Job: Ensembl Software Engineer - Comparative Genomics
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6 months ago by
Emily_Ensembl20k wrote:

Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: 3 years
Grading: 5 (£2,676 per month after tax) or 6 (£2,994 per month after tax)
Closing Date: 7 January 2020
Reference Number: EBI01550

We are seeking a highly motivated software engineer to work on comparative genomics in Ensembl, a world leading provider of genomics data resources and bioinformatics software tools.

The Darwin Tree of Life (DToL) project plans to sequence, assemble and annotate all 66,000 eukaryotic species in the UK. This will offer unprecedented molecular-level insights into evolution and biodiversity, and for the first time will enable the study of the genomics of whole ecosystems. Ensembl are partners in the DToL and will provide a platform for the annotation and comparison of these genomes.

The Ensembl comparative genomics team has expertise in software development, large-scale compute, big data, workflow management and automation. We collaborate with consortia and communities from all over the world to compare an ever-increasing number of genomes and infer their evolutionary history.

As part of the team, you will help develop methods and pipelines that will support the DToL and other large-scale genomic projects taking place under the banner of the Earth BioGenome Project ( A particular area of interest is Whole Genome Multiple Sequence Alignment. In collaboration with a group at University of California Santa Cruz, you will further develop the multiple genome aligner Cactus ( and its associated Hierarchical ALignment (HAL) format. A particular focus will be on the efficient deployment of the tool in a large-scale production environment to support potentially thousands of genomes. You will also contribute to the on-going development of the Cactus algorithms to improve performance and accuracy (especially in the case of complex genomes).

Your role

Your main responsibilities will involve both the integration and the expansion of genome multiple genome tools into our genome comparison pipelines. Specifically, you will:

  • Further develop and extend the Cactus aligner and the HAL format for efficient deployment in a high-throughput production environment
  • Contribute significantly to the optimisation of Ensembl genome alignment pipelines
  • Work in a release-based environment and coordinate with other Ensembl teams
  • Collaborate with international partners on a shared code-base
  • Participate in training users on our genome alignment workflow

You have

You should hold a post-graduate degree (MSc/PhD) in Computer Science or a related field and have significant experience developing scientific software. Specific skills and experience we require include:

  • The ability to understand, maintain and write complex code in C/C++
  • Domain experience with scaling and optimising algorithms and data structures
  • Experience with cloud compute environments (e.g. AWS)
  • Experience with software containerisation (e.g. Docker, Singularity)

You will also have good communication and interpersonal skills, and be a self-starter 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 will be expected communicate computational ideas, both orally and in writing.

You might also have

Previous experience with biological sequence analysis would be advantageous, including an understanding of sequence alignment algorithms, or graph algorithms applied to biological sequences. Evidence of working in a dynamic, team-based environment or contributing to a large, shared code-base is desirable.

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.

This position is limited to the project duration specified.

To apply please submit a covering letter and CV through our online system.

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.

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

Apply now

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