Software Developer


Key information

  • Location: EMBL-EBI Hinxton
  • Staff category: Staff Member - Technology
  • Contract duration: 3 years (renewable)
  • Grading: Grade 5 or 6 (starts at £2,738 or £3,063 per month after tax)
  • Closing date: 19 August 2020
  • Reference number: EBI01667

Continue reading for more information about this position, or apply now.




About this position

Ensembl is one of the leading providers of genome annotation. We seek a highly motivated, talented and experienced software developer to contribute to our 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. Our 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 (VEP). Our resources are some of the most highly used by scientists across the globe and are distributed freely.

Your role

Your primary responsibilities will include:

  • Developing and maintaining efficient methods for the management of large-scale variation data; tools for the functional annotation of variants; and APIs for data access (in Perl and REST),
  • Integrating new sources of genomic variation and phenotype association data into our resources,
  • Collaborating with members of the broader Ensembl team both on specific development projects and to coordinate our regular data/software releases,
  • Liaising with other groups at EMBL-EBI and our external collaborators to add new functionalities to our tools and agree standards for data representation,
  • Supporting our users and presenting our work at internal meetings and scientific 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/programmers and interact with other groups at the EMBL-EBI beyond.

You have

  • Proficiency working in a UNIX/Linux environment.
  • Extensive programming experience, preferably object-oriented.
  • Strong knowledge of Perl or Python.
  • Experience using version control systems, preferably Git.
  • Experience working with large scale databases, preferably including familiarity with MySQL.
  • Experience employing robust testing strategies.
  • Many years’ experience working in a production development environment, ideally creating both efficient large-scale data analysis pipelines, user-friendly tools and APIs.
  • Familiarity with all stages of the software development process
  • Ability to work to deadlines.
  • Experience collaborating on software development projects and working with colleagues from different disciplines.
  • Skills and motivation to deliver a high-quality product with excellent attention to detail.
  • Good communication and interpersonal skills.
  • Ability to work independently while also interacting in a team of international scientists.
  • Scientific curiosity and initiative

You might also have

  • Experience of managing genomics data.
  • Experience with bioinformatics or statistical tools.
  • Familiarity with C.
  • Familiarity with the Ensembl APIs

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 over 27 member states and two associate member states. We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 850 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.


Join EMBL and you’ll join a community of world-class researchers and skilled professionals working together to uncover the secrets of life.

We offer attractive conditions and benefits to attract and retain the brightest talent. Learn more.

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The European Molecular Biology Laboratory is a single organisation spread across six European locations. Each of our sites hosts its own research units, services and facilities.

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EMBL seeks to better understand the molecular basis of life. In the process, we’re changing European science.