Software Developer
Location:EMBL-EBI Hinxton near Cambridge, UK
Staff Category:Staff member
Contract Duration:3 years
Grading:5 (monthly salary starting at £2,507 after tax). For more information about pay and benefits click here
Closing Date:12 February 2017
Reference Number:EBI_00854

Job Description

The Ensembl Production Team is looking to appoint a skilled and highly motivated Software Developer to join the team at the European Bioinformatics Institute (EMBL-EBI), which is located on the Wellcome Trust Campus near Cambridge in the UK.

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

  • Coordination of the production of new releases of Ensembl and Ensembl Genomes data;

  • Developing new automated pipelines for use in the production process;

  • Designing and implementing infrastructure for automated production processing;

  • Ensuring the quality and integrity of data for release.

Specific day-to-day duties will include:

  • Design and implementation of software infrastructure components for automated processing using messaging queues and microservices;

  • 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 Dan Staines (Ensembl Production Coordinator) in the team of Andy Yates (Genomics Technology Infrastructure Team Leader).

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 and proud to be an equal-opportunity employer. Our 600 staff are engineers, technicians, scientists and other professionals from all over the world.

Qualifications and Experience

You must hold a degree in computer science or bioinformatics or a degree in biological sciences and a post-graduate qualification in computer science or bioinformatics. You should have one of the following: a minimum of two years professional programming experience, a bioinformatics based PhD; or research experience with next generation sequencing data. It would be highly desirable if experience had been gained working in other areas of genomic biology or bioinformatics.

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

The post holder must be highly self-motivated and interested in biological science (although biological qualifications are not themselves essential) and be able to work independently. They 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 must have knowledge of Perl, though experience in a related scripting language (e.g. Python, Ruby) or compiled programming language (e.g. Java) would be applicable. Knowledge of MySQL, writing SQL statements and designing database schemas is essential. Experience of handling large data sets, and knowledge of other database technologies (NoSQL and traditional RDBMS) would be desirable. Experience of messaging queues (e.g. ActiveMQ and the STOMP protocol) and modern reporting frameworks (e.g. Kibana) would also be desirable.

Benefits

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.



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.

Additional Information

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.

Applications will close at 23:00 GMT on the date listed above.