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Software Developer

22 August 2018

Our environment provides an exciting opportunity for candidates looking to work with extremely large databases and complex distributed processing workflows. You will work in a close collaboration with other developers within the team and with our internal, European and international collaborators and clients. The team follows agile software development practices and uses Git, JIRA and Slack in a collaborative programming environment.

ENA is one of the world’s largest public scientific data archives and contains PetaBytes of experimental and computational nucleotide sequence data. Experimental sequence read data is generated by sequencing platforms, such as Illumina, Oxford Nanopore or PacBio, while computational data, such as genome assemblies, is derived from the sequence reads. Data is deposited into ENA to make if freely available to the scientific community.

The Role:

We are looking for an experienced Software Developer to join the Molecular Archival cluster of the European Bioinformatics Institute (EMBL-EBI). Your primary focus will be on developing, improving, maintaining and operating Java-based data archival and processing pipelines for the European Nucleotide Archive (ENA) resource. You will be responsible for several high-throughput processing pipelines executing millions of tasks on EMBL-EBI’s HPC clusters. In coming years, the processing and archival infrastructure will be migrated to containerised deployment environments in remote co-located cloud infrastructures.

Qualifications and Experience:

You should have a university degree in computer science or software engineering and have several years of experience building distributed data processing applications in Java. 

Required experience:
  • A strong command of Java, JDBC, and the Spring framework
  • Good understanding of workflow and distributed data processing software
  • Familiarity with continuous integration and deployment methodologies
  • Self-motivated and capable of working both independently and as part of a team
  • Willingness to learn new skills as the project requires
  • Excellent communication, interpersonal and English language skills
Desirable experience:
  • Prior experience in building web services using Java
  • Proficiency with relational databases
  • Proficiency with MongoDB
  • Prior experience working in a multidisciplinary scientific environment


At EMBL-EBI, we help scientists realise the potential of ‘big data’ in biology by enabling them to exploit complex information to make discoveries that benefit mankind. Working for EMBL-EBI gives you an opportunity to apply your skills and energy for the greater good. As part of the European Molecular Biology Laboratory (EMBL), we are a non-profit, intergovernmental organisation funded by 22 member states and two associate member states. We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 600 staff are engineers, technicians, scientists and other professionals from all over the world.

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. The remuneration package comprises a competitive salary, a comprehensive pension scheme and health insurance, educational and other family related benefits where applicable, as well as financial support for relocation and installation. For more information about pay and benefits click here

We have an informal culture, international working environment and excellent professional development opportunities but one of the really amazing things about us is the concentration of technical and scientific expertise – something you probably won’t find anywhere else.

If you’ve ever visited the campus you’ll have experienced first-hand our friendly, collegial and supportive atmosphere, set in the beautiful Cambridgeshire countryside. Our staff also enjoy excellent sports facilities including a gym, a free shuttle bus, an on-site nursery, cafés and restaurant and a library.

Application Instructions:

To apply please submit a covering letter and CV, with two referees, through our online system at[]=SDE

Applications are welcome from all nationalities - visa information will be discussed in more depth with applicants selected for interview.
EMBL-EBI is committed to achieving gender balance and strongly encourages applications from women, who are currently under-represented at all levels. Appointment will be based on merit alone.
The initial contract is for a period of three years with the possibility of a fixed-term extension.

Closing Date: 23 September 2018