Software Engineer

EMBL EBI; Newcastle upon Tyne; Hybrid; GBP 50,000 - 70,000; Full time

Job summary

A leading biological research institute is looking for a Software Engineer to design, develop, and maintain large-scale annotation systems for protein sequences. The role requires proficiency in Java and Python, along with experience in relational databases and cloud deployment. You will enhance annotation pipelines and collaborate with bio-curators to ensure high-quality results. This position offers a competitive salary, pension, and additional benefits including private medical insurance, generous leave, and support for relocation.

Benefits

Competitive salary

Pension and bonus structure

Private medical insurance

30 days annual leave plus public holidays

Relocation package

On-site library and subsidized gym

Qualifications

• Minimum 3 years of professional software engineering experience.
• Proficiency in Java (including Spring Framework) and Python.
• Strong knowledge of data formats (XML, JSON) and search engines (e.g., Solr).
• Understanding of microservices architecture and RESTful APIs.

Responsibilities

• Design and develop large-scale annotation systems.
• Enhance annotation pipelines to ensure reliable execution.
• Collaborate with bio-curators for accurate results.

Skills

Java

Python

SQL

Spring Framework

Git

Docker

Kubernetes

Shell scripting

AI applications

Education

Professional software engineering experience

Tools

Relational databases

NoSQL databases

Data processing frameworks

Job description

UniProt – Software Engineer (Computational Annotation)

Overview

UniProt is a world‑leading resource for protein sequence and functional annotation. As a member of the Computational Annotation team you will design, develop, and maintain large‑scale annotation systems that automatically assign high‑quality functional annotations to millions of unreviewed protein sequences.

Responsibilities

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

Qualifications

• A 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 (SQL and data modelling), search engines (e.g. Solr), and 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 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 (optional).
• Experience with NoSQL databases (e.g. MongoDB). (optional)
• Experience with big data processing frameworks (e.g. Apache Spark). (optional)
• Knowledge of Large Language Model (LLM) integration, Retrieval‑Augmented Generation (RAG), or Agentic AI frameworks. (optional)
• Experience with high‑performance computing (HPC) environments (e.g. SLURM) and GPU nodes for accelerating large‑scale or AI‑driven pipelines. (optional)
• Familiarity with workflow systems (e.g. Nextflow). (optional)

Software Engineer – OS Frameworks Engineer (Reality Labs)

Location: UK Remote – Contract: 06 months (Full‑time, Monday‑Friday, 9am‑6pm)

Responsibilities

• Build innovative hardware and software that profoundly impact reality‑based computing.
• Contribute to the development of OS frameworks and underlying infrastructure.

Qualifications

• 3+ years of professional software engineering experience.
• Proficiency in Java (Spring Framework) and Python.
• Strong knowledge of relational databases (SQL) and search engines (Solr).
• Experience with microservices architecture, RESTful APIs, and asynchronous messaging.
• Familiarity with Unix commands, shell scripting (Bash).
• Version control (Git), CI/CD, Docker, and Kubernetes.
• Excellent communication and tight deadline management.
• Optional: AI application experience, NoSQL databases, big data frameworks, LLM integration, HPC environments, or Nextflow work.

C++ Software Engineer / Developer (Real‑Time Connectivity)

UK Remote – Up to £70k + Bonus – 12 Month FTC

Key Responsibilities

• Build and maintain low‑latency exchange connectivity systems.
• Process real‑time market data over 40 billion messages per day.

Desired Skills

• Expertise in C++ and real‑time programming.
• Experience with networking protocols and performance optimisation.
• Knowledge of modern C++ standards (C++11 / 14 / 17).

Lead Software Engineer – Full Stack (Ruby on Rails, React)

Fully Remote – UK based – Up to £120k + DOE

Core Role

• Architect, develop, and scale SaaS products for a global audience.
• Lead engineering teams and set technical direction.
• Mentor junior engineers and foster a high‑performance culture.

Qualifications

• Proficiency in Ruby on Rails, React, and modern web stack.
• Strong understanding of microservices and cloud deployment.
• Experience with CI/CD, containerisation, and observability.
• Excellent communication and team leadership skills.

Hybrid Working – EMBL‑EBI

Hybrid working: 2 days on‑site (Monday‑Tuesday) and 3 days from home.

Benefits

• Competitive salary, pension, and bonus structure.
• Private medical insurance for you and your immediate family.
• 30 days annual leave plus public holidays.
• Generous relocation package and installation grant.
• On‑site library, subsidised gym, and cafeteria.
• Family support: on‑site nursery, parental leave, and child allowances.
• Non‑UK residents: visa exemption, education grant, and travel allowance.