GA4GH Bioinformatician/Software Developer
Location:EMBL-EBI Hinxton near Cambridge, UK
Staff Category:Staff Member
Contract Duration:2 years
Grading:5 (monthly salary starting at £2,552 after tax). For more information about pay and benefits click here
Closing Date:27 July 2018
Reference Number:EBI_01240

Job Description

The Samples, Phenotypes and Ontologies team are looking for an enthusiastic, highly motivated GA4GH Bioinformatician/Java software developer to join the BioSamples database team. This post offers the challenges and excitement of working at the forefront of genomics and clinical data science.

The project

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 over 5 million samples in 2017. It plays a key role in biological knowledge to the raw data, stored in the many archive databases at EBI and outside. The GA4GH initiative underlies the foundation of data sharing and processing for genomic medicine. The Clinical & Phenotypic work stream of GA4GH is designing datamodels to ensure sample, individual and technical metadata is completely interoperable and can be used by research groups across the globe.

The Biosamples team is a multidisciplinary team of bioinformaticians and programmers with experience in ontologies, databases, backend java technologies and user interfaces.

Your role

As a GA4GH Bioinformatician/software developer for BioSamples you will be in charge of making the BioSamples metadata available to GA4GH members, and retrieve associated raw data from other EMBL-EBI archives such as ENA and EGA.

You will use many techniques, including big data techniques, to explore and analyse sample data. This will include: data mining, analysis and the presentation of results in a clear manner with a view to processing, cleaning, and verifying the integrity of data stored in BioSamples, with a specific focus on human diseases. In this role, you’ll be building tools to automate the capture, validation and storage of ontology- and metadata-rich descriptions of biological samples. This will involve development of automated data validation and curation tools. You will also need to identify and support evolving user requirements, as well as develop training materials in collaboration with the EMBL-EBI training team.

You’ll be working locally within the SPOT team at EBI alongside developers, bioinformaticians and ontologists. Internationally you will be part of the GA4GH consortium and be involved in regular conference calls with diverse partners. You will have the opportunity to travel to face to face meetings. For example, our next plenary will be in Basel early October 2018.

Qualifications and Experience

You will have:

  • An undergraduate degree in a Biomedical Science, with a masters degree in bioinformatics or a computer science. Demonstrated equivalent experience will also be considered.
  • Previous experience of software development in at least one programming language
  • A desire to engage with both the user community and project collaborators, which requires good communication skills and ability to work as part of a team of people with a range of skills and a diversity of backgrounds.
  • Interest in integrating data to solve biological problems, specifically in genomics with a view towards human health

You might also have:

  • Experience with collaborative projects and/or Agile software development
  • Data formats for expressing biological data and data management
  • UI Design
  • Semantic technologies such as ontologies and RDF


In addition to highly competitive salary and fantastic benefits package 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 individual, especially one with previous experience in bioinformatics interested in practical applications development on a large scale.

Opportunities will be provided for self-growth. These include working in a highly-skilled team on the Wellcome genome campus, a hub of scientific and technical expertise with many trainings and seminars available.

We know the importance of and value a healthy work life balance. The campus provides an on site nursery and since 2017 a holiday club for children 4-14 years old. Cambridge is a vibrant city which is culturally diverse and has many excellent schools and family-friendly amenities.

Application Instructions

To apply please submit a covering letter and CV, with two referees, through our online system.

Additional Information

Applications are welcome from all nationalities - 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.

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