Software Engineer - Bioinformatics

We are looking for an experienced Software Engineer and/or Bioinformatician to join us in the important role of developing new annotation procedures for proteomics and structural data in one of the world’s leading scientific resources, the Universal Protein resource (UniProt) at the EMBL-European Bioinformatics Institute (EBI) located on the Wellcome Genome Campus near Cambridge in the UK.

The successful candidate will have the wonderful opportunity of working with software engineers and scientists in the UniProt, PDBe and PRIDE at EMBL-EBI as well as our collaborators in UK and US. S(he) will be working in the integration of proteomics and structural data into UniProt and the rule-based automatic annotation system (UniRule) developed by UniProt. As part of his/her daily work s(he) will analyse data, design and develop production software, create technical documents, take part in the daily Scrum meeting, as well as communicate with other teams at EMBL-EBI and/or with our international collaboration partners. Scalability will be an important feature of his/her clear, concise, well tested and documented code. S(he) will be based in a multidisciplinary team within the Protein Function group and will respond to the Protein Function development Team Leader at EMBL-EBI. You will be working in the PTMXchange and 3DGateway Project.

The Protein Function development team maintains bioinformatics infrastructure of the world leading Universal Protein Resource (UniProt), Gene Ontology Annotation and Enzyme resource. This is a very dynamic and interdisciplinary team comprising talented and enthusiastic software engineers and bioinformaticians working closely together with the biocurators in these resources. The UniProt resource is one of the most internationally used protein databases serving a large and diverse research community in genomics, proteins and proteomics.

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).

Your Role:
We are looking for a Software Engineer and/or Bioinformatician with strong record in software development to work in the architectural design and development of robust and scalable data integration pipelines.

Responsibilities include:

Design, development, test, document and maintenance of software for a new scalable data integration production pipeline
Assist with the data analysis and data processing algorithms in the data integration pipeline
Design and develop software for our computational annotation procedures
Support and maintain the resource production and service release
Engage and coordinate work with different teams in the organization and internationally
Assist with innovative programming and big data technologies
Assist with programming standards to promote best practices

You Have:
A degree in Computer Science, Computational biology or a related discipline
At least 2 years of working experience in software using Java
Familiar with standard development tools (continuous integration e.g. Jenkins, build management e.g. Maven, and source code management systems e.g. GIT, etc).
Experience in relational database querying (e.g. MySQL, PostgreSQL)
Understanding of good coding practices and approaches (OOP, IoC, automated testing, clean code principles, code review)
Knowledge of standard development tools and concepts (VCS, CI, etc)

You might also have:

Knowledge of NoSQL/graph databases
Experience working in bioinformatics and biological resource development would be an advantage.
Knowledge/experience of proteomics and genomics
Knowledge of UniProtKB, InterPro, Ensembl, ENA, RefSeq would be very valuable
Familiarity working with computing cluster such as LSF or SGE

Why join us:
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 over 27 member states and two associate member states. 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.

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. For more information about pay and benefits please visit our website

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 view a copy of the full job description please visit our website

To apply please submit a covering letter and CV through our online system.

Applications are welcome from all nationalities and this will continue after Brexit. For more information please see our website. 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.

Application Closing Date: 
26 December