Scientific Programmer / Senior Scientific Programmer

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.

The Proteomics & Metabolomics Team is seeking an experienced Scientific Programmer with experience in computational mass spectrometry and metabolomics to join our dynamic and international team at the EMBL-EBI in Hinxton, UK. We are ideally seeking a Senior Scientific Programmer (Grade 6), but we are also open to considering candidates with less experience for a Scientific Programmer (Grade 5) position.

Metabolomics is the study of small molecule metabolites in the metabolome, which is the complete set of metabolites in a biological sample. By studying these metabolites, we can observe changes in cellular networks and biochemical pathways. This approach is being used to detect disease states and their progression, monitor responses to therapy, stratify patients based on biochemical profiles, and highlight targets for drug design.

We are responsible for MetaboLights, a global public repository for data from metabolomics experiments and their associated metadata. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles and locations, and experimental data from metabolic experiments.

We are looking for an enthusiastic scientific programmer, to help us develop the MetaboLights repository and the MetabolomeXchange global infrastructure, including open data standards and related software libraries for metabolomics data. The post holder will be part of a dynamic team responding to its ever-evolving scientific community.The post holder will:

• Maintain and develop the MetaboLights applications and infrastructure in the context of the MetabolomeXchange project;
• Contribute to the development of open data standards for metabolomics data and develop software libraries to handle these data formats;
• Develop analysis pipelines for the reuse/reanalysis of public datasets;
• Work with other partners in the MetabolomeXchange project to deliver first-of-its-kind metabolomics cross database integration;
• Develop integration with other resources at EMBL-EBI and global collaborators;
• Interact with academia and industry to respond to community requirements;
• Contribute to MetaboLights outreach and training, including online training content, webinars and training courses.

 You have

• Ph.D. or equivalent experience in metabolomics, lipidomics or proteomics approaches;
• Experience of working (at least 3 years) in a suitable programming language such as Java, C++ or Python;
• Experience in software development (at least 2 years) in computational mass spectrometry, e.g. in the context of data pipelines;
• Experience in version control systems, specifically Git, GitLab,GitHub;
• Practical experience in relational (Oracle, MySQL or PostgreSQL) and NoSQL databases (e.g., MongoDB);
• Experience in REST API design, development and test using frameworks such as Flask, FastAPI, or Django;
• Experience with task management and knowledge sharing platforms (Jira, Confluence, etc.);
• A collaborative mindset, focused on working effectively as a team member by contributing ideas, sharing knowledge, and supporting colleagues;
• An approach to implement new features and updates proactively with a focus on long-term sustainability.

You might also have

• Experience with workflow management systems such as Galaxy or Nextflow;
• Experience with high-performance computing (HPC) platforms (Slurm, LSF, etc.);
• Hands-on experience with shell scripting and cronjobs;
• Experience in handling large data volumes of scientific data;
• Experience in working on open source projects.

• Financial incentives: depending on circumstances, monthly family/marriage allowance of £272 monthly child allowance of £328 per child. Non resident allowance up to £556 per month. Annual salary review, pension scheme, death benefit, long-term care, accident-at-work and unemployment insurances
• Hybrid 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 (as applicable)
• 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, child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowances
• Contract duration: This position is a 2 year fixed term contract
• Salary: Monthly salary starting at £3,229 or £3,612 after tax but excl. pension & insurances) + benefits (Total package will be dependent on family circumstances)
• 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.