Job:Ensembl Bioinformatics Developer
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3.8 years ago
Emily 23k

Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: 3 years
Grading: Grade 5 (monthly salary starting at £2,676 after tax)
Closing Date: 7 January 2020
Reference Number: EBI01549

We are seeking a talented bioinformatician to help develop exciting new genome resources at the European Bioinformatics Institute (EMBL-EBI).

Mice, rats, zebrafish, flies, worms and yeast are studied extensively by scientists around the world to reveal fundamental mechanisms of human biology.  The Alliance of Genome Resources (AGR) is a major new initiative to develop infrastructure, analysis pipelines, and curation workflows for model organism genomic data, together with an integrated website and tools (

You will join a team that acts the genomics hub for the AGR, analysing and integrating genomic data across the model organisms on behalf of the Alliance.  You will develop and deploy bioinformatics tools and pipelines on model organism genomic data sets, using the Ensembl platform ( developed at EMBL-EBI, and working closely with Ensembl developers. You will also contribute to the development of the AGR central data portal,  as part of a larger team of developers spread across multiple institutions in Europe and North America. This an excellent opportunity to join a dynamic and high-impact international project.

Your role

You will develop and deploy bioinformatics tools and workflows on model organism genomic data on behalf of the Alliance of Genome Resources. Specifically, your work will include the following:

  • Pipelines for the integration and annotation of model organism genomic variants using the Ensembl Variant Effect Predictor (VEP) and associated tools
  • Resources for model organism gene- and genome-level sequence homology, including protein multiple sequence alignments and synteny.
  • Pipelines for efficient ingest of large genomic data sets
  • A shared data model, API and tools for the AGR portal

You have

You should hold a degree in biological or computer science, and at least two years experience working in bioinformatics. We are specifically looking for:

  • High degree of proficiency in at least two programming languages (e.g. Python and Java)
  • Practical experience working with relational Databases platforms (e.g. MySQL, Postgres)
  • Experience working with genome analysis and annotation tools
  • Familiarity with cluster compute environments and/or workflow management systems
  • Excellent communication skills

You might also have

Experience with the following will be considered a plus:

  • Working in a cloud computing environment (e.g. AWS)
  • Practical experience with NoSQL database platforms (e.g.  Neo4j, Elasticsearch)
  • Working within a geographically distributed international project
  • Working with the Ensembl platform

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 over 27 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 Grant duration specified.

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

Apply now

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