Electron Microscopy Data Bank Coordinator

Key information

  • Location: EMBL-EBI Hinxton
  • Staff category: Staff Member
  • Job type: Bioinformatics
  • Contract duration: 3 years
  • Grading: Grade 8 (starting salary from £3,999.80 per month after tax) + other paid benefits
  • Closing date: 19 February 2021
  • Reference number: EBI01761

Continue reading for more information about this position, or apply now.

About this position

EMBL-EBI is a world-leader in archiving and disseminating 3D biomacromolecular and cellular structure data and plays a key role in the dissemination of 3D electron microscopy (EM) data through the EMDB (Electron Microscopy Data Bank; emdb-empiar.org) and EMPIAR (Electron Microscopy Public Image Archive; empiar.org) public archives.

We develop and provide advanced tools and web-resources for searching, analysing and visualising structural data for the benefit of structural biologists and the wider scientific community. The team consists of an international and inter-disciplinary mix of professionals (scientists and IT specialists).


Your role

We are looking to recruit an EMDB Coordinator to lead the activities surrounding the EMDB archive.

EMDB, founded at EMBL-EBI in 2002, will become a core archive of the Worldwide Protein Data Bank organisation (wwPDB; wwpdb.org) in 2021, and its future development will be carried out in collaboration with the wwPDB partners.

The EMDB Coordinator will lead a small team (presently 7 staff members, a mixture of structural biologists and computational scientists) and be responsible for leading EMDB’s archival, curation, integration, visualisation and dissemination activities, its production processes (weekly release preparation, updates of databases, websites, ftp areas, etc.), and the active involvement of the team in the wwPDB-related work (annotation of EMDB data, planning and implementing updates of the unified wwPDB deposition system OneDep, validation software, data model, etc.). Currently, the EMDB activities are funded by EMBL-EBI and two grants from the Wellcome Trust. We expect the EMDB Coordinator to play an important role in attracting future external funding.

This is a senior role, reporting directly to Dr Ardan Patwardhan who has overall responsibility of EMBL-EBI’s EM-archiving activities. It provides a rare and exciting opportunity for a scientist with experience in this rapidly expanding and developing field to have a huge impact on how the scientific community archives, validates and re-uses EM data.

The duties of the EMDB Coordinator will include (but are not limited to):

  • To lead and take responsibility for all the activities of the EMDB team, including its work as a wwPDB partner on joint projects (software development, validation, annotation, etc.), the operation of the production processes, and the planning and implementation of new dissemination and outreach activities, maintenance and development of the team’s internal infrastructure, website, services, etc. This includes all aspects of managing a technical/scientific team, including work planning, definition of specifications, reviewing, progress tracking, etc.
  • Active involvement in recruitments, grant writing and management, staff assessments, writing publications, organising workshops, etc.
  • To work with external collaborators on enhancing the functionality and services that the EMDB resource at EMBL-EBI offers.
  • Where opportune, to (co-)organise workshops with community experts to obtain advice about on-going and future developments in the field to ensure that EMDB remains an up-to-date and relevant resource for the EM and wider scientific community.
  • To be visible in the community and represent EMDB in online forums, at conferences, in the context of CCP-EM etc. and to take a proactive role in ensuring that EMDB is heard and seen in the community.

You have

As the successful candidate it is likely that you will have:


  • Education and Qualifications
    • PhD in a relevant field
    • At least 5 years of post-doctoral experience, ideally in the EM field
  • Professional experience
    • Good understanding of data collection, handling, processing, analysis, visualisation, interpretation, archiving, dissemination etc. in cryo-EM, cryo-ET or both
    • Demonstrated project and people-management experience
    • An understanding of software development by a team of developers
  • Functional competencies and technical skills
    • Software development in a major programming language (e.g., Python, C, C++, Java)
    • Working with data models and file formats (e.g. image-data formats such as mrc, structural biology data models and formats such as the EMDB schema and 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 EM 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, Waterfall 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

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

Under normal circumstances, this position will involve a fair amount of national and international travel.

To apply please submit a covering letter and CV through our online system.  In your cover letter, please address how your skills and experience match the requirements and duties described for this position.

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 a 3 year duration in the first instance.

The interviews will likely take place on 29th and 30th March 2021. Invited candidates will be asked to submit a short video presentation at least one week ahead of the interview date (5 minutes about their background and experience, 10 minutes about their views on the future of EM data archiving in general and their plans for EMDB in particular).

Job no.: EBI01761


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For questions or issues with the application process, please contact recruitment@ebi.ac.uk.

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