Ensembl Production Software Developer
Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: 3 years
Grading: 5-6 (Monthly salary starting at £2,728 - £3,063) Plus other paid benefits
Closing Date: 31 March 2021
Reference Number: EBI01781
A highly motivated, Python Software developer is wanted to help implement the next-generation of genome-scale Ensembl processing automation in the Ensembl production team. 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 datasets across multiple platforms.
  • Developing new automated pipelines for use in the production process
  • Designing and implementing infrastructure for automated production processing, delivery automation
  • Designing and developing automated CI / CD pipelines for our services platforms
  • 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 Project 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 or have gained equivalent vocational experience. Candidates should have a minimum of two years professional programming experience, preferably in a bioinformatics or large scale data processing environment. It would be 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 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 or ETL (Extract Transform Load) processes. Evidence of working in a dynamic, 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, and willing to conform and contribute to standard working practices. Candidates 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 NoSQL database technologies (e.g. MongoDB, Elastic)
  • Messaging queues (e.g. RabbitMQ or the STOMP protocol)
  • Knowledge of service oriented architecture and micro-services
  • Containerisation (e.g. Docker, CaaS, Kubernetes or Singularity)
  • Automated testing and deployment (e.g. Gitlab-ci / Travis)
  • RDBMS knowledge (e.g. MySQL, PostgreSQL or SQLite)
  • A working knowledge of SQL and writing RDBMS database schemas

Why join us

EMBL-EBI is a worldwide leader in bioinformatics. We encourage personal and professional development and are committed to ensuring our employees feel valued, supported and empowered to reach their potential at work.

Surrounded by beautiful South Cambridgeshire countryside, our state-of-the-art Campus provides employees with a relaxed atmosphere where the pursuit of scientific discovery and meaningful work, underpin every role. In addition, our employees have access to a wide range of benefits including:
  • 30 days annual leave per year plus 8 bank holidays
  • Flexible work arrangements
  • Unique pension scheme including 17% employer contribution
  • Annual salary review
  • Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover)
  • Death benefit, long-term care, accident at work and unemployment insurances
  • Relocation package including installation grant (if required)
  • On-site library and subsidised on-site gym and cafeteria
  • Casual dress code
  • Free shuttle bus to and from Campus
  • Extensive sports and social club activities (run on campus and remotely)
  • Family benefits: Onsite nursery, 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
 

What else you need to know

To apply please submit a covering letter and CV through our online system. 

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. Visa exemptions will be offered to international candidates and details will be discussed during interview. We believe in science without borders and this continues after Brexit.

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. More info on how we are recruiting in this period is available on our page: Recruitment and Onboarding during Covid19.