European Bioinformatics Institute/European Molecular Biology Laboratory (EMBL-EBI)
Job Location
Wellcome Trust Genome Campus
CB10 1SD
United Kingdom

EMBL-EBI staff enjoy many benefits including sports facilities, a free shuttle bus to Cambridge and other nearby centres, and an attractive working environment set in 55 acres of parkland. Our salary scales are very competitive.

Job Description

The Vertebrate Genomes Team seeks an enthusiastic developer to work on comparative genomics for the Ensembl team at the European Bioinformatics Institute (EMBL-EBI), which is located on the Wellcome Trust Genome Campus near Cambridge in the UK.

Ensembl ( is one of the most successful large-scale bioinformatics projects and one of the leading projects for genome annotation. Large-scale sequencing projects are now collecting genome sequences from hundreds of new species, and further orders of magnitude will be reached in the next years (for example the Genome 10K project). These data will contribute to improving our knowledge and understanding of the evolutionary history of vertebrate genes and genomes, and the connection between genome evolution and speciation. In light of these new resources, we are looking for an additional member for the team to expand and develop the comparative genomics databases for Ensembl.

The successful candidate will be involved in creating the Ensembl comparative genomics resources as well as in maintaining and developing the production pipeline and the associated Perl API.

Reporting to the Ensembl Comparative Genomics Project Leader, the developer's primary task will be to maintain and develop the whole-genome alignment component of the Ensembl project. This will include working closely with collaborators and keeping up-to-date with scientific research in the area of genome alignments, including aligners (eg Cactus) and file formats (e.g. HAL - Hierarchical Alignment Format). Derived resources that are currently produced, such as GERP and synteny analysis, may also be expanded to new resources of interest to the Ensembl project and community.

In particular, and in addition, to the above, this role will involve:

  • Maintaining and developing the Ensembl Comparative Genomics pipelines, databases and API.
  • Helping with coordination of the Ensembl comparative genomics release process.
  • Supporting the Ensembl Genomes team and other external users in their use of the comparative genomics pipelines.
  • Collaborating and coordinating with peers at the UCSC genome browser on the development of the tools and creation of resources.
  • Teaching the usage of the Ensembl Compara Perl API at the quarterly PI workshops (
  • Participation in collaborations between Ensembl and research groups/consortia.
  • Representing the project and the institute at conferences.


The EBI is part of the European Molocular Biology Laboratory(EMBL) and is Europe's leading provider of information services to biological researchers in academia and industry. EMBL-EBI staff enjoy many benefits including sports facilities, a free shuttle bus to Cambridge and other nearby centres, and an attractive working environment set in 55 acres of parkland. Our salary scales are very competitive.

For further information please visit


The ideal candidate will hold a PhD in molecular biology, bioinformatics or a related field or a Masters degree with appropriate experience. Previous experience of working in a production software environment and organising tasks to fit defined release cycles is desirable but not essential.

You will have experience of working in a UNIX/Linux environment and must have programming experience: the ideal candidate will have at least 2 years experience of Perl programming or will have a computational background and a demonstrable knowledge in comparative genomics.

A high proficiency in object-orientated Perl and shell scripting is essential and the post holder will be expected to be comfortable working in a Unix environment working with relational databases. Experience of the following would be highly beneficial but not essential:

  • Python programming
  • C++ programming
  • The HAL/HDF5 file formats
  • Compute grid engines (such as Platform LSF)
  • Version control systems, especially GIT 


The successful candidate will be self-motivated and capable of working both independently and within a closely interacting team of scientists in an international academic environment. They should be comfortable with detail-orientated work, project deadlines, and enjoy the challenges and excitement associated with working in a fast moving field.

Excellent English, written and oral, communication and interpersonal skills are essential

How to Apply

Please apply online through

About Our Organization

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

We welcome applications irrespective of gender and appointment will be based on merit alone. Applications are welcome from all nationalities. Visa information will be discussed in more depth with applicants selected for interview.

Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.

Applications will close at midnight German time on the date listed above.

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