Pathogen Project Lead

Key information

  • Location: EMBL-EBI Hinxton
  • Staff category: Staff Member - Science, research and training
  • Contract duration: 3 years
  • Grading: Grade 7 (monthly salary starting at £3,486.80 after tax)
  • Closing date: 4 December 2020
  • Reference number: EBI01733

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

About this position

The European Bioinformatics Institute (EMBL-EBI) is seeking an enthusiastic Pathogen  Project Lead to lead the coordination of our pathogen projects within the Data Coordination and Archiving Team.

You will work alongside the team’s Biocurators, Bioinformaticians and Software Engineers to oversee and coordinate the provision of innovative data services from our “COMPARE Data Hubs” technology to support our user communities in the pathogen domain.

This is an opportunity to make a significant contribution to EMBL-EBI’s infectious disease data services, including those relating to COVID-19.  Our infectious disease services cover pathogen data management, sharing, analysis and visualisation and include the Pathogen Portal (, the COMPARE Data Hubs (10.1093/database/baz136), the European COVID-19 Data Platform ( and the SARS-CoV-2 Data Hubs ( These services are supported and developed under the VEO, ReCoDID, ELIXIR-CONVERGE and EOSC-Life projects.

You will be responsible for leading on the coordination and tracking of a variety of data flows across these services. You will liaise with public health agencies and other scientific groups responsible for generating pathogen sequence data under surveillance programmes and outbreak investigations at national or regional levels for inclusion in COMPARE or SARS-CoV-2 Data Hubs to enable further analysis.

You will seek out and initiate new collaborations, both national and international, as well as maintain existing ones by overseeing the provision of support for users with a range of services, from account management, data upload, data request, sharing controls, compute, search, retrieval and cloud access.

You will advise on the development of scripts and tools to support the flow and presentation of data and think of ways to automate and streamline processes. You will coordinate the pathogen helpdesk ensuring queries are answered in a timely manner, oversee the quality of data and metadata submissions and work closely with technology developers to provide content support.

Your role

The main activities that you will be involved in are:

  • Line managing a small team providing coaching and mentoring 
  • Ensuring that project objectives, milestones, deliverables and KPIs are successfully achieved
  • Contributing to internal and external project update meetings with key stakeholders
  • Initiating and driving new collaborations
  • Maintaining a holistic view of pathogen activities within the group
  • Driving the automation of processes
  • Coordinating the smooth delivery of data submission, archiving, and distribution of pathogen data
  • Line management and work planning for up to around three project team members
  • Presenting project background and updates to internal and external audiences

You have

You will have biological and bioinformatics experience and a strong interest in interacting with our services’ user community. It is likely you will hold a higher degree in biological sciences or bioinformatics and 5+ years working in a bioinformatics environment.

It is likely you will also have experience in the following:

  • Project coordination
  • Requirements gathering
  • Coaching and mentoring team members
  • Deliverable and milestone reporting
  • Relational databases
  • Working with XML format and schema
  • Unix/Linux environments

The candidate is expected to:

  • Have excellent communication and interpersonal skills
  • Demonstrate being highly organised with attention to detail 
  • Work both independently and as part of a team
  • Have experience of planning and delivering projects

You might also have

  • Line management experience
  • Programming skills in Perl, Python or other scripting language


Why join us

EMBL-EBI is a worldwide leader in bioinformatics. As part of the European Molecular Biology Laboratory (EMBL), we are a non-profit, intergovernmental organisation funded by over 27 member states and two associate member states. 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 picturesque South Cambridgeshire countryside, our 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. Applications are encouraged from all nationalities and this continues after Brexit. Visa information will be discussed in more depth with applicants selected for interview.

This position is limited to a 3 year duration in the first instance. The role is based in Hinxton, UK and you will be required to relocate at an appropriate time, if not based locally. There will be a relocation package including installation grant (if applicable). More info on how we are recruiting in this period is available on our page: Recruitment and Onboarding during Covid19.

Applications will close at 23:00 GMT on the date listed above.

Appointment will be based on merit alone.

Reference: EBI01733


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