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Ensembl Production Software Developer

European Molecular Biology Laboratory (EMBL)

Location: Cambridge, Hinxton
Salary: £2,631.99 to £2,944.48 monthly starting salary after tax (Grade 5 or 6).
Hours: Full Time
Contract Type: Fixed-Term/Contract
Placed On: 7th June 2019
Closes: 19th July 2019
Job Ref: EBI01446

About the team/job

Ensembl is looking for a talented and motivated software developer to help build next-generation genome-scale data processing pipelines. This successful candidate join the Ensembl Production team at the European Bioinformatics Institute (EMBL-EBI), which is located on the Wellcome Genome Campus near Cambridge in the UK.

The Software Developer will focus on creating software used for data production releases working with the Ensembl and Ensembl Genomes resources, as part of the Ensembl Production Team. The team is responsible for:

  • Coordination of the production of new releases of Ensembl and Ensembl Genomes
  • Developing new automated pipelines for use in the production process
  • Designing and implementing infrastructure for automated production processing
  • Provide Production processing services to other Ensembl / Ensembl Genomes teams
  • Ensuring the quality and integrity of data for release 

Your role

As a software developer your specific day-to-day duties will include:

  • Design and implementation of software infrastructure components for automated processing using messaging queues and micro-services
  • Design and implementation of new production pipelines
  • Participating in the planning and coordination of Ensembl and Ensembl Genomes releases, including collaboration with other members of the Ensembl and Ensembl Genomes teams
  • Execution of production processes and pipelines

The candidate will report to Marc Chakiachvili (Ensembl Production Team Leader) in the team of Andy Yates (Genomics Technology Infrastructure Team Leader). 

You have

You must hold a degree in computer science, bioinformatics or biological sciences. You must have a post-graduate qualification in computer science or bioinformatics or similar qualification/experience. Candidates should ideally hold two years professional programming experience, preferably in a bioinformatics or large scale data processing environment. It would be highly desirable if experience had been gained working in other areas of genomics.

You must have good knowledge of Python and be happy to work scripts and pipelines written in Perl. You should also have knowledge of a compiled programming language (e.g. Java). Knowledge of databases (e.g. MySQL, PostgreSQL, Oracle), writing SQL statements and designing database schemas is essential.

You must have experience of data processing workflows either with traditional compute farms (e.g. LSF, SGE) or with distributed processing systems (e.g. Luigi) and demonstrate understanding of data workflows. Evidence of working in a team-based environment or contributing to a large, shared code-base is desirable.

You must be highly self-motivated, interested in biological science and be able to work independently. A successful candidate must be open to working in a production team (willing to conform and contribute to standard working practices); and are expected to have good communication skills, written and verbal, both to facilitate effective communications with other team members and to communicate with external collaborators and users.

You might also have

Experience of the following would be advantageous.

  • Python web frameworks (e.g. Django, Flask)
  • Knowledge of newer database technologies (e.g. NoSQL)
  • Messaging queues (e.g. RabbitMQ and/or the STOMP protocol)
  • Knowledge of service oriented architecture and micro-services
  • Containerisation (e.g. Docker, CaaS, Kubernetes, Singularity)
  • Automated testing and deployment (e.g. Gitlab-ci / Travis) 
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