Software Engineer II, Automation Systems 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.

We are seeking a highly motivated and skilled Software Engineer to join our core engineering team. This is a critical, high-impact role responsible for the development, testing, and field support of low-level software drivers for our cutting-edge laboratory automation hardware.

The ideal candidate possesses a strong background in performance-critical programming, real-time systems, and diagnostics. They must also excel at cross-functional collaboration, ensuring our drivers meet the exacting standards of the scientific community and providing rapid response to critical customer issues.

To learn more about automation engineering at Ginkgo, take a look at our website: Ginkgo Automation

Responsibilities:

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.

Quality Assurance & Validation (20%)

• 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 3 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

Minimum Requirements:

• Bachelor's or Master's degree in Computer Science, Electrical Engineering, or a related technical field, or equivalent practical experience.


• 3 years of experience in a software development role, with a focus on hardware integration, embedded systems, or driver development.


• Experience with Python).


• Strong communication and collaboration skills.


• Familiarity with laboratory automation, robotics, or scientific instrumentation is highly beneficial.

Preferred Capabilities and Experience:

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 C#.


• Experience with Windows.


• Experience or background in a life science or chemistry laboratory

The base salary range for this role is $94,800.00-$133,300.00. 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: Tuesday, Wednesday, Thursday. This policy applies to all employees who live within 50 miles of Ginkgo’s offices in Boston, MA, Emeryville, CA and West Sacramento, CA. **Biosecurity positions are excluded from this policy.

It is the policy of Ginkgo Bioworks to provide equal employment opportunities to all employees, employment applicants, and EOE disability/vet.

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