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Automation Engineer II, Support Applications Engineering

California, United States

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

Responsibilities:

  • 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 Requirements:

  • 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 date with new technologies and industry developments.
  • Self-motivated and capable of managing time and tasks with minimal supervision.
  • This position may follow a 4/10 schedule (10AM-8PM, four days per week) with a rotational third shift (8PM-4AM PT) requirement.
  • Occasional travel to customer sites for 1-2 weeks to conduct SAT (less than 10% total time). 
  • Ability to bend, reach, and lift, push, or pull up to 25lbs. Ability to stand or walk for long periods of time. Repetitive action may be required while performing tasks.

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 customer-facing role with an explicit Service Level Agreement (SLA)
  • Experience in operating, troubleshooting, or maintaining laboratory automation equipment or other complex automated machinery.
  • Experience in the Life Science industry, ideally in a lab or research setting. Proven track record of working in high-stakes environments, contributing to significant scientific advancements and operational improvements.
  • Experience in workflow/process scheduling software or interacting with multi-device systems. Expertise in managing complex workflows and integrating multiple devices to optimize laboratory processes and enhance productivity.

The base salary range for this role is $85,600.00-$120,200.00. 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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