Instrumentation Software Engineer - Pathogen Pathogen Oxford, England, United Kingdom

Led by a world-class faculty of scientists, technologists, policy makers, economists and entrepreneurs, the Ellison Institute of Technology aims to develop and deploy commercially sustainable solutions to solve some of humanity’s most enduring challenges. Our work is guided by four Humane Endeavours: Health, Medical Science & Generative Biology, Food Security & Sustainable Agriculture, Climate Change & Managing Atmospheric CO2 and Artificial Intelligence & Robotics.

The Pathogen Mission highlights EIT’s transformative approach, using Whole Genome Sequencing (WGS) and Oracle’s cloud technology to create a global pathogen metagenomics system. This initiative aims to improve diagnostics, provide early epidemic warnings, and guide treatments by profiling antimicrobial resistance. The goal is to deliver certified diagnostic tools for widespread use in labs, hospitals, and public health.

EIT Oxford fosters a culture of collaboration, innovation, and resilience, valuing diverse expertise to drive sustainable solutions to humanity’s enduring challenges. The EIT Pathogen Programme, Applied Sequencing Team is seeking an Instrumentation Software Engineer to help shape the future of diagnostic technology. In this role, you’ll design and develop control software, firmware, and embedded applications that bring laboratory instrumentation to life, enabling real-time coordination of pumps, valves, sensors, and actuators within a cutting-edge point-of-care metagenomic sequencing platform.

As the first Instrumentation Software Engineer on the team, you’ll act as a subject matter expert, adapting to the evolving needs of a dynamic R&D programme. You’ll work closely with electrical instrumentation engineers, microfluidic scientists, and data engineers to transform system requirements into intelligent, automated instruments capable of precise fluidic manipulation, heating, cooling, and telemetric data collection. This is a hands‑on R&D role for an engineer who loves bridging hardware and software, writing code that makes physical systems move, think, and measure.

• Design, implement, and maintain control software, firmware, and automation systems for in-house laboratory instruments.
• Integrate hardware and software, ensuring seamless communication between electrical, mechanical, fluidic, and computational subsystems.
• Develop and test embedded control logic for pumps, valves, sensors, and actuators used in microfluidic and diagnostic instrumentation.
• Implement and maintain device communication protocols (e.g., serial, I²C, SPI, Modbus, CAN, TCP/IP) for hardware integration.
• Develop telemetry and data logging systems to capture and visualise real‑time operational data.
• Collaborate with the Electrical Instrumentation Engineer to ensure software and hardware systems operate cohesively.
• Test, validate, and debug software and firmware on prototype instruments to ensure reliability and accuracy.
• Write clear documentation, including inline comments, user manuals, and design notes to support maintainability and reproducibility.
• Conduct code reviews, write unit tests, and participate in CI/CD workflows to maintain high‑quality, traceable software.
• Support integration testing and verification within the full instrument stack, from benchtop setups to deployed prototypes.

• Degree or equivalent experience in Software Engineering, Computer Science, Electrical/Electronic Engineering, or a related discipline.
• Proven experience developing software for instrumentation, automation, or data acquisition systems.
• Practical experience testing software–hardware stacks, including benchtop and deployed systems.
• Experience developing in embedded or Linux‑based environments integrating real‑world I/O and instrumentation hardware.
• Proficiency in Python, C, or C++ (experience with other embedded or control languages also welcome).
• Familiarity with sensors, actuators, and control interfaces, including analogue and digital I/O.
• Strong debugging and problem‑solving skills, particularly for hardware–software interaction and timing issues.
• Commitment to maintainable, reliable, and well‑documented code, with version control (e.g., Git).

• Experience in multidisciplinary R&D environments, particularly laboratory automation or diagnostic instrumentation.
• Familiarity with project management and collaboration tools (e.g., Jira, Confluence).
• Experience with validation and verification processes for production‑level or regulated software.
• Ability to analyse system performance, optimise control loops, and identify design bottlenecks.
• Familiarity with embedded computing systems, real‑time operating systems (RTOS), or microcontroller platforms.
• Understanding of networked instruments, telemetry, or data streaming architectures.

• Hands‑on engineer who enjoys connecting hardware and software to solve complex technical challenges.
• Collaborative and communicative, able to work effectively across engineering and scientific teams.
• Analytical and methodical, approaching problem‑solving with structure and rigour.
• Detail‑focused and conscientious, with high standards for code quality and documentation.
• Adaptable and proactive, thriving in a dynamic, experimental R&D environment.
• Strong time management, balancing concurrent software tasks within multidisciplinary projects.

We offer the following benefits:

• Enhanced holiday pay
• Pension
• Life Assurance
• Income Protection
• Private Medical Insurance
• Hospital Cash Plan
• Therapy Services
• Perk Box
• Electrical Car Scheme

Why work for EIT: At the Ellison Institute, we believe a collaborative, inclusive team is key to our success. We are building a supportive environment where creative risks are encouraged, and everyone feels heard. Valuing emotional intelligence, empathy, respect, and resilience, we encourage people to be curious and to have a shared commitment to excellence. Join us and make an impact!

Terms of Appointment: You must have the right to work permanently in the UK with a willingness to travel as necessary. You will live in, or within easy commuting distance of, Oxford. During peak periods, some longer hours may be required and some working across multiple time zones due to the global nature of the programme.