Thursday, September 28, 2023
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PDBe Coordinator

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About the team/job

We are looking for an individual to coordinate the Protein Data Bank in Europe Team (PDBe; team at the European Bioinformatics Institute (EMBL-EBI). This role is central for delivering data services that significantly impact on how the scientific community uses bio-macromolecular structure data now and in the future.

The PDBe team manages three core structural biology resources – the Protein Data Bank; the Protein Data Bank in Europe Knowledge Base (PDBe-KB;; and the AlphaFold Protein Structure Database (AFDB; PDBe is a founding member of the Worldwide Protein Data Bank organisation (wwPDB; and the PDBe-KB consortium and collaborates with Google Deepmind on the AlphaFold Database.

The team develops data archiving and analysis tools for structural biologists and the wider scientific community. The team consists of an international and interdisciplinary mix of professionals: scientists, software engineers, and database engineers. 

Your role

This position is for a Scientist, interested in open data, who wants to impact the development of key resources for global, public 3D-structure data. We need a person who understands the importance of teamwork and is focused on the delivery of key tasks.

As the PDBe Coordinator, you will be expected to:

  • Work with the PDBe team leader and other senior members of the team to formulate and refine the team and resource strategy;
  • Liaise with wwPDB and PDBe-KB consortium members, AFDB collaborators and other internal and external collaborators;
  • Represent the PDBe team in various forums;
  • Keep abreast of relevant developments in the field of structural bioinformatics and related disciplines;
  • Lead, manage and coordinate PDBe team projects with respective project leads;
  • Line management of several project leaders, software developers and bioinformaticians working on PDBe projects;
  • Contribute to funding applications;
  • Be in constant communication with the PDBe Archive Project Leader to coordinate and prioritise team projects;
  • Work with the PDBe training and outreach lead to formulate and deliver an effective training and outreach strategy for the PDBe resources;
  • Work with the PDBe technical lead to ensure timely delivery and robust maintenance of PDBe infrastructure, website and other data access tools

As a Senior Scientific Officer, the successful candidate will report directly to Sameer Velankar, PDBe team leader. This is an opportunity for the right person to deliver significant impact in the area of 3D-structure data via PDBe data resources, tools and services. 

You have

Education and Qualifications

  • PhD in a relevant field
  • Ideally, at least 5 years of post-doctoral experience, with extensive knowledge in the area of structural biology and structural chemistry, broad knowledge of molecular biology or biochemistry, and in-depth knowledge of protein structure.

Professional experience

  • Good understanding of structural biology data collection, handling, processing, analysis, visualisation, interpretation, archiving, dissemination etc.
  • Demonstrated project and people-management experience.
  • An understanding of software development by a team of developers

Functional competencies and technical skills

  • Excellent written and oral communication skills, fluency in English, and attention to detail
  • Software development in a major programming language (e.g., Python, C, C++, Java)
  • Working with data models and file formats (e.g. structural biology data models and formats such as the PDBx/mmCIF, XML, JSON)

Interpersonal and Communication skills

  • A strong affinity with and enthusiasm for the goal of EMBL-EBI to provide world-class open data and services to the global community
  • Proven ability to collaborate with people inside and outside an organisation, with the requisite diplomacy skills
  • Ability (and enthusiasm) to engage within the user community.
  • Enthusiasm and drive to lead the development of an already successful resource for a rapidly changing field of science

You might also have

Professional experience

  • Demonstrated experience or substantive involvement in writing successful grants

Functional competencies and technical skills

  • Project and people management skills and experience (e.g., in Agile software development, project management, conflict resolution)
  • Working with relational and non-relational database technologies (e.g., SQL, Oracle, Mongo DB, Neo4J)
  • Web and front-end development (e.g., Django framework, Javascript frameworks/libraries, HTML 5)
  • Working with collaborative computing technologies and concepts (e.g., GitHub/GitLab/SVN, JIRA and other issue-tracking systems, continuous integration) 

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, 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 3 year contract, renewable to a maximum of 9 years.
  • 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.
  • EMBL is a signatory of DORA: Find out how we apply DORA principles to our recruitment and performance assessment processes here.
  • Job location: This role is based in Hinxton, near Cambridge, UK. You will be required to relocate if you are based overseas and you will receive a generous relocation package to support you.
  • How to apply: To apply please submit a cover letter and a CV through our online system. In your application letter, please demonstrate how you fit each of the key requirements and desirable qualifications.
  • Interviews: Candidates invited for an interview will be asked to give a brief (15 minute) presentation that demonstrates their previous experience and what they would bring to the role (5 minutes) and what their approach and vision would be for PDBe resources, and what they think the challenges will be (10 minutes). Interviews will be virtual and are expected to take place beginning October 2023. 

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