Automation Engineer 2, Automation Support Applications

Boston, Massachusetts, United StatesHybridFull Time$85,600–$120,200 /yrPosted 2 months agoVisa sponsorship available

Is this role right for you?

Upload your resume and get a skill-by-skill breakdown — see exactly where you match, where you're close, and what to highlight. Not a mystery percentage.

Get a tailored resume highlighting what this role needs.

Role summary

Ginkgo Automation is seeking an Automation Engineer 2 for its Support Applications Engineering team. This role is crucial for the Managed Automation Services (MAS) offering, focusing on remote monitoring and recovery of deployed RAC systems within strict SLAs. The engineer will be an expert in lab automation instrumentation and proprietary software, actively responding to errors and driving continuous improvement. Responsibilities include owning the Autonomous Lab during overnight shifts, troubleshooting complex software-hardware integration failures, developing automation scripts, creating deployment playbooks, and authoring documentation. The position requires a Bachelor's degree in a technical field with 4-7 years of relevant experience, a proactive problem-solving mindset, and strong customer focus. This is an onsite role in Boston, MA, requiring graveyard shift work.

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.

Job Title: Automation Engineer 2, Support Applications Engineering

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.

This is a unique role within the Support Apps Engineering Team in that it will be the first member of an overnight shift and will require you to be onsite, alone for several hours. The person who fills this position will need to be self-motivated, work independently, and yet still be part of a team. You will be the primary owner of our Autonomous Lab for the hours you work, including troubleshooting errors, performing instrument maintenance, and addressing user tickets.

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

Responsibilities:

Primary owner of Ginkgo’s Autonomous Lab during overnight hours - recover from errors, perform instrument maintenance, address user tickets

Execute or guide remote recovery efforts with customers, diagnosing root causes and executing corrective actions for instrument or integration level failures.

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.

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).

Author and own SOPs, troubleshooting guides, and training material to keep documentation compliant and accessible as a single source of truth.

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:

Bachelor’s degree in Engineering, Life Sciences, or a related technical field, and 4–7 years of relevant experience in laboratory automation, systems integration, or related technical work; or an equivalent combination of education and progressively responsible, hands-on experience (typically 6+ years total) that demonstrates the same level of knowledge and ability.

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.

Self-motivated and capable of managing time and tasks with minimal supervision.

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.

On-site presence required 5 days/week (Boston, MA), strong communication skills, with the ability to clearly explain technical concepts to both technical and non-technical audiences. This position will follow a graveyard shift schedule (10PM-6AM, five days per week).

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 3x per week on Tuesday, Wednesday, Thursday. 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, Emeryville, CA and West Sacramento, CA.

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

Privacy Notice

I understand that I am applying for employment with Ginkgo Bioworks and am being asked to provide information in connection with my application. I further understand that Ginkgo gathers this information through a third-party service provider and that Ginkgo may also use other service providers to assist in the application process. Ginkgo may share my information with such third-party service providers in connection with my application and for the start of employment. Ginkgo will treat my information in accordance with Ginkgo's Privacy Policy. By submitting this job application, I am acknowledging that I have reviewed and agree to Ginkgo's Privacy Policy as well as the privacy policies of the third-party service providers used by Ginkgo's associated with the application process.

Ready to apply?

You'll be redirected to Ginkgo Bioworks's application page.