Data Engineer at EMBL

✨ The Stack take on this EMBL job

• 🏢 EMBL has 15 jobs here, 15 with visa sponsorship see all
• 🛂 Skilled Worker visa. Standard minimum salary: £41,700 a year guide

Updated 2026-11-05, from our data and official sources.

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About the role

Responsibilities:
- Analyse and optimise existing data pipelines for performance, scalability and reliability.
- Design and implement ETL processes and new pipeline architectures for large-scale structural biology datasets.
- Integrate pipelines with PDBe, PDBe-KB, AFDB and internal tools in collaboration with bioinformaticians and annotators.
- Monitor pipeline health, investigate incidents, tune queries and resolve bottlenecks to maintain throughput.
- Lead and execute database migration tasks (notably Oracle → PostgreSQL) ensuring data integrity and minimal disruption.
- Document pipelines, workflows, runbooks and operational procedures for handovers and knowledge sharing.
- Research and recommend tools, techniques and best practices to improve data infrastructure and cost/performance trade-offs.

Requirements:
- MSc in Computer Science, IT, Bioinformatics or related field with demonstrated IT expertise.
- Strong data modelling skills and advanced SQL capability across complex schemas.
- Proficient in Python and experienced with ETL tooling for large-volume data processing.
- Hands-on experience with relational databases: deep PostgreSQL knowledge (architecture, partitioning, indexing, tuning), Oracle (PL/SQL) and MySQL/MariaDB.
- Proven record of migrating databases between RDBMS platforms, especially Oracle to PostgreSQL.
- Familiarity with data warehousing concepts and cloud analytics (Redshift, BigQuery) is desirable.
- Good communicator able to work effectively in interdisciplinary, international teams.

Responsibilities

The Data Engineer will optimize and enhance data pipelines to ensure efficient processing, storage, and retrieval of macromolecular structure databases. Key tasks include analyzing existing pipelines for scalability, integrating systems with bioinformaticians, and documenting workflows.

Requirements

Candidates must have an MSc in Computer Science, IT, or Bioinformatics with expert skills in data modelling, SQL, Python, and ETL processes. Extensive experience in RDBMS platforms and database migration, specifically from Oracle to PostgreSQL, is required.

Key skills

• Data Modelling — in 24 other listings on The Stack
• Advanced SQL — in 1 other listing on The Stack
• Python — in 1200 other listings on The Stack
• ETL — in 40 other listings on The Stack
• PostgreSQL — in 296 other listings on The Stack
• Oracle — in 15 other listings on The Stack
• MySQL — in 93 other listings on The Stack
• MariaDB — in 15 other listings on The Stack
• Database Migration
• Data Warehousing
• Redshift
• BigQuery
• Communication
• Collaboration
• English Proficiency
• PL/SQL

On The Stack (as of 2026-11-05)

• EMBL has 14 other listings on The Stack, 14 of them marked as offering visa sponsorship.
• 214 visa-sponsored jobs in the United Kingdom on The Stack, posted in the last 60 days.
• 47 visa-sponsored data engineer jobs in Europe on The Stack, posted in the last 60 days.

Frequently asked questions about EMBL

Is this Data Engineer role still open?

It was posted on 2026-06-08. Listings more than 30 days old may no longer be active, so check EMBL's site before applying.

Does EMBL offer visa sponsorship?

This listing is marked as offering visa sponsorship. Eligibility rules are set by the employer, so check the details on EMBL's site.

Where is this role located?

The listing gives the location as Hinxton, United Kingdom. It is marked on-site.

What skills does this role ask for?

The listing names: Data Modelling, Advanced SQL, Python, ETL, PostgreSQL, Oracle, MySQL, MariaDB, Database Migration, Data Warehousing, Redshift, BigQuery, Communication, Collaboration, English Proficiency, PL/SQL.