COVID-19 Bioinformatician
Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: 1 year or until 28/02/2023
Grading: Grade 5 (monthly salary starting at £2,738 after tax) + other paid benefits
Closing Date: 26 April 2021
Reference Number: EBI01768
We are seeking a Bioinformatician to join the Data Coordination and Archiving Team at the EMBL-European Bioinformatics Institute (EMBL-EBI). The team provides data coordination services for partners around the world for a portfolio of sequencing-based studies. With underlying infrastructure for these services based around the European Nucleotide Archive – one of life science’s largest and longest standing data resources – this is an opportunity to rise to the challenges of ‘big data’ and make contributions that advance the reach and utility of sequence data.

Your role

This is an exciting opportunity to make a significant contribution to the EMBL-EBI COVID-19 rapid scientific response. To combat COVID-19 we need to refocus wherever possible research efforts as well as research infrastructure provision into enabling the scientific community to understand the biology, epidemiology, transmission and evolution of the virus responsible for the outbreak, SARS-CoV-2. EMBL-EBI has recognised the urgency to identify and consolidate needs around creating a European COVID-19 Data Platform for data/information exchange, connected to the European Open Science Cloud (EOSC).

As part of the EMBL-EBI COVID-19 task force you will be part of the team that coordinates and develops automated workflows to process SARS-CoV-2 datasets. Adapting and developing innovative workflows to process and present COVID-19 data held across EMBL-EBI archives and the wider scientific community. You will also contribute to the Embassy Cloud Analysis workflow platform that automates the analysis of incoming COVID-19 data.

You will design and extend workflows, including investigating and selecting appropriate technologies, to meet the data processing and presentation needs of the projects. You will work with teams from across EMBL-EBI and collaborate with expert scientists to provide innovative services.

You have

You should have a university degree in the computer sciences or life sciences and have several years’ experience in a bioinformatics or software developer capacity.

Required experience:
  • Experience developing and maintaining bioinformatic pipelines
  • Python
  • Containerisation (Docker or similar) and orchestration
  • RESTful APIs
  • Proficiency with database connectivity. Relational and noSQL databases
  • Experience in full software development cycle including design, implementation, testing, version control and deployment
  • Willingness to learn new skills as the project requires
  • Self-motivated and capable of working both independently and as part of a team
  • Excellent communication, interpersonal and English language skills

You might also have

  • Experience with Kubernetes
  • Experience with Phylogenetics
  • Experience with viral sequence data and/or ‘omics sequencing
  • Experience with NexfFlow and/or Snakemake
  • Experience with CI/CD pipelines
  • Experience with Jupyter ipython notebooks
  • Experience with microservices architecture
  • Experience with Cloud deployment
  • Prior experience working in a multidisciplinary scientific environment.

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

At EMBL-EBI, we strongly believe that inclusive and diverse teams benefit from higher levels of innovation and creative thought. We encourage applications from women, LGBTQ and individuals from all nationalities. Visa exemptions will be offered to international candidates and details will be discussed during interview. We believe in science without borders and this continues after Brexit.

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.

This position is limited to project duration until end February 2023.

We aim to provide a response within two weeks after the closing date. 

Job no.: EBI01768