We’re looking for a software engineer to join our production team, responsible for creating and running software for Ensembl production releases. We’re looking for postgrad qualifications in computer science or bioinformatics, with experience in bioinformatics, Python, MySQL and data processing workflows. Closes 19th July.
Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: 3 years
Grading: 5 or 6 (monthly salary starting at £2,631.99 or £2,944.48 after tax)
Closing Date: 19 July 2019
Reference Number: EBI01446
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 have a minimum of 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 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 (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)
Why join us
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.
What else you need to know
To view a copy of the full job description please click here
To apply please submit a covering letter and CV through our online system. Applications are welcome from all nationalities and this will continue after Brexit. For more information please see our website. 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.
Applications will close at 23:00 GMT on the date listed above.
