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Data Engineer

European Molecular Biology Laboratory (EMBL)
Closing date
12 May 2024

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Life Science
Job Type
Employment - Hours
Full time
Fixed term

About the team/job

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 (wwPDB;, 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

We seek a skilled and motivated Data Engineer to join our dynamic team. 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.

The tasks for this post include the following:

    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.

The successful candidate will report directly to the PDBe Technical Project Lead as a Technical Officer. This post is an opportunity for the right person to bring IT skills and innovative ideas to help sustain the growing amount of structural biology data in the PDB and ensure that PDBe, PDBe-KB and AFDB services remain sustainable.

You have

  • MSc in computer science, IT or a related field, or in bioinformatics with a 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 (Oracle, PostgreSQL) and experience optimising database performance.
  • Proficiency in data warehousing (Redshift, BigQuery)
  • Strong communication and collaboration skills, with the ability to work effectively in a team environment.
  • Proficiency in oral and written English

You might also have

  • PhD in computer science, IT or a related field, or in bioinformatics with a demonstrated IT expertise
  • Experience in big data technologies and frameworks, such as Apache Spark, Hadoop or similar platforms
  • Hands-on experience with CI/CD (GitLab CI/GitHub Actions)
  • Familiarity with Java
  • Familiarity with Google Cloud Platform or AWS
  • Familiarity with data modelling techniques for AI (Artificial Intelligence) and ML (Machine Learning) applications
  • Familiarity with Neo4J or other graph databases is an added advantage
  • Familiarity with data visualisation (Tableau, PowerBI)
  • Knowledge of, or affinity with, structural biology and bioinformatics
  • Experience working in international teams

Why join us

Do something meaningful

At EMBL-EBI, you can apply your talent and passion to accelerate science and tackle some of humankind's most significant challenges. EMBL-EBI, part of the European Molecular Biology Laboratory, is a worldwide leader in the storage, analysis and dissemination of large biological datasets. We provide the global research community with access to publicly available databases and tools crucial for advancing healthcare, food security, and biodiversity.

Join a culture of innovation

We are located on the Wellcome Genome Campus, alongside other prominent research and biotech organisations, and surrounded by beautiful Cambridgeshire countryside. This is a highly collaborative and inclusive community where our employees enjoy a relaxed atmosphere. We are committed to ensuring our employees feel valued, supported and empowered to reach their professional potential.


Enjoy lots of benefits:

  • Financial incentives: Monthly family, child and non-resident allowances, annual salary review, pension scheme, death benefit, long-term care, accident-at-work and unemployment insurances
  • Flexible 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 (if 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, 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 your home country every second year and a monthly non-resident allowance.

For more details please see our employee benefits page.

What else you need to know

  • Contract duration: This position is a fixed-term project-limited contract for 1 year 8 months (20 months), estimated 01/07/2024-31/01/2026.
  • International applicants: We recruit internationally and successful candidates are offered visa exemptions. Read more on our page for international applicants.
  • 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, UK and you will be required to relocate once it is safe to do so, if you are currently based abroad. Read more about how we are recruiting during the pandemic.
  • How to apply: To apply please submit a cover letter and a CV through our online system. We aim to provide a response within two weeks after the closing date.

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