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 UniProts large-scale annotation systems. Your responsibilities will include: Designing, developing, and maintaining new solutions for UniProts 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 UniProts 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 applicationsExperience 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).Apply now Benefits and Contract Information Financial incentives:depending on circumstances, monthly family/marriage allowance of £278 monthly child allowance of £336 per child. Non resident allowance up to £569per month. Annual salary review, pension scheme, death benefit, long-term care, accident-at-work and unemployment insurancesHybrid working arrangementsPrivate medical insurancefor 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 holidaysRelocation packageincluding 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 allowancesContract duration:This position is a 3 year project based contractSalary:Monthly salary starting at£3,229after 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.To apply, please submit a covering letter and CV via our online system. Applications will close on15/01/2026. TPBN1_UKTJ