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

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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.

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.

• 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…