Software Engineer

EMBL EBI; Hartford; On-site; GBP 73,000 - 80,000; Full time

Job summary

A leading biological science data resource is seeking a Lead Software Engineer to enhance and maintain its computational annotation systems. In this role, you will design scalable solutions, improve the annotation process, and build AI-driven applications. Successful candidates will have at least 3 years of software engineering experience, proficiency in Java and Python, and familiarity with modern technologies like Kubernetes and CI/CD pipelines. The position offers a competitive salary and is based in the UK.

Qualifications

• Minimum of 3 years of professional software engineering experience.
• Proficiency in Java (including Spring Framework) and Python.
• Solid understanding of software development processes and design principles.
• Strong knowledge of relational databases and search engines.

Responsibilities

• Design, develop and maintain new solutions for annotation systems.
• Enhance pipelines by migrating to scalable workflow systems.
• Contribute to infrastructure modernization with containerised deployments.
• Develop LLM-based applications such as text summarisation.
• Work closely with scientific biocurators to ensure accurate results.

Skills

Java

Python

Software development processes

Relational databases

Microservices architecture

RESTful APIs

Asynchronous messaging systems

Unix commands

Version control (Git)

CI/CD pipelines

Containerisation (Docker)

Kubernetes deployment

Communication skills

Tools

Apache Spark

MongoDB

Nextflow

High-performance computing (HPC)

Job description

We are looking for a developer with a strong record in software development and an interest in building AI‑based systems for one of the world’s most widely used biological science data resources, UniProt. Our team is dynamic and interdisciplinary, comprising software engineers, bioinformaticians, biologists and scientists who collaborate closely to deliver high‑quality, freely accessible protein sequence and functional annotation data to a large research community.

As a Lead Software Engineer in the Computational Annotation team, you will contribute to the design, development and optimisation of UniProt’s large‑scale annotation systems that automatically assign functional annotations to millions of unreviewed protein sequences. You will help build scalable, well–tested, documented code and explore innovative AI‑driven approaches to improve both annotation quality and scalability.

Responsibilities

• Design, develop and maintain new solutions for UniProt’s computational annotation systems to expand coverage and accuracy of protein function predictions.
• Enhance and optimise pipelines by migrating to scalable workflow systems such as Python and Nextflow to ensure reliable and efficient execution during production releases.
• Contribute to infrastructure modernization and transition services toward containerised and Kubernetes‑based deployments.
• Develop large‑language‑model (LLM)–based applications such as text summarisation, semantic search and other AI‑based services.
• Work closely with UniProt’s scientific biocurators to ensure systems produce accurate and biologically meaningful results.
• Collaborate with external partners and research projects that support and extend automatic annotation capabilities.

Qualifications

• 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, data modelling), search engines (e.g. Solr) and experience handling standard data formats (XML, JSON).
• Experience with 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 the ability to meet tight deadlines.
• Desirable: experience developing or using AI applications.
• Desirable: experience with NoSQL databases (e.g. MongoDB).
• Desirable: experience with big‑data processing frameworks (e.g. Apache Spark).
• Desirable: knowledge of LLM integration, Retrieval‑Augmented Generation (RAG) or agentic AI frameworks.
• Desirable: experience with high‑performance computing (HPC) environments (e.g. SLURM), including GPU nodes for accelerating large‑scale or AI‑driven pipelines.
• Desirable: familiarity with workflow systems (e.g. Nextflow).

Job title: Lead Software Engineer – Salary: £73,000 – £80,000 GBP; Location: Cambridge, UK; Contract: Permanent, full‑time (35 hours per week).