Software Developer

Job Location
Wellcome Genome Campus
CB10 1SD
United Kingdom
5 or 6 (monthly salary starting at £2,475 net of tax plus mobility and other allowances where applicable)

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.

Job Description

The Genomics Technology Infrastructure team seeks a talented and motivated software developer to work in the Ensembl project at the European Bioinformatics Institute (EMBL-EBI).

Ensembl ( is one of the most successful large-scale bioinformatics projects and one of the leading projects for genome annotation. Ensembl has developed one of the most mature database schemas and APIs for genomic annotation storage and access. This is extensively used in our sister project Ensembl Genomes (

You will be responsible for designing a new annotation storage system to sit alongside our existing infrastructure. This new system is responsible for the archiving, checksums and retrieval of transcripts across multiple releases of Ensembl and Ensembl Genomes annotation sets. It will provide infrastructure to track transcripts in a stable manner, which is critical for implementing genomics in the clinic. In addition this system will be capable of loading transcript annotation directly from an Ensembl database and from externally submitted files and will form a key part of our internal production infrastructure. The system will also be capable of tagging transcripts across multiple sources and disseminating all of this information via a public REST API to be feedback into the Ensembl ecosystem. You will report to the Ensembl Core Project Leader.


You will have a Master's degree, or equivalent qualification/experience, in a biological or computer science. Previous experience of working in a large software development team would be advantageous as would experience in API development. Working knowledge of biology, biochemistry, genomics (especially gene annotation) is desirable but not essential.

You should be experienced in a mainstream programming language such as Java, Perl or Python and have experience of working with collaborative tools e.g. Git. Knowledge of the Unix command line and of RDBMS is essential and experience with REST API frameworks and NoSQL technologies would be seen as an advantage.

You must be team oriented, ready to contribute to Ensembl's 40+ development team, and will be expected to work in step with the procedures and time constraints of the entire project. You must also be thorough, timely and detail-oriented in your work, as you will have to keep track of many parallel tasks. Communication and presentation skills will be highly valued.

How to Apply

Please apply online through

About Our Organization

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 21 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.

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.

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