Software Engineer

European Bioinformatics Institute (EMBL-EBI)
Job Location: 
Wellcome Trust Genome Campus near Cambridge in the UK
Job Description: 

We are looking for a self-starting Software Engineer to join the Expression Atlas development team at the European Bioinformatics Institute (EMBL-EBI), located on the Wellcome Trust Genome Campus near Cambridge in the UK.

EMBL-EBI is part of the European Molecular Biology Laboratory (EMBL) and is a world-leading bioinformatics centre providing biological data to the scientific community, with expertise in data storage, analysis and representation. Expression Atlas is a value added database servicing queries for gene expression patterns (e.g. genes over-expressed in a particular tissue or disease state) as well as broader exploratory searches for biologically interesting genes/samples.

Expression Atlas is currently undergoing a major transformation to include proteomic data, as well as baseline and differential expression of genes, proteins, smallRNAs and pathways. A variety of quality control and statistical analysis approaches for both microarray and RNA-seq experiments are also being developed. The increasing sophistication of biological analysis and representation in turn requires increasingly complex and intuitive user interface solutions, often demanding novel technological approaches to implement them.

The post holder will be fully involved in developing, delivering into production environment and maintaining the new Expression Atlas software. Evaluation and benchmarking of various state-of-the-art user interface and back-end candidate technologies, frameworks and patterns will also be required.

The Expression Atlas team is interdisciplinary, consisting of software engineers, scientists and bioinformaticians. The successful candidate will be expected to work closely with other Atlas team members, but have direct interactions with end-users, as well as other teams within the Functional Genomics group and across EMBL-EBI.

The post holder will report to the Expression Atlas coordinator and the Functional Genomics group leader.

At EMBL-EBI we provide a dynamic, international working environment and have close ties with both the University of Cambridge and the Wellcome Trust Sanger Institute. EMBL-EBI staff enjoy many benefits including 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.


Applicants will possess a BSc or equivalent in computer science or a related technical subject (e.g. mathematics).

The successful candidate will have had 3 or more years of verifiable experience in web development with a proven track record in this area (applications should include references to contributed projects and open source repositories).

The ideal candidate will possess excellent skills in at least 2 of the following technical areas:

•Java software engineering and TDD skills.
◦Core Java and open source extensions (Guava, Commons, etc.)
◦Object Oriented code quality metrics
◦xUnit, Hamcrest, Selenium WebDriver
◦Dependency Injection
◦Maven and Continuous Integration
◦JDBC / JPA / SQL (NoSql is a plus)
◦UML / ER (ability to read and clearly understand models, at least)

•Web UI / REST development
◦UI Sketching , Mocking, Composition
◦TDD Javascript (Jasmine or QUnit or other equivalent technology)
◦Web MVC + Front End Templating
◦Content negotiation◦Data binding (with Java or with JSo REST)
◦Build processes

•System Integration
◦Solr / Lucene
◦Web application performance
◦Distributed Data
◦Linux / Scripting (Shell or Python or equivalent)

Strong technical, interpersonal and communication skills are key to this position. We place high value on self-motivation and a drive for quality.

An interest in bioinformatics, working in R&D environment and providing high quality service to help scientific discovery will be a plus.

Contact Information: 

Please apply online through

About Our Organization: 

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

We welcome applications from all nationalities. Visa information will be discussed in more depth with applicants selected for interview.

Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.