Senior Scientific Programmer

Hinxton near Cambridge, UK
Job Description: 

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.

    How to Apply

    Please apply directly via the EBI website:

    Applications from Canadian citizens are welcome.