Software Engineer
Location:EMBL-EBI Hinxton near Cambridge, UK
Staff Category:Staff Member
Contract Duration:3 years
Grading:5 or 6 (monthly salary starting at £2,552 or £2,855 after tax). For more information about pay and benefits click here
Closing Date:24th June 2018
Reference Number:EBI_01229

Job Description

The Samples, Phenotypes and Ontologies team are looking for an experienced software developer to join their group. You will be working on a project specific to the Open Targets initiative to help develop the infrastructure behind the high-profile GWAS Catalog. The GWAS Catalog is a manually curated, high quality repository of all published genome wide association studies that has been running since 2008. It is considered the “go-to” resource for looking up findings relating human genotype to phenotype associations.

Open Targets is a platform for target identification and prioritisation and performs large-scale biological data analysis and integration using EFO as the core ontology for the semantic annotation of data about disease and phenotype. GWAS Catalog data makes up a very important part of the Open Targets platform.

If you’re an experienced developer with an interest in helping solve big biological problems about the genetic basis of disease, this job is perfect for you! Most of the GWAS Catalog infrastructure is written in Java, so you’ll need previous Java experience, but we also have data pipeline services developed in Python and we make use of modern javascript frameworks for our user interfaces. We make good use of tools and frameworks like Spring and Docker to deliver our resources. SPOT is a multitalented team, so you should also be flexible enough to learn new languages to find the right tool for the right problem. You should be enthusiastic about full-stack development, as you’ll be expected to develop, test and deploy tools from database to user interface. You should be keen to advance your knowledge of the latest industry standard toolkits to help continuously innovate the catalog.

In this role, we’ll be asking you to help develop the infrastructure that manages the data in the GWAS Catalog - this means you’ll be building tools and pipelines to capture new data from submitters, and to serve it back to the community through the Open Targets platform, via APIs. Individual GWAS datasets can be very large - tens or hundreds of gigabytes - and we’re storing billions of records, so this requires someone who can get creative to build solutions to these sort of big data problems.

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 23 member states and two associate member states and proud to be an equal-opportunity employer. We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 600 staff are engineers, technicians, scientists and other professionals from all over the world.

Qualifications and Experience

The Samples, Phenotypes and Ontologies team follows agile techniques in our approach to development, so if you’re the sort of person who likes to work in sprints, has worked with tools like Jira in the past to prioritise user requirements, or have ever tried pair-programming or code reviews, then you’ll be a good fit for our team. All of our software is built and published using continuous integration and version control, so you should at least be familiar with GitHub, and you should be confident in making your code public for others to install and run.

Our ideal candidate will be self-motivated and capable of working both independently and with a closely interacting team of scientists in an international academic environment. This post offers the challenges and the excitement of working at the forefront of genomics and clinical data, and as such requires an eager individual with excellent communication skills.

This position represents a fantastic opportunity to get hands-on in applying your software engineering skills to a resource with major scientific impact in a world-leading bioinformatics institute. It comes with the chance to work with a strong team of curators and developers at the interface of big data architecture and expert biologists to help deliver services with real scientific impact and a variety of clinical applications.


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.

This position is limited to the project duration specified.

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