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Bioinformatician/Software Engineer

14 May 2018

Job Description

We are seeking to recruit a Bioinformatician/Software Engineer to join the Protein function development team at the EMBL-European Bioinformatics Institute (EBI) located on the Wellcome Genome Campus near Cambridge in the UK. This team is responsible for major international protein sequence resources including the Universal Protein resource (UniProt).

The candidate will be part of the development team that maintains the databases, software and analysis pipelines for the production and release of the UniProt protein sequence databases. (S)he will be expected to gain a good understanding of the group projects and design, organize and develop the full lifecycle of our resources in close interaction with the team members at EBI as well as at the international teams involved in these projects. This is a central role in the production and development of services for crucial biological services for the scientific community.

The post holder will be working specifically within data production group that is responsible for scheduling, producing and release UniProt data monthly. This is a dynamic, challenging environment, provides an excellent opportunity to handle and organise large-scale complex biological data; observe emerging trends and methods from forefront and be part of working within an international environment. The primary responsibilities include:

  • Design and develop new data production pipelines for biological databases in the Protein Function development team
  • Maintain and optimise existing production pipeline scripts and software modules
  • Organise, execute, monitor, and troubleshoot production procedures on daily basis in synchronisation with other staff members
  • Assess new technologies and methods to improve database production environment
  • Evaluate and develop pipelines for importing new data sources
  • Maintain and ensure highest quality and consistency of the data throughout data production
  • Evaluate and propose solutions to biological challenges within data production
  • Communicate and coordinate production work with UniProt Consortium members, software developers, and biologists involved in the database release cycle

The EBI is a world-leading bioinformatics centre providing biological data to the scientific community, with expertise in data storage, analysis and representation. The Universal Protein Resource (UniProt) provides a central resource on protein information and a solid set of services and computational analysis of protein data. UniProt is produced by the UniProt Consortium – a collaboration between the EBI, the Protein Information Resource (PIR) and the Swiss Institute of Bioinformatics (SIB).

As part of the European Molecular Biology Laboratory (EMBL), we are a non-profit, intergovernmental organisation funded by 24 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

Essential Skills

  • Minimum 2 years or adequate demonstrable experience in working with biological data and writing complex code
  • Masters or higher degree in bioinformatics or computer science
  • Good understanding and/or interest of biological data
  • Strong programming skills: Bash, Perl, Python
  • Strong knowledge of SQL: Oracle, PostgreSQL
  • Comfortable operating in a Unix/Linux environment
  • Excellent problem-solving skills with an ability to understand, debug and fix both data and production code
  • Work under pressure to complete production tasks within specified deadlines
  • Work independently or with minimal supervision
  • Excellent communication and interpersonal skills
  • Enthusiastic to learn and help the scientific community

Ideal Skills

  • Specific experience in production pipelines or analysis workflows is highly desirable
  • Knowledge/experience of proteomics and genomics
  • Knowledge of UniProtKB, InterPro, Ensembl, ENA, RefSeq would be very valuable
  • Experience in working with computing cluster such as LSF or SGE
  • Understanding/experience with widely used biological file formats, methods and tools
  • Experience in Object-oriented programming: Java
  • Experience using team collaboration tools: Git, Jira, Confluence


EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation.

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.