Bioinformatician (PDBe Team)
Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: approximately 3 years or until end of grant/project on 30/09/2024
Grading: 5 or 6 (monthly salary starting at £2,738 or £3,063 per month after tax + other paid benefits)
Closing Date: 14 July 2021
Reference Number: EBI01851
The Protein Data Bank in Europe Team (PDBe; is part of the worldwide Protein Data Bank organisation (wwPDB;, which maintains the global archive of structural data on biomacromolecules - the PDB. The PDBe Team also maintains several databases that support deposition and advanced search services for structural biologists and the wider scientific community. It has recently launched a new resource – PDBe Knowledge Base (PDBe-KB) of functional annotations for PDB data. The Team consists of an international and inter-disciplinary mix of professionals: scientists, software engineers, and database engineers. The PDBe is part of the Molecular and Cellular Structure cluster within the EBI.

We seek to recruit a bioinformatician interested in structural biological data and functional annotations to work within the Protein Data Bank in Europe Team (PDBe) on the PDBe – Knowledge Base (PDBe-KB) at the European Bioinformatics Institute (EMBL-EBI). The post holder will create and improve biological data processing pipelines, perform data analysis, and develop user-facing web pages. The post holder will be creative, curious, and ambitious and tackle challenging biological data analysis problems.

Your role

The post holder will be in a scientific, technical role. They will ensure that the PDBe-KB annotation processing pipeline will support variation data and macromolecular interaction interface-specific annotations. The post holder will have an experimental, innovation-driven mindset and investigate the annotations, designing methods for comparing data provided by various PDBe-KB partner resources. They will also be interested in designing and developing user-facing web pages to display macromolecular structural complexes in their biological context.

The successful candidate will report to the PDBe-KB project leader.

You have

We are looking for a scientific programmer/bioinformatician with strong structural biology background and software engineering skills. You should be able to work both independently and in close collaboration with the PDBe team members. Excellent communication and interpersonal skills, as well as excellent knowledge of English, are therefore required.

You should hold a PhD in Structural biology, Bioinformatics or a related field and a minimum of 2 years of work experience in Structural biology, Bioinformatics or related subjects. Strong knowledge of structural biology and excellent knowledge of Python and API frameworks is expected.

You should have:
  • A proven track record of data analysis using Python libraries
  • Experience in data visualisation
  • Proficiency in Python3+
  • Knowledge of standard data science procedures
  • Experience with programmatic access frameworks (e.g. FastAPI)

You might also have

It is an advantage if you have:
  • Experience in full-stack web development
  • Scientific publications on the field of protein/nucleic acid annotations
  • Experience with Apache Spark
  • Knowledge of front-end development with experience in HTML5, CSS3, JS/TS
  • Knowledge of and experience with JavaScript libraries (e.g. Angular.js, D3.js)
  • Experience in presenting scientific themes at conferences and/or workshops

Why join us

Do something meaningful
At EMBL-EBI you can apply your talent and passion to accelerate science and tackle some of humankind's greatest challenges. EMBL-EBI, part of the European Molecular Biology Laboratory, is a worldwide leader in the storage, analysis and dissemination of large biological datasets. We provide the global research community with access to publicly available databases and tools which are crucial for the advancement of healthcare, food security, and biodiversity. Join a culture of innovation
We are located on the Wellcome Genome Campus, alongside other prominent research and biotech organisations, and surrounded by beautiful Cambridgeshire countryside. This is a highly collaborative and inclusive community where our employees enjoy a relaxed atmosphere. We are committed to ensuring our employees feel valued, supported and empowered to reach their professional potential.  Enjoy lots of benefits:
  • Financial incentives: Monthly family, child and non-resident allowances, annual salary review, pension scheme including 17% employer contribution, death benefit, long-term care, accident-at-work and unemployment insurances
  • Flexible working arrangements
  • Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover)
  • Generous time off: 30 days annual leave per year, in addition to eight bank holidays
  • Relocation package including installation grant (if required
  • Campus life: Free shuttle bus to and from work, on-site library, subsidised on-site gym and cafeteria, casual dress code, extensive sports and social club activities (on campus and remotely)
  • Family benefits: On-site nursery, 10 days of 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.
For more details please see our employee benefits page.

What else you need to know

  • Contract duration: This position is a grant/project-limited fixed-term contract foreseen for a duration of 3 years or until  30/09/2024 (whichever is shortest).
  • International applicants: We recruit internationally and successful candidates are offered visa exemptions. Read more on our page for international applicants.
  • Diversity and inclusion: 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.
  • Job location: 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. Read more about how we are recruiting during the pandemic.
  • Your application: To apply please submit a cover letter and a CV through our online system. We aim to provide a response within two weeks after the closing date: 14 July 2021