Senior Scientific Programmer
Location:EMBL-EBI Hinxton near Cambridge, UK
Staff Category:Staff Member
Contract Duration:3 Years
Grading:6 (monthly salary starting at £2,805 after tax). For more information about pay and benefits click here
Closing Date:25 June 2017
Reference Number:EBI_00958

Job Description

Are you an experienced scientific programmer looking for an exciting new opportunity?

The Ensembl Project, based at the European Bioinformatics Institute (EMBL-EBI), is one of the leading providers of genome annotation. The Variation Annotation Team is looking to recruit a highly motivated, talented and experienced Senior Scientific Programmer to contribute to Ensembl variation resources.

Large-scale sequencing projects are producing genomic data on an unprecedented scale, providing extensive variant catalogues in many species and leading to the discovery of rare human variants. These data have the potential to drive an improved understanding of genetic disease, evolution and population genetics. The Ensembl Team aggregates and annotates large quantities of data from public archives and develops tools for data access, visualisation and variant interpretation, including the Ensembl Variant Effect Predictor. Our resources are some of the most highly used by scientists across the globe.

Your primary responsibilities will include:

  • Designing, developing and maintaining software tools for the functional annotation of variants;
  • Developing and maintaining our Perl and REST APIs;
  • Investigating and implementing efficient methods for the management of large scale variation data;
  • Identifying and integrating new annotation methods or sources of variation and phenotype data;
  • Developing effective ways of displaying variation data;
  • Coordinating with members of the broader Ensembl team and other groups at EMBL-EBI; representing the variation team and taking a lead in technical discussions as required
  • Teaching courses on Ensembl tools, providing user support and presenting our work at conferences;
  • Collaborating on international projects such as GA4GH.

This position offers the motivated candidate a unique opportunity for significant scientific involvement in a rapidly moving field development of domain area expertise in bioinformatics. You will work closely with a team of bioinformaticians and programmers, and interact with other groups at the EMBL-EBI and alongside our international collaborators.

The EMBL-EBI is part of the European Molecular Biology Laboratory (EMBL) and is Europe's leading provider of information services to biological researchers in academia and industry. The institute is located on the Wellcome Genome Campus at Hinxton, near Cambridge, UK. We enjoy many benefits including sports facilities, a free shuttle bus to Cambridge and other nearby centres, and an attractive working environment set in 55 acres of parkland. Our salary scales are very competitive. For further information please visit

Qualifications and Experience

You should have a first degree and either a higher degree or equivalent experience in genetics, biological or computational sciences.

You will have several years experience of working in a production development environment, ideally creating both efficient large-scale data analysis pipelines and user-friendly tools and APIs. You should be familiar with all stages of the software development process and be used to working to deadlines. Experience of managing genomics data and working with bioinformatics or statistical tools will be an advantage.

You will be highly proficient at working in a UNIX/Linux environment and have extensive programming experience, preferably using OOP. Ideally, you will have a strong knowledge of Perl; familiarity with Python and C will also be an advantage. You will have experience of employing robust testing strategies and using version control systems, preferably Git. You will have experience of designing and optimising RDMS, preferably with MySQL. Familiarity with the Ensembl APIs will be an advantage.

We are seeking highly motivated candidates with good communication and interpersonal skills. You will have experience of taking the lead on technical or scientific projects and collaborating with colleagues from different disciplines. You must have scientific curiosity and initiative. You will work both independently and as part of a closely interacting team of international scientists. Skill in delivering a high quality product with excellent attention to detail is essential.


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.