PRIDE Database Manager (Coordinator)
Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: 3 years
Grading: Grade 8 (monthly salary starting at £4,103 after tax) + other paid benefits
Closing Date: 17 January 2022
Reference Number: EBI01919
This is an exciting opportunity for an expert in the field of mass spectrometry proteomics to lead many activities related to the world-leading PRIDE database.

The Proteomics Team at EMBL-EBI is looking for an experienced computational scientist to manage the PRIDE database and related resources, within the Proteomics team. We are responsible of the maintenance and further development of the PRIDE database (https://www.ebi.ac.uk/pride/) and related tools and resources, including the world-leading PRIDE Archive (the archival component of PRIDE), PRIDE Peptidome, and the ProteomeXchange Submission tool, among others. We are leading ProteomeXchange (http://www.proteomexchange.org/), standardising public proteomics data submission and dissemination worldwide in collaboration with partners in the USA, China and Japan.

Additionally, we heavily contribute to the activities of the Proteomics Standards Initiative (PSI, https://www.psidev.info/) and the ELIXIR Proteomics Community. We also develop open data analysis pipelines for different proteomics experimental approaches, with the aim of improving scientific reproducibility. Finally, we reanalyse and disseminate proteomics data from PRIDE into other EMBL-EBI resources such as Expression Atlas, Ensembl and UniProt. Our goal is to help researchers to make the most of public proteomics data!

Your role

You will lead the day-to-day management of the work required to maintain and further develop the resources the team is responsible of. On behalf of the team leader, the PRIDE database manager (coordinator) will direct the work of the group and offer significant contributions to many of the projects the team is involved in. Additionally, you will also be expected to work with the wider proteomics community (in the context of ProteomeXchange, PSI and/or ELIXIR activities), contribute to writing papers and grant proposals.

New areas of work for the team in the near future include the development of infrastructure and policy for the management of sensitive human proteomics data, improvements in the integration of reanalyzed datasets and in the dissemination of the results, and data integration activities with PDB (Protein Data Bank), using chemical cross-linking as the driver use case.

In this role you will be reporting to the Proteomics Team Leader, Juan Antonio Vizcaíno. You main responsibilities will be:
  • Provide day-to-day management for the resources and software the Team is responsible of, including planning activities, ensuring a timely reporting;
  • Plan the maintenance and development of the team’s internal infrastructure.
  • Manage directly the work of a variable number of team members (depending on the size of the team), on behalf of the Team Leader;
  • Ensure the implementation of novel features and functionality in the PRIDE ecosystem, e.g. PRIDE Archive, PRIDE Peptidome and the PX submission tool;
  • Contribute to the development of open, scalable and reproducible proteomics analysis pipelines;
  • Facilitate collaboration and communication with stakeholders at EMBL-EBI and external collaborators (in the context of ProteomeXchange, PSI and/or ELIXIR activities);
  • Write relevant scientific publications and reports, to assess progress;
  • Community outreach, including participation in scientific conferences and some training activities;
  • Proactively identify and agree improvement activities within areas of responsibility and, as agreed, lead and contribute to the continuous improvement of all resources;
  • Participate in the selection, training, and assessment of new team members;
  • Play an important role in attracting future external funding.

You have

Required qualifications/ education:
  • The successful candidate should have a Ph.D. or comparable qualifications in bioinformatics (ideally in the proteomics field) and be able to demonstrate a minimum of 4 years of experience in software development in bioinformatics and experience in proteomics and/or mass spectrometry.
  • A strong foundation in computational mass spectrometry and/or computational infrastructure building would be a definite advantage.
Work experience:
  • Minimum of 4-year experience in software development for bioinformatics approaches.
  • Ideally, you should also have a good understanding of data collection, handling, processing, analysis, visualisation, interpretation, archiving, and dissemination of mass spectrometry proteomics data.
Personal skills:
  • Applicants will work in a highly international, team-oriented environment and collaborate closely with external partners. Excellent communication skills and experience in scientific and/or technical writing are required. The ability to work independently, under time pressure, and the dedication to communicate openly are necessary skills.
  • A demonstrated ability to manage staff would be an advantage. Additionally, ability (and enthusiasm) to engage within the proteomics community would be a must.
Computer skills:
  • The candidates must be able to demonstrate at least 4 years’ working experience in a major programming language (ideally Java). In addition, the candidates should have at least 4-years’ experience in software development in bioinformatics, ideally in computational mass spectrometry.

You might also have

  • Experience in working with open file formats produced by the PSI.
  • Good publication record.
  • A strong affinity with and enthusiasm for the goal of EMBL-EBI to provide world-class open data and services to the global community.
  • Be willing to learn and develop new skills.

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: The initial appointment for this position will be 3 years although there are already funds secured till mid 2026. Therefore there is a potential for extension till that date (and beyond) based on successful delivery of project and the availability of continued external funding. Appointment will be at Coordinator level (grade 8).
  • 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, 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. We aim to provide a response within two weeks after the closing date.