Bioinformatician/Software Developer

Job Location
Wellcome Trust Genome Campus
CB10 1SD
United Kingdom
Grade 5 Competitive salary
Job Description

We are looking to recruit an enthusiastic, highly motivated bioinformatician and Java software developer to join the Samples, Phenotypes and Ontologies (SPOT) team at the European Bioinformatics Institute (EMBL-EBI) located on the Wellcome Trust Genome Campus near Cambridge in the UK.

In this role, you’ll be building tools to automate the capture, validation and storage of plant phenomics data. You’ll be embedded into the Biosamples team, a multidisciplinary team of bioinformaticians and programmers with experience in ontologies, databases, and backend java technologies as well as user interfaces.
The Biosamples database at EMBL-EBI is a resource that integrates biological samples from a wide variety of sources to provide a single location to apply standards and ontologies to sample data. It has grown from 14,000 samples in 2010 to almost 4 million samples in 2014. Biosamples will become an important component in a new bioinformatics platform to enable genomics research in crop science, helping to integrate the growing wealth of plant genomic and phenomic information to empower the research community as it addresses global challenges relating to plant security, bioenergy and environmental change.
 You’ll be expected to work on all aspects of the stack, as well as data processing pipelines behind the scenes, to help acquire and process the data on the way in. You’ll also work directly with plant scientists to help develop a plant phenotype data submission service that capitalises on the ontologies and data standards that are available in the plant community. As part of your day to day job, you can expect to interact with other groups at EMBL-EBI as well as our external collaborators in order improve submission of and access to plant phenomics data in the biosamples database.
 This position offers exciting opportunities, both to work as part of a team on a large, established bioinformatics database, and to take the initiative in the development of new data processing and submission tools. It would be perfect for a dynamic and motivated programmer, especially one with previous experience of plant genomics.
 EMBL-EBI is part of the European Molecular Biology Laboratory (EMBL) and is Europe's leading provider of information services to biological researchers in academia and industry. 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.



  • Undergraduate degree in biology or several years’ experience working in a bioinformatics environment, and a master’s degree in either computer sciences or bioinformatics
  • Good Java programming skills
  • Experience of working in a Unix/Linux environment and coding against relational databases
  • Experience of working with version control technologies - ideally Git or SVN
  • SPOT is a multidisciplinary team, who believe in Agile development methods, so you’ll either need to have worked in agile teams in the past or be comfortable adapting to one



  • Experience with Solr, Lucene or ElasticSearch
  • Familiarity with SQL databases
  • Experience with semantic web technologies such as OWL, RDF or SPARQL would be an advantage
  • Experience with other languages, such as Python or perl would also be useful
  • A background or prior experience in plant genomics data would be an advantage but is not required
About Our Organization

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

Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review. Applications are accepted welcomed from all nationalities, visa information will be discussed in details with those selected for interview. 

At Nature, Johns Hopkins' Gundula Bosch describes her graduate program that aims to get doctoral students thinking about the big picture.

Patricia Fara writes about childcare funding, and women in science and science history at NPR.

National Institute of Environmental Health Sciences researchers have visualized the career paths of former postdocs.

A new survey from the Pew Research Center finds that half of women working in STEM have experienced gender discrimination at work.