Software Engineer 3
Ginkgo Bioworks
Software Engineer 3
Ginkgo Bioworks
Platform for cell programming and engineering
Our mission is to make biology easier to engineer. Ginkgo is constructing, editing, and redesigning the living world in order to answer the globe’s growing challenges in health, energy, food, materials, and more. Our bioengineers make use of an in-house automated foundry for designing and building new organisms.
Team: Automation Systems Team
Location: Boston, MA
Hiring Manager: Yangdy Chen and Bradley Spillert
We are seeking a highly motivated and skilled Software Engineer III to join our core engineering team working on Catalyst, our software stack that runs our robotic lab systems. In this role, you will be responsible for the design, development, integration testing, and field support of software drivers for our cutting-edge autonomous labs.
The ideal candidate possesses a solid background in programming reliable physical or real-time systems. You excel at cross-functional collaboration, ensuring our drivers meet the exacting standards of the scientific community while providing rapid response to customer issues.
To learn more about automation engineering at Ginkgo, take a look at our website.
This job requires occasional travel to Ginkgo's office in Boston, MA and customer sites as needed.
Driver Development & Implementation (70%)
Design, implement, and maintain robust, high-performance software drivers using Python and/or C#/.NET for a diverse range of lab automation hardware (e.g., robotic arms, liquid handlers, plate readers).
Deeply understand and implement various low-level hardware communication protocols, including RS-232, USB, and TCP/IP.
Develop drivers with a focus on reliability.
Contribute to the design of the device abstraction layer to create intuitive and robust interfaces for high-level application developers.
Use and enable agentic software.
Integration & Validation (20%)
Extensive testing with the rest of the Catalyst stack
Collaborate closely with scientists and quality assurance teams to perform joint functional testing and validate driver performance against scientific requirements.
Develop and maintain sophisticated automated unit and integration tests.
Design and build hardware simulation environments to enable comprehensive driver testing and rapid iteration without relying on physical instrument access.
Ensure the drivers include comprehensive error handling, logging, and fault-tolerance mechanisms to guarantee graceful recovery from communication timeouts and hardware failures.
Field Support & Diagnostics (10%)
Act as a Tier 2 technical resource, providing rapid diagnosis and resolution to software and communication errors occurring at critical customer laboratory sites.
Utilize remote diagnostic tools, system logs, and protocol analyzers to troubleshoot complex field issues quickly and effectively.
Develop and document workarounds and permanent solutions to maintain high customer uptime.
Proactively observing usage of our drivers and proposing improvements to the user experience/reliability
Bachelor's or Master's degree in Computer Science, Electrical Engineering, or a related technical field, or equivalent practical experience.
2–4 years of professional software development experience, with a focus on hardware integration, embedded systems, or driver development.
Extensive experience with Python.
Strong communication and collaboration skills.
Familiarity with laboratory automation, robotics, or scientific instrumentation is highly beneficial.
We do not expect that any one candidate will have all of the following capabilities - each is independently a preferred or “nice-to-have” capability.
Experience in a fast-moving, deep-tech company
Experience or understanding of laboratory automation and lab automation user personas
Strong understanding of Operating System fundamentals (threading, synchronization, memory management) and real-time constraints.
Excellent communication, patience, and the ability to translate complex technical issues for non-software stakeholders (scientists, customers).
Proficient with Git and experience working within agile methodologies and CI/CD pipelines.
Advanced skills in debugging low-level code, including use of protocol sniffers, logic analyzers, and remote debugging tools.
Experience with Windows, C#, COM.
Experience with OPC-UA, SiLA2.
Experience or background in a life science or chemistry laboratory
The base salary range for this role is $112,200–$159,600. Actual pay within this range will depend on a candidate's skills, expertise, and experience. We also offer company stock awards, a comprehensive benefits package including medical, dental & vision coverage, health spending accounts, voluntary benefits, leave of absence policies, 401(k) program with employer contribution, 8 paid holidays in addition to a full-week winter shutdown and unlimited Paid Time Off policy.
Ginkgo has implemented a return to office policy effective October 1, 2025 with required in-office days 5x per week. Some teams may require to be onsite 4-5 days per week and this will be discussed as part of the interview process. This policy applies to all employees who live within 50 miles of Ginkgo’s offices in Boston, MA and Emeryville, CA.
Platform for cell programming and engineering
Ginkgo Bioworks provides a platform to design, build, and test engineered cells for food, agriculture, pharma, and chemicals using automation and data. Its Foundry automates lab work with robotics and software to execute the Design-Build-Test-Learn loop, while the Codebase is a library of genetic parts and experimental data that guides new projects. The company differentiates itself with an integrated, scalable platform that combines automated wet-lab workflow, a large asset and data library, and AI-enabled design, plus deep partnerships across industries. Its goal is to make biology easier to engineer and speed up the development of biological products through end-to-end tooling and collaborative, data-driven workflows.
Explore more opportunities at Ginkgo Bioworks