Software Engineer

Job Location
Wellcome Genome Campus
Hinxton, near Cambridge
CB10 1SD
United Kingdom

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. We provide a dynamic, international working environment and have close ties with the University of Cambridge and the Wellcome Trust Sanger Institute.

EMBL-EBI staff also enjoy excellent sports facilities, a free shuttle bus to Cambridge and other nearby centres, an active sports and social club and an attractive working environment set in 55 acres of parkland.

Job Description

We are seeking to recruit an experienced Software Engineer to join the UniProt protein resources team at the European Bioinformatics Institute (EMBL-EBI) located on the Wellcome Genome Campus near Cambridge in the UK.

UniProt 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 EBI, the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR).

You will manage and develop software supporting the automatic annotation pipelines for complete genomes in UniProt. You will be responsible for the design, development and maintenance of software for the Java data services providing protein annotations to the scientific community and computational biologists. The role involves close interaction with the UniProt international consortium and team members. You are expected to be innovative and work with the team in the extension of the current software components as well as to evaluate and promote new software methods, tools and programming models for a robust and interoperable programming framework.

The primary responsibilities include:

  • Design, development and maintenance of software for the automatic annotation of large data sets
  • Design, development and maintenance of software for the provision of data services, including the Java API for the scientific community
  • Assist with programming standards to promote best practices
  • Support the databases and develop and execute production release pipelines of the UniProt resources
  • Assist with innovative programming technologies.

You will have a background in computing, and/or bioinformatics. Proven work experience of programming with Java and related technologies such as Spring/Guice, Lucene/Solr, and Java RESTful services are essential.

You will be familiar with relational databases (preferably Oracle) and have a general understanding of NoSQL databases, as well as knowledge of SQL and Unix shell scripting (preferably bash).

You will also be familiar with standard development tools (continuous integration e.g. Jenkins, build management e.g. Maven, and source code management systems e.g. GIT, etc).

Knowledge of Perl and/or Python would be advantageous, and knowledge of JavaScript and frameworks such as AngularJS would be beneficial.

You will be able to work as part of a focussed team, but at the same time self-driven and able to work independently. You will be a structured worker with good communication skills.

How to Apply

Please apply online through

About Our Organization

The 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 academic and industry. 

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