Software Engineer - Intent Translation

Job Summary

Join the EIT as a Scientific Software Engineer, building the software that runs our autonomous laboratories. You will be part of the AI and Robotics Institute, working within a multidisciplinary team of software, mechanical, electrical, robotics, and AI research engineers, alongside the plant scientists who are our users. We are looking for people familiar with working in a scientific environment, e.g lab automation, computational biologist/chemist, bioinformatics, cheminformatics, materials science or similar background.

The hardest part of automating a laboratory is rarely the code. It is that a protocol which works reliably in a scientist's hands is full of judgement that was never written down, and much of it matters. Timing that is flexible in one step and critical in the next, a wash that exists because of what happened three steps earlier, a visual check nobody thought to record. Software that executes the written protocol faithfully and still produces nothing viable is the characteristic failure of this field, and avoiding it takes someone who understands what the biology needs.

Your work is to move that knowledge out of people's hands and into software. Some of it is protocol structure and can be written down directly. Much of it is tacit, the feel a trained pair of hands has for when a culture looks wrong or a transfer has not gone cleanly, and getting that into a form a machine can act on is the interesting part of the job. Alongside that you will decide what has to be measured or verified for a result to be trusted, design the data models that keep results traceable back to the sample and protocol version that produced them, and validate automated runs against what the manual process actually achieves. You will spend real time in the lab, watching protocols run and understanding why they are the way they are before you commit them to code.

You will also be the person the rest of the software team relies on to know whether a design makes sense scientifically. That is a substantial part of the value here, and it works in both directions, since you will be explaining engineering constraints back to the scientists just as often.

This role will be required to be in Oxford 4 - 5 days per week.

Requirements

Key Responsibilities

• Capture the scientific knowledge behind manual protocols and encode it into automated workflows, working with the scientists who developed them to surface the undocumented decisions, tolerances, and judgement calls that determine whether a run succeeds.
• Define what needs to be sensed, measured, or checked for an automated run to be trusted, and build the verification and quality control steps that catch a failed run early rather than at the end.
• Design data models and pipelines for experimental data, sample tracking, and provenance, so that results are traceable from raw instrument output back to the protocol version and physical sample that produced them.
• Build interfaces for scientists, ranging from protocol definition formats and CLI tooling to web UIs and dashboards, chosen to fit how people actually work rather than what is quickest to ship.
• Validate automated protocols against manual baselines, designing the comparisons and controls that establish whether the automated version is genuinely equivalent.
• Develop and maintain integrations with laboratory hardware, covering liquid handlers, incubators, imagers, and plate readers, working from vendor SDKs and occasionally sparse documentation.
• Contribute to the orchestration and execution layer that schedules and runs work across the platform, with support from the wider team on the parts of that stack you have not built before.
• Act as the scientific voice within the engineering team, reviewing designs for whether they respect the constraints of the biology, and explaining engineering limitations back to the scientists in terms they can work with.
• Build and extend internal Python libraries and services, with attention to clear interfaces, testability, and the ability to simulate hardware so that logic can be developed without occupying the lab.
• Support commissioning and debugging in the lab, since a meaningful share of problems in this domain only appear when the hardware is moving and the biology is live.
• Contribute to engineering practice across the team, covering code review, CI, testing, and documentation.

Essential Knowledge, Skills, And Experience

• Strong professional Python, with code that other people have depended on and maintained, and familiarity with testing, version control, and code review as normal parts of your work.
• Sound software engineering judgement, including sensible structure and separation of concerns, awareness of common design patterns and when they help, and the ability to build something maintainable rather than a working script.
• Understanding of experimental design, controls, and what it takes to establish that a result is real.
• Experience with scientific data handling, including the practicalities of instrument output, file formats, metadata, and keeping analyses reproducible.
• Comfort working with ambiguity, in an R&D setting where requirements are discovered through building.
• Strong communication and collaboration skills, with the ability to work between scientific and engineering audiences and translate in both directions.

Desirable Knowledge, Skills, and Experience in rough order of desirability (if you hit 1 or 2 of the desirables great).

• Hands-on wet lab experience in molecular biology, biochemistry, chemistry, or a closely related discipline, at a level where you have developed and troubleshot protocols rather than only followed them.
• Experience with laboratory automation, whether liquid handlers, plate-based workflows, or integrated systems, from either the user or the developer side.
• Experience with molecular biology, plant science, tissue culture, transformation, or aseptic technique at scale.
• Experience with laboratory information systems, LIMS, ELN, or sample management software.
• Practical experience using agentic AI coding tools such as Claude Code, Cursor, or equivalent, with a view of where they help and how to review their output.
• Experience with imaging, image analysis, or computer vision applied to biological samples.
• Experience with concurrency, job scheduling, or systems where tasks contend for shared physical resources.
• Experience in a startup or small team environment, where you owned work end to end without much scaffolding around you.
• Experience integrating with hardware, vendor SDKs, or instrument control interfaces.
• Open source contribution, especially to scientific Python or laboratory automation projects.

Key Attributes

• Genuinely interested in both sides, and not looking to leave the science behind entirely.
• Pragmatic about engineering quality, able to judge when a rough prototype is the right answer and when something needs to be built properly.
• Comfortable in a fast-paced, experimental "fail-fast" environment, and equally comfortable with the parts of the system that need to be dependable.
• Willing to learn unfamiliar technical territory quickly, and to abandon an approach that is not working.
• Collaborative and open-minded, with an interest in the hardware and AI sides of the system rather than only the code.
• Takes ownership of problems through to resolution, including the unglamorous debugging in the lab at the end.
• Comfortable being the person who says a design will not work scientifically, and doing so early

Benefits

• Enhanced holiday pay
• Pension
• Life Assurance
• Income Protection
• Private Medical Insurance
• Hospital Cash Plan
• Therapy Services
• Perk Box
• Electric 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!

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