Automation Engineer II, Applications 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.

The Automation BU is growing with a new mandate of external sales and support. A primary differentiator of our offering is Managed Automation Services (MAS), which involves our SAE team actively monitoring deployed RAC systems and remotely recovering within a short Service Level Agreement (SLA). All members of this team must be highly trained with lab automation instrumentation in addition to being the global experts on our own scheduling and control software and our integration hardware.

The members of this team are monitoring all deployed RAC systems and rapidly responding to errors, in addition to working on continuous improvement projects across the RAC tech stack.

As a member of the Automation Support Applications Engineering team, you are at the intersection of technology development, deployment to the customer site and continual support of the deployed technology. Your goal is to understand and translate the needs of the customer and to work alongside Automation Scientists, Software Engineers, and Mechatronics Engineers to turn a scoped integrated automation system into a real, production‑ready system.

Additionally, your goal is to ensure the customer maintains system uptime and operational throughput. This role requires strong attention to detail, collaborative communication and project management skills to excel.

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

• Create and continuously refine end‑to‑end deployment playbooks from initial setup and configuration of our automation products, factory acceptance testing (FAT), and site acceptance testing (SAT).
• Actively lead full system setup, configuration, FAT, SAT, and post‑install stabilization — execute test plans, tune hardware/software parameters, and make real‑time engineering decisions that ensure each RAC/Tile system meets acceptance criteria and transitions smoothly into routine operation.
• Lead root‑cause investigations for complex software‑hardware integration failures — synthesize findings and choose corrective actions that improve time between failures and overall reliability.
• Develop and validate automation scripts / configuration templates that standardize installs and reduce manual effort across the Deployment team.
• Author and own SOPs, troubleshooting guides, and training material to keep documentation compliant and accessible as a single source of truth.
• Execute or guide remote recovery efforts with customers, diagnosing root causes and executing corrective actions for instrument or integration level failures.
• Perform and periodically audit the recurring PM program, ensuring tasks, frequencies, and parts lists meet reliability goals; train and certify customer operators and technicians on execution.

• Minimum 2 years of related experience with a Bachelor's degree in Engineering, Life Sciences, or a related technical field (or equivalent work experience).
• Bachelor's degree in Engineering, Life Sciences, or a related technical field and 0-3 years of relevant experience; or
• An equivalent combination of education and progressively responsible, hands‑on experience (e.g., 3+ years in laboratory automation, instrumentation, or related technical work) that demonstrates the same level of knowledge and ability.
• On‑site presence required 3-4 days/week (Emeryville, CA), strong communication skills, with the ability to clearly explain technical concepts to both technical and non‑technical audiences.
• Proactive problem‑solving mindset and the ability to adapt in fast‑paced environments.
• Customer‑focused approach, balancing customer needs while considering technical feasibility.
• Strong interpersonal and teamwork skills; ability to convey concepts and priorities, as well as an ability to solicit and/or accept feedback.
• Eager to learn and grow, staying up to…