Location:EMBL-EBI Hinxton near Cambridge, UK
Staff Category:Staff member
Contract Duration:3 years
Grading:5 (monthly salary starting at £2,552 after tax). For more information about pay and benefits click here
Closing Date:24 September 2017
Reference Number:EBI_01018

Job Description

EMBL-EBI seeks an enthusiastic software developer to lead our software development and informatics efforts supporting manual genome annotation within the GENCODE project.

GENCODE seeks to annotate all evidence-based features in the human and mouse genomes with high accuracy and then release these annotations for the greatest possible benefit to biomedical research and genome interpretation. Given how intensively reference genomes are used by hundreds of thousands of biologists and clinicians across the world, it is imperative that the annotation error rate is brought down as close to zero as possible.

A unique aspect of the GENCODE approach is manual comparison of the final gene annotation with supporting evidence. This process involves expert human curators viewing experimental data, the results of automated algorithms and other information to create the final gene annotations.

To keep the process efficient, the GENCODE project counts a number of developers who provide these curators with specialised tools to visualise the data, report errors and correct annotations. You will help support and extend the existing tools, in particular:

  • Maintain the MySQL backend and its Perl API,

  • Migrate this infrastructure from the Sanger Institute to EMBL-EBI,

  • Ensure compatibility between the GENCODE backend and that of its sister project, Ensembl,

  • Add new features, in collaboration with the GENCODE curators,

  • Ensure this backend communicates well with the frontend (Zmap).

Within EMBL-EBI, you will work within the Genome Analysis team (led by Daniel Zerbino) and collaborate closely with the HAVANA curation team (led by Adam Frankish). EMBL-EBI is part of the European Molecular Biology Laboratory (EMBL) and is located on the Wellcome Genome Campus, near Cambridge in the UK. EMBL-EBI is Europe's leading provider of information services to biological researchers in academia and industry.

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 and proud to be an equal-opportunity employer. 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

Qualifications and Experience

An ideal candidate should have:

  • Degree, MSc or PhD level or equivalent qualification/experience in a Computational, Physical or Biological Sciences;Experience of communicating and working with expert technical users (e.g. in a science community);

  • Experience in working in large scientific projects, especially in the field of genomics, would be strongly preferred.

You must be capable of autonomously leading your work in a thorough, timely and detail-oriented fashion, as you will have to keep track of many parallel tasks. Communication and presentation skills within multidisciplinary teams will be highly valued.

You must have extensive experience with computers and be fully fluent with one or more of the following technologies:

  • Perl

  • MySQL

  • Git

Knowledge of C++ would be highly advantageous.


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.

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.

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 contract duration specified.

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