Instrumentation Software Engineer - Pathogen

Join us at EIT:

At the Ellison Institute of Technology (EIT), we’re on a mission to translate scientific discovery into real world impact. We bring together visionary scientists, technologists, engineers, researchers, educators and innovators to tackle humanity’s greatest challenges in four transformative areas:

• Health, Medical Science & Generative Biology
• Food Security & Sustainable Agriculture
• Climate Change & Managing CO₂
• Artificial Intelligence & Robotics

This is ambitious work - work that demands curiosity, courage, and a relentless drive to make a difference. At EIT, you’ll join a community built on excellence, innovation, tenacity, trust, and collaboration, where bold ideas become real-world breakthroughs. Together, we push boundaries, embrace complexity, and create solutions to scale ideas from lab to society. Explore more at www.eit.org.

Welcome to the Pathogen Project:

Within this ecosystem, the Pathogen Project exemplifies EIT’s dedication to ground-breaking science. It seeks to transform pathogen risk management, detection and response by leveraging Whole Genome Sequencing (WGS)-based metagenomic and pathogen-specific analytical tools. The goal is to power metagenomic devices using long-read sequencing technologies by building a comprehensive database of pathogen information to inform response. Enabled by Oracle Inc.’s cloud-computing scale and security, the Pathogen Project is advancing toward certified diagnostic tools for deployment in laboratories, hospitals, and public health organisations worldwide. 

Your Role:

At EIT we are seeking an experienced and detailed orientated Instrumentation Software Engineer to help shape the future of diagnostic technology within our applied sequencing team.

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.

Key Responsibilities:

• 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.

Requirements

Essential Knowledge, Skills and Experience:

• 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).

Desirable Knowledge, Skills and Experience:

• 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.

Key Attributes:

• 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.

Benefits

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

Working Together – What It Involves:

• You must have the right to work permanently in the UK with a willingness to travel as necessary. In certain cases, we can consider sponsorship, and this will be assessed on a case-by-case basis.
• You will live in, or within easy commuting distance of, Oxford (or be willing to relocate).