European Molecular Biology Laboratory (EMBL)

Software engineer

European Molecular Biology Laboratory (EMBL)

Hinxton, Cambridge, United Kingdom

About the team/job

An exciting opportunity has arisen for an enthusiastic software engineer to work in the field of biological “Big Data” within a highly motivated engineering team. 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. UniProt is an international Consortium, a collaboration between the EMBL-EBI, the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR) in US.

Your role

We are looking for a Software engineer with strong record in software development and interested in solving scientific questions related to Big data in biology. The successful candidate will be working in one of the most challenging projects in the UniProt protein resource developing and implementing methods and production software for the computational prediction and functional annotation of protein sequences. Proteins are the building blocks of live and knowing how they function in the cells of living organisms gives us an insight on their health and disease states. With knowledge in biology generated at an unprecedented accelerating pace, the number of protein sequences in the database has increased dramatically and computational methods are needed more than ever for predicting and annotating protein function.

The significance of automated annotation of protein sequences is increasing due to the exponential growth of available protein sequence data. In this context scalability will be an important feature of your clear, concise, well tested and documented code. You will also be interested in applying analytic engines and technical approaches to distributed processing of big data.

As part of your daily work you will 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. The ability to work towards tight deadlines is essential.

Your main responsibilities will be:

  • Develop, maintain, run and monitor computational annotation production pipelines

  • Contribute to the team’s novel developments by suggesting Machine Learning / Data Analysis algorithms and approaches, and implementing them

  • Develop, maintain and deploy web-based curation tools

  • Develop and maintain the computational annotation database backend

  • Write and maintain documentation; proactively participate in group meetings and discussions with the team about solutions for the ongoing tasks and new issues

  • Communicate with scientific experts to understand and efficiently collect project requirements

You have

  • A university degree in Computer Science / STEM or a related field with at least 2 years of proven professional experience in developing Java software in a team environment, and in supporting production systems in an academic or commercial setting

  • A Background in computing with at least 2 years of experience programming in Java

  • Proven working experience of writing production quality software in Java

  • Understanding of good coding practices and approaches (OOP, IoC, automated testing, clean code principles, code review)

  • Familiarity with HTML5/CSS3/JavaScript/JQuery, SQL and relational database design principles, Unix shell scripting

  • Knowledge of standard development tools and concepts (VCS, CI, etc)


You might also have

  • Knowledge of Machine Learning and Data Analysis algorithms is a strong plus

  • Experience with agile development practices and the full software development life cycle

  • Knowledge of the Spring framework

  • Experience with data mining approaches and the “BigData” concept

  • Experience with HPC schedulers like LSF

  • Knowledge of “Big Data” processing technologies like Apache Spark

  • Knowledge of NoSQL/graph databases, experience with Apache Lucene/Solr

  • Knowledge of a scripting language such as Python/Perl

  • Knowledge of biology or relevant science

Why join us

This is an excellent opportunity for a software engineer interested and/or with experiment in data mining techniques to help us shape the future of computational annotation in a world leading database (UniProt) used by thousands of scientists around the world.

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 22 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 click here

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.

What else you need to know

To view a copy of the full job description please click here.

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.

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

Please apply via recruiter’s website.

Quote Reference: embl-EBI01436