Bioinformatician - parasite genomics
Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: 3 years
Grading: 5 (monthly salary starting at £2,632 after tax)
Closing Date: 23 November 2020
Reference Number: EBI01718
We are seeking a motivated bioinformatician to work on resources for parasitic worm genomics at the EMBL European Bioinformatics Institute (EMBL-EBI).

Parasitic worms are responsible for more than one billion human infections globally and also have a devastating impact on our food supply. WormBase ParaSite ( facilitates genomics-based approaches to the understanding, treatment and prevention of parasitic worm infection by integrating, analysing, comparing and displaying genomes for hundreds of diverse species.

WormBase ParaSite is a database, website and set of tools developed in partnership between the WormBase and Ensembl ( groups at EMBL-EBI, and the Parasite Genomics group at the Wellcome Sanger Institute. You will work closely with genome scientists and bioinformaticians in all three groups in a dynamic and collaborative environment.

Your role

You will develop and maintain the technical infrastructure for WormBase ParaSite (databases and software) and will work on a range of genomic data analysis and integration activities, participating in the exciting next phase of development for the resource. You will also have the opportunity to engage directly with the research community by participating in training workshops and international conferences. Your main responsibilities will be:
  • Maintain and develop the WormBase Parasite database and software infrastructure (based on Ensembl) for storing and presenting parasitic worm genomes and genomic data
  • Write and deploy high-throughput bioinformatics analysis pipelines for annotation and comparison of parasitic worm genomes
  • Develop processes and pipelines for the integration of diverse parasitic worm genomic datasets (e.g. gene expression, genomic variation, phenotypic screens)
  • Collaborate on extending the platform to deal with new cutting-edge data types as they emerge
  • Help develop and deploy cloud-based tools to support expert curation of genomic data for parasitic worms

You have

You are a bioinformatician who is motivated to create robust, well-designed and well-documented infrastructure, code, pipelines and processes. Specifically, you should have:
  • A post-graduate degree (Masters or PhD) in bioinformatics or a related subject
  • Proficiency in at least two programming languages (ideally including Perl and Python)
  • Practical experience working with relational database systems (e.g. MySQL, PostgreSQL)
  • Experience developing high-throughput analysis pipelines using a workflow management system (such as Snakemake or Nextflow)
We do not expect you to know everything on day one, but you need to have solid experience in at least one of our core areas (genomics, bioinformatics or software development) and display an eagerness and ability to quickly expand your knowledge in other areas. You should also have good communication skills to operate effectively within an environment where biologists, bioinformaticians software engineers work closely together.

You might also have

Ideally, you will also have practical experience working with the Ensembl platform, and with deploying software in a cloud computing environment. Experience working with AWS will be considered a major plus.

Why join us

EMBL-EBI is a worldwide leader in bioinformatics. We encourage personal and professional development and are committed to ensuring our employees feel valued, supported and empowered to reach their potential at work.

Surrounded by beautiful South Cambridgeshire countryside, our state-of-the-art Campus provides employees with a relaxed atmosphere where the pursuit of scientific discovery and meaningful work, underpin every role. In addition, our employees have access to a wide range of benefits including:
  • 30 days annual leave per year plus 8 bank holidays
  • Flexible work arrangements
  • Unique pension scheme including 17% employer contribution
  • Annual salary review
  • Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover)
  • Death benefit, long-term care, accident at work and unemployment insurances
  • Relocation package including installation grant (if required)
  • On-site library and subsidised on-site gym and cafeteria
  • Casual dress code
  • Free shuttle bus to and from Campus
  • Extensive sports and social club activities (run on campus and remotely)
  • Family benefits: Onsite nursery, child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowances
  • Benefits for non UK residents: Visa exemption, education grant for private schooling, financial support to travel back to your home country every second year and a monthly non-resident allowance

What else you need to know

To view a copy of the full job description please click here

This role is based in Hinxton, UK and you will be required to relocate once it is safe to do so if you are currently based abroad. More info on how we are recruiting in this period is available on our page: Recruitment and Onboarding during Covid19.

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.