At a Glance
- Tasks: Optimise data pipelines and enhance data processing for global macromolecular structure databases.
- Company: Join an international team at a leading biotechnological research institute.
- Benefits: Enjoy flexible working, generous leave, and comprehensive health insurance.
- Other info: Hybrid working options and a vibrant campus life with various activities.
- Why this job: Make a real impact in life sciences while working with cutting-edge data technologies.
- Qualifications: MSc in relevant field, strong SQL and Python skills, and experience in data engineering.
The predicted salary is between 39636 - 39636 £ per year.
About the Team
The Velankar team maintains macromolecular structure databases that form essential resources for biologists and other life scientists worldwide. PDBe is a founding partner of the Worldwide Protein Data Bank organisation, which maintains the global archive of 3D structural data on macromolecules the Protein Data Bank (PDB). The PDBe team also develops the PDBe Knowledge Base (PDBe-KB) and AlphaFold Protein Structure Database (AFDB). The PDBe team is international and inter‑disciplinary and consists of expert data curators, bioinformaticians, scientific software developers and IT specialists.
Your Role
As a Data Engineer, you will play a crucial role in optimising and enhancing our data pipelines, ensuring efficient data processing, storage and retrieval. You will work closely with cross‑functional teams to analyse requirements, propose new data pipeline architectures, and implement solutions to improve performance and scalability.
Responsibilities
- Analyse existing data pipelines and identify areas for improvement, optimisation, and scalability.
- Work closely with Bioinformaticians and annotators to integrate data pipelines with existing systems and applications.
- Monitor data pipeline performance, troubleshoot issues, and implement solutions to ensure reliability and efficiency.
- Stay current with industry trends and best practices in data engineering and recommend new technologies or tools to enhance data infrastructure.
- Document data pipelines, processes, and workflows for internal reference and knowledge sharing.
Qualifications
- MSc in computer science, IT, or a related field, or in bioinformatics with demonstrated IT expertise.
- Expert in data modelling and advanced SQL.
- Proficiency in Python programming.
- Proficiency in ETL (Extract, Transform, Load) processes and tools for large‑scale data processing.
- Strong understanding of relational databases with hands‑on experience across multiple RDBMS platforms: PostgreSQL, Oracle, MySQL/MariaDB.
- Experience in database migration, especially Oracle to PostgreSQL, with knowledge of compatibility layers, stored procedure conversion, data type mapping, trigger migration, and handling of Oracle‑specific features in PostgreSQL.
- Experience with migration tools such as Oracle Data Pump, GoldenGate, custom ETL scripts, and data validation strategies.
- Planning and executing migration projects, including downtime management, data consistency verification, and rollback strategies.
- Cross‑platform optimisation: Knowledge of leveraging PostgreSQL features to improve performance during migration scenarios.
- Proficiency in data warehousing (Redshift, BigQuery).
- Strong communication and collaboration skills, with ability to work effectively in a team environment.
- Proficiency in oral and written English.
- Optional: PhD in related fields; experience in big data technologies such as Apache Spark, Hadoop; CI/CD; familiarity with Java, Google Cloud Platform or AWS; data modelling for AI/ML; graph databases; data visualisation tools.
Other helpful information
Hybrid working: at EMBL‑EBI we offer hybrid working options with a dedicated desk available every day; the team works two days on site and three from home.
Benefits
- Monthly family, child and non‑resident allowances; annual salary review; pension scheme; death benefit; long‑term care; accident‑at‑work and unemployment insurance.
- Flexible working arrangements, including hybrid working patterns.
- 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, plus public holidays.
- Relocation package including installation grant (if required).
- Campus life: free shuttle bus to and from work, on‑site library, subsidised gym and cafeteria, casual dress code, extensive sports and social club activities on campus and remotely.
- Family benefits: on‑site nursery; 10 days of child sick leave; generous parental leave; holiday clubs on campus and monthly family and child allowances.
- Benefits for non‑UK residents: visa exemption; education grant for private schooling; financial support to travel back to home country every second year; monthly non‑resident allowance.
International Applicants
We recruit internationally and successful candidates are offered visa exemptions. For further information please consult our International Applicants page.
Contract and Salary
Contract length: grant‑based contract for 3 years. Salary: Grade 5 monthly salary starting at £3,303 per month after tax (excluding pension and insurance contributions). Plus generous benefits.
Diversity and inclusion
We believe that diverse teams drive innovation and scientific excellence. We encourage applications from candidates of all genders, identities, nationalities and any other diverse backgrounds.
How to apply
To apply please submit a cover letter and a CV through our online system. Applications will close at 23:59 CET on the date shown below. We aim to provide a response within two weeks after close date.
Closing date: 28/06/2026
Data Engineer employer: 1000 European Molecular Biology Laboratory
At EMBL-EBI, we pride ourselves on being an exceptional employer, offering a collaborative and innovative work culture that fosters professional growth and development. As a Data Engineer, you will benefit from flexible hybrid working arrangements, generous annual leave, and comprehensive family benefits, all while contributing to groundbreaking research in the life sciences. Our international team is dedicated to diversity and inclusion, ensuring that every employee feels valued and empowered to make a meaningful impact.
Contact Details:
1000 European Molecular Biology Laboratory Recruitment Team
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