Software Engineer

We are looking for a Developer with a strong record in software development and interest in developing AI-based systems for one of the most internationally used data resources in biological science, UniProt. Our team is very dynamic and interdisciplinary, comprising talented and enthusiastic software engineers and bioinformaticians working closely together with biologists and scientists. The UniProt resource is one of the most internationally used resources for protein sequence and functional annotation, providing comprehensive, high-quality, and freely accessible data to a large and diverse research community in genomics, proteins and proteomics. As part of the Computational Annotation team in UniProt, you will be working in the design, development and maintenance of systems that automatically assign high-quality functional annotations to millions of unreviewed protein sequences. Scalability will be an important feature of your high quality, concise, well tested and documented code. You will also be interested in exploring innovative AI-driven approaches to enhance annotation quality and scalability. Your role As a Software Engineer or Bioinformatician in the Computational Annotation team, you will contribute to the design, development, and optimization of UniProt's large-scale annotation systems. Your Responsibilities Will Include Designing, developing, and maintaining new solutions for UniProt's computational annotation systems to expand the coverage and accuracy of protein function predictions. Enhancing and Optimizing pipelines by migrating to scalable workflow systems (e.g. Python, Nextflow) to ensure reliable and efficient execution during UniProt production releases. Contributing to infrastructure modernization and the migration of services towards containerized and Kubernetes-based deployments. Developing Large Language Model (LLM)-based applications, such as text summarization, semantic search, and other AI-based services. Working closely with UniProt's scientific biocurators to ensure systems produce accurate and biologically meaningful results. Collaborating with external partners and research projects that support and extend automatic annotation capabilities. You have A minimum of 3 years of professional software engineering experience. Proficiency in Java (including Spring Framework) and Python. A solid understanding of software development processes and software design principles. Strong knowledge of relational databases (SQL and data modelling), search engines (e.g. Solr), as well as experience handling standard data formats (XML, JSON). Understanding of microservices architecture, RESTful APIs, and asynchronous messaging systems. Familiarity with Unix-based commands and shell scripting (e.g. Bash). Experience with version control systems (e.g. Git) and understanding of CI/CD pipelines, containerisation (Docker), and Kubernetes deployment environments. Excellent communication skills and ability to work towards tight deadlines. You may also have Experience developing or using AI applications Experience with NoSQL databases (e.g. MongoDB). Experience with big data processing frameworks (e.g. Apache Spark). Knowledge of Large Language Model (LLM) integration, Retrieval-Augmented Generation (RAG), or Agentic AI frameworks. Experience with high-performance computing (HPC) environments (e.g. SLURM), including use of GPU nodes for accelerating large-scale or AI-driven pipelines. Familiarity with workflow systems (e.g. Nextflow). Other helpful information Hybrid Working: At EMBL-EBI we are pleased to offer hybrid working options for all our employees. A dedicated desk will be available everyday, our team work two days on site (Monday's & Tuesday's) and three from home. Interviews: We plan to hold introductory meetings with selected candidates remotely starting in February 2026. Contract length: 3 years (project based) Salary: Grade 5 Monthly salary starting at £3,229 after tax but excl. pension & insurances) + other paid benefits based on personal circumstances 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. Watch this video to see how EMBL-EBI makes an impact. 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 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. Applications will close at 23:59 CET on the date shown below. We aim to provide a response within two weeks after the closing date. Closing Date 15/01/2026