Software Engineer
Location:EMBL-EBI Hinxton near Cambridge, UK
Staff Category:Staff member
Contract Duration:Until 30.11.2019
Grading:5 (monthly salary starting at £2,552 after tax). For more information about pay and benefits click here
Closing Date:23 July 2018
Reference Number:EBI_01246

Job Description

We are seeking a full-time Software Engineer/Bioinformatician to join the Data Coordination and Archiving Team at the EMBL European Bioinformatics Institute (EMBL-EBI), located on the Wellcome Genome Campus near Cambridge in the UK. The team provides data coordination services for partners around the world for a portfolio of sequencing-based initiatives. With underlying infrastructure for these services based around the European Nucleotide Archive – one of life science’s largest and longest standing data resources – this is an opportunity to rise to the challenges of ‘big data’ and make contributions that advance the reach and utility of sequence data.

The post holder will work on our major EU-funded COMPARE project (, that is establishing the analytical framework, globally linked data and information sharing platform for the rapid identification, containment and mitigation of emerging infectious diseases and foodborne outbreaks. The successful applicant will continue development of the COMPARE Workflow Engine, which supports cloud-based data analyses using quality-assured workflows developed as part of the project. The role will include the maintenance and extension of these workflows and the delivery of the outputs of the workflows into the COMPARE data management system for user access. Tasks will cover the design, coding, testing, documentation and maintenance of software. You will also support our international network of collaborators providing workflow and data output solutions.

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

You should hold a university degree in software engineering, bioinformatics, data science, computer science, or a related field. It is desirable to have previous experience in bioinformatics, database technologies and biological data analysis. You will have a proven track record of working on large-scale data analysis projects and an understanding of the challenges posed by collaborative projects including flexibility, tight deadlines, and use of state-of-the-art approaches.

You must have significant experience in the following:

  • Shell scripting in a Unix/Linux environment
  • Python
  • Distributed Programming
  • Cloud computing and workflow environments
  • SQL (Oracle/PostgreSQL/MySQL)

You must also have experience in the following:

  • Linux system administration
  • Deployment of software in cloud-based environments, workflow systems and shared codebases

The candidate is expected to:

  • Travel to external international meetings
  • Work in a production team, conforming and contributing to standard working practices
  • Have good communication skills, both written and verbal
  • Be able to communicate effectively with external collaborators and users
  • Work as part of a focused team, but at the same time be self-driven and able to work independently.

And the following would be desirable:

  • Java


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.