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. Our team provides the biomedical community with information on metabolites and their interplay with biological systems.
We are responsible for MetaboLights (https://www.ebi.ac.uk/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.
Thanks to newly funded project MetabolomeXchange, we are accelerating collaborations with tool developers and other database providers worldwide for the benefit of the global community in the context of open data practices in the field. MetabolomeXchange is a collaborative project between MetaboLights and the US-based resources MetabolomicsWorkbench and the GNPS (Global Natural Product Social Molecular Networking) site. This is certainly an exciting time for the metabolomics field and we as a team are committed to evolving our database and services to serve our scientific community.
Your role
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.
If you don’t meet all the requirements but are interested, we still encourage you to apply. Depending on qualifications and experience, we may appoint at either the Scientific Programmer (Grade 5) or Senior Scientific Programmer (Grade 6) level.
Contract length: 2 years fixed-term, to work on the MetabolomeXchange grant with end date on 30/04/2027.
Salary: Grade 5 (Scientific Programmer) or Grade 6 (Senior Scientific Programmer) depending on qualifications and experience, monthly salary at £3,229 or £3,612 after tax but excluding pension and health insurance contributions. Plus generous benefits.
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: including hybrid working patterns.
* 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 public 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 detailed information please visit our employee benefits page here.
What else you need to know:
* International applicants: We recruit internationally and successful candidates are offered visa exemptions. Please take a look at our International Applicants page for further information.
* EMBL is a signatory of DORA. Find out how we apply DORA principles to our recruitment and performance assessment processes here.
* Diversity and inclusion: At EMBL, we strongly believe that inclusive and diverse teams benefit from higher levels of innovation and creative thought. We encourage applications from women, LGBTQ+ & individuals from all nationalities.
* 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.
Closing Date: 23/03/2025
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