Software Engineer / Bioinformatician

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.

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.

Responsibilities

• 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.

• 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.

• 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).