Ensembl Developer – Genebuild

We’re looking for a bioinformatics developer to join our genebuild team, creating and running pipelines to annotate genes onto genomes. We’re looking for PhDs or MScs in Computer Science, Bioinformatics, Genetics or related fields, with experience in genome annotation using pipelines and compute clusters and knowledge of object-oriented programming and Unix. Closes 25th February.

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: 25 February 2018
Reference Number: EBI_01122

Job Description

The Vertebrate Annotation team are looking to recruit a highly motivated bioinformatics developer to join the Ensembl Genebuild project at the European Bioinformatics Institute (EMBL-EBI), located on the Wellcome Genome Campus, near Cambridge in the UK.

Ensembl Genebuild produces gene annotation for vertebrate species, including the reference gene sets for human and mouse. We are one of the world’s leading groups for identifying the location, structure and tissue-specific expression of genes and their transcripts for large numbers of vertebrate species.

Your main responsibilities will involve running our large-scale annotation system to produce gene annotation. As part of Ensembl Genebuild, you will:

  • Run production pipelines on a large compute cluster to download, process and integrate data from various public sequence archives
  • Produce high-quality, evidence-based gene sets for vertebrate species including protein-coding genes, noncoding RNA genes and pseudogenes
  • Produce tissue-specific RNA-seq alignments and transcript models
  • Collate these data into appropriate databases and files for the Ensembl release cycle
  • Document the data and processes used in gene annotation
  • Contribute to the Ensembl code-base including the design and implementation of new annotation pipelines and software
  • Work collaboratively with other members of Ensembl on data production around the Ensembl release cycles
  • Communicate the team’s work internally and to researchers in the field, including user support

The Ensembl Genebuild project is a component of the Vertebrate Annotation team. As part of Ensembl Genebuild, you will join seven bioinformaticians and developers who are experts in gene annotation. We have domain area expertise in public archives, alignment methods, software development, large-scale compute, pipeline workflows and automation. Future projects for the team include: scaling up gene annotation pipelines, improving our annotation of noncoding genes, automating and enhancing our RNA-seq annotation pipeline, and developing methods of analysing new data including full-length transcriptomic reads.

This is a unique opportunity to contribute to Ensembl’s mission to analyse, store and disseminate genomic annotation. For further information about Ensembl, please visit: www.ensembl.org and https://github.com/Ensembl.

For further information about Ensembl Genebuild, please check here

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 23 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

You should hold an MSc, PhD or equivalent experience in Computer Science, Bioinformatics, Genetics or related fields and be able to write, understand and maintain complex code. You will also have domain experience of eukaryotic genome annotation, the biology of gene expression, current methods for DNA sequencing and sequence alignment.

Previous experience of processing large biological data sets in a production environment would be advantageous, including an understanding of compute clusters, pipeline workflows, software design and automation. Evidence of working in a dynamic, team-based environment or contributing to a large, shared code-base is desirable.

We are looking for a new team member who has good communication and interpersonal skills, is a self-starter, and who can manage their own time to meet the needs of several projects. The key attributes sought are the ability to work in a team, excellent attention to detail, solid problem solving skills, and the desire to learn and improve. Furthermore, you should demonstrate your ability to communicate both biological and computational ideas (orally and in writing), time management to deadlines, and a desire to work in an international environment.

Proficiency in object-oriented programming and developing software in a primarily Unix-based environment is essential. Familiarity with compute clusters and development tools such as Git would be an advantage. In addition, experience in developing computationally efficient solutions, working on a large but continually-evolving codebase, and familiarity with relational databases would be an advantage.


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.

The initial contract is for a period of three years with the possibility of a fixed-term extension. The appointed candidate must start before 01.10.2018.

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