly interact with high-resolution images and gene expression overlays.
• System Integration: Act as the technical liaison between the BioImage Archive and Functional Genomics, as well as with central EMBL-EBI storage and search infrastructure teams, ensuring that the new portal integrates seamlessly with our existing high-performance systems.

You have: You should have a university degree in computer science, life sciences, or a related discipline and experience in a software development capacity.

• Substantial experience developing full-stack web applications.
• Solid experience with Java or Python for backend development.
• Extensive hands-on experience with JavaScript and modern frontend frameworks (e.g., React).
• Experience with Containerisation (Docker) and deploying applications to Kubernetes environments.
• Experience configuring CI/CD pipelines (e.g., GitLab CI, Jenkins) for automated testing and deployment.
• Experience working with databases (Relational or NoSQL) and designing data models.

Personal Attributes: A strong affinity with the goal of EMBL-EBI to provide open data to the global scientific community. Excellent communication skills, with the ability to bridge the gap between technical and scientific requirements. A self-starter attitude, comfortable working on a greenfield project with evolving requirements.

You may also have: Experience designing data systems that operate at scale. Experience working with biological data, particularly BioImaging or Genomics formats. Experience with search infrastructure (e.g., Solr, Elasticsearch). Familiarity with data standards or validation frameworks (e.g., JSON Schema, RO-Crate).

Benefits and Contract Information:

• Financial incentives: depending on circumstances, monthly family/marriage allowance of £278, monthly child allowance of £336 per child. Non-resident allowance up to £569 per month. Annual salary review, pension scheme, death benefit, long-term care, accident-at-work and unemployment insurances.
• Hybrid working arrangements.
• Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover).
• Generous time off: 30 days annual leave per year, in addition to eight bank holidays.
• Relocation package including installation grant (as applicable).
• Campus life: Free shuttle bus to and from work, on-site library, subsidised on-site gym and cafeteria, casual dress code, extensive sports and social club activities (on campus and remotely).
• Family benefits: On-site nursery, child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowances.
• Contract duration: This position is a 1 year project-based contract.
• Salary: Monthly salary starting from £3,303 or £3,695 after tax but excluding pension & insurances (Total package will be dependent on family circumstances).
• International applicants: We recruit internationally and successful candidates are offered visa exemptions.
• Diversity and inclusion: At EMBL-EBI, we strongly believe that inclusive and diverse teams benefit from higher levels of innovation and creative thought. We encourage applications from women, LGBTQ and individuals from all nationalities.
• Job location: This role is based in Hinxton, near Cambridge, UK. You will be required to relocate if you are based overseas and you will receive a generous relocation package to support you.

To apply, please submit a covering letter and CV via our online system. Applications will close on 18/03/2026.