European Molecular Biology Laboratory (EMBL)

Bioinformatician

European Molecular Biology Laboratory (EMBL)

Hinxton, Cambridge, United Kingdom


About the team/job


The Archival Infrastructure and Technology team is looking for an enthusiastic, highly motivated bioinformatician to join the Human Cell Atlas (HCA) project to help us integrate data from labs using cutting-edge single cell techniques.

The HCA is using single-cell gene expression techniques as the basis for both understanding human health and understanding different disease mechanisms. So if you are interested in the Human Cell Atlas, or if you’d like to help us work towards developing comprehensive reference maps of all human cells, this job will be perfect for you!

With the help of our collaborators, we are collecting data and building process to make data
Findable, Accessible, Interoperable and Reproducible (FAIR), as part of  the Data Coordination Platform (HCA-DCP) for the HCA community.  As part of this team, you will have the chance to engage with our collaborators from the Broad Institute, the Chan Zuckerberg Institute, the University of California Santa Cruz and Stanford University.


Your role


This position is a fantastic opportunity to gain hands-on experience, working on a high-profile project with major scientific impact in a world-leading bioinformatics institute.

We are looking for a bioinformatician or a software developer with experience in handling biological data and biological requirements. You should have a biological background but you should also be able to find your way around a terminal. Programming experience in at least one programming language (such as Python, Perl or Java) and experience with managing data or data processing pipelines would be desirable. Previous experience of working in a bioinformatics-focused environment would be beneficial.

You will help us describe all data collected from HCA scientists using well-structured, FAIR metadata that takes advantage of many pre-existing ontologies. This approach provides rich and consistent information so users can query the Atlas using many facets of a sample’s identity, such as tissue source and donor age, as well as project and experimental details. You will help build the tools that support metadata FAIRification, annotation and discovery for the HCA.

We follow agile techniques in our approach to development, so if you’re the sort of person who likes to work in sprints, has worked with tools like Jira or Zenhub in the past to prioritise user requirements, or have ever tried pair-programming or code reviews, then you’ll be a good fit for our team. All of our software is built and published using continuous integration and version control, so you should at least be familiar with GitHub, and you should be confident in making your code public for others to install and run. 

You’ll be working within the AIT team at EBI alongside developers, bioinformaticians and ontologists. 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 to improve submission of data to the HCA-DCP.


You have


  • Experience of at least one programming language including Python and/or Java
  • Practical experience of data management
  • Knowledge of common data formats, in particular, JSON and JSON schema
  • Excellent interpersonal and communication skills and an ability to work as part of a team of people with a range of skills and a diversity of backgrounds.

You might also have


  • Research experience in single-cell genomics or bioinformatics
  • Several years of experience with other programming languages, such as Python or Java
  • Some familiarity with semantic technologies and use of ontologies for annotating metadata 
  • Experience of working in an agile development environment
  • Interest in Cloud technologies

We value people who demonstrate that they’re eager to learn about specific aspects to support our users’ requirements.


Why join us


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.

This position is limited to the project duration specified.

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

Please apply via recruiter’s website.

Quote Reference: embl-EBI01477

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