Bioinformatician/Scientific Programmer, Variation Annotation
Location:EMBL-EBI Hinxton near Cambridge, UK
Staff Category:Staff Member
Contract Duration:3 years (initially, renewable)
Grading:5 (monthly salary starting at £2,552 after tax). For more information about pay and benefits click here
Closing Date:5 August 2018
Reference Number:EBI_01247

Job Description

Are you an experienced bioinformatician/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 seeking to recruit an experienced and highly motivated bioinformatician/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:

  • Developing efficient methods for the management of large scale variation data;
  • Developing and maintaining tools for the functional annotation of variants;
  • Designing and building databases of genomic variation;
  • Developing and maintaining our Perl and REST APIs;
  • Identifying and integrating new sources of genomic variation and phenotype data;
  • Analysing and annotating genomic data;
  • Developing effective ways of displaying variation data;
  • Liaising with members of the broader Ensembl team and other groups at EMBL-EBI;
  • Supporting our users, delivering training courses and presenting at conferences.

This position offers the motivated candidate a unique opportunity for significant scientific involvement and 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 our international collaborators and participate in projects such as GA4GH.

EMBL-EBI is part of the European Molecular Biology Laboratory (EMBL) and it is a world-leading bioinformatics centre providing biological data to the scientific community with expertise in data storage, analysis and representation. EMBL-EBI provides freely available data from life science experiments, performs basic research in computational biology and offers an extensive user training programme, supporting researchers in academic and industry. We have close ties with both the University of Cambridge and the Wellcome Trust Sanger Institute.

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 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.

Comfort working in a UNIX/Linux environment and extensive programming experience, preferably using OOP, are required. Ideally, you will have a strong knowledge of Perl; familiarity with Python and C will also be an advantage. You will have experience of RDMS, preferably with MySQL. Familiarity with the Ensembl APIs and tools will be an advantage.

We are seeking highly motivated candidates with good communication and interpersonal skills. 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 on time and 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