Bioinformatics 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_01228

Job Description

We are seeking to recruit an enthusiastic, highly motivated Bioinformatics Software Engineer to work at the European Bioinformatics Institute (EMBL-EBI) located at the Wellcome Genome Campus near Cambridge in the UK.

You will be working in the highly dynamic Web Production Team led by Rodrigo Lopez, across a number of activities aimed at providing and improving access to bioinformatics core services including text search and biological sequence analysis tools. You will be experienced with software development technologies and best practices (i.e. Agile/DevOps). Prior knowledge of bioinformatics data and tools as is experience with visualisation frameworks based on SVG/JavaScript is highly desirable.

The Web Production team provides robust and reliable services to the community. You will be working with 11 highly skilled professionals that provide robust services and support a fast growing audience of scientists from around the world. You will be highly visible and participate regularly in internal and external training and dissemination events such as seminars, workshops and conferences at the international level. You will be a proactive individual and learn new skills quickly.

The EMBL-EBI is part of the European Molecular Biology Laboratory (EMBL) and it is a world-leading bioinformatics centre providing biological data to the scientific community with expertise in data storage, analysis and representation. EMBL-EBI provides freely available data from life science experiments, performs basic research in computational biology and offers an extensive user training programme, supporting researchers in the academic and industrial sectors.

Qualifications and Experience

You will have a Master’s or higher degree in computer science, software development or have equivalent qualifications. You will be required to document your experience in full-stack web applications development (i.e. back-end and front-end tiers, including web-based clients, programmatic access APIs, and data access layers). Java, Python, C and C++ technologies and frameworks (e.g. Spring) are widely used within the organization, so experience with these is required as well as with CI/CD methodologies.

Prior work experience should include three or more years' software development in a team environment and supporting production systems in an academic or commercial setting. The ability to work within a team is critical to this position and excellent English communication skills, verbal and written are essential. You will be required to communicate technical documents, take part in the daily Scrum, as well as provide user orientated communication with external and internal users of the systems. An ability to work to tight deadlines is essential.


  • Expert knowledge of Java and Spring (MVC, Security, Integration) and related technologies
  • Experience in Web Services technologies (REST, SOAP, AWS, CWL, etc.) and API driven development and PaaS solutions
  • A good knowledge of modern front-end technologies such as AngularJS
  • Use of version control (e.g. Git, subversion) and experience of gitlab CI/CD methodologies
  • Experience using high performance computing frameworks such as Hadoop, Condor, Apache Spark or IBM/LSF.
  • Experience with running and troubleshooting web application servers (e.g. Java web containers such as Tomcat)
  • Experience in communicating and working with expert users (e.g. in a science community) in a co-development model.


  • Previous experience evaluating open-source software and its subsequent integration to a production system
  • Familiarity with agile development practices and the full software development lifecycle in a team environment
  • Knowledge of scripting languages such as Perl/Python as well as Unix/Linux shells
  • Experience with VMs and/or container (e.g. Docker, Singularity) deployment in public or private cloud environments
  • Experience of working within a DevOps environment

You will be able to pay attention to detail but also meet deadlines. You will also demonstrate innovation and a willingness to take on new challenges and a passion for code development and making software that can be used. You have the knowledge and experience to make technical decisions with minimal supervision.


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.

The initial contract is for a period of three years with the possibility of a fixed-term extension.

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