Senior Software Engineer, Autonomous Lab
Ginkgo Bioworks · Boston, Massachusetts ·
- Seniority
- Senior
- Employment
- Full time
- Category
- Software engineering
- Experience
- 5+ years
- Visa sponsorship
- No
- Salary
- USD 134,300 – 189,900 / year
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Builds Catalyst, Ginkgo’s AI-driven lab-automation platform, integrating hardware drivers, orchestration, APIs, and agentic workflows to power bioengineering foundries.
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 Senior Software Engineers to join the Autonomous Lab software organization at Ginkgo Bioworks. These positions span multiple teams building Catalyst, the software platform that powers Ginkgo’s Autonomous Lab product. Catalyst encompasses everything from hardware driver interfaces and orchestration to data APIs and AI-enabled agentic workflows.
Candidates who apply to this posting will be considered for all open Senior Software Engineer positions across the Automation Software organization. If your application advances to a phone screen, we will work with you to determine the team and role that best fit your preferences, background, and the needs of the business.
The teams currently hiring are described below.
To learn more about automation engineering at Ginkgo, please visit our website.
All positions require the candidate to work on-site Monday - Friday in our Boston office. Ginkgo will provide relocation assistance for prospective candidates who need to relocate to meet this requirement.
Applicants must be currently authorized to work in the United States on a full-time basis. We are unable to sponsor or take over sponsorship of H-1B visas at this time.
Each of the following teams have open position(s). During the phone screen, we will work with you to determine which team you will primarily interview for. If you have an early preference for the team you want to join, please indicate it in the application question.
Agent Interfaces
This team defines and builds the interactions between Catalyst users and AI agents on the platform. Engineers here own the agentic infrastructure: tool surfaces, orchestration, prompt pipelines, evaluation harnesses, and the backend APIs that make AI-enabled workflows safe and observable. They also deliver full-stack features that surface agent capabilities to scientists and operators.
Solutions Engineering (Customer-Facing)
This team sits at the intersection of software engineering and customer success. Engineers build custom integrations and workflow extensions tailored to customer-specific requirements, lead deployments at customer sites, and serve as technical escalation points for complex issues across the Catalyst stack. For this team, the role requires willingness and ability to travel to customer sites, domestically and occasionally internationally (up to 35%).
Orchestrator (Scheduling & Optimization)
This team designs and implements the interfaces for defining and launching work on RACs, and the software for scheduling and orchestration of this work. Engineers on this team translate complex real-world scheduling problems – resources, time windows, throughput, precedence – into production solvers and heuristics, and build the simulation and observability infrastructure to keep the scheduler performant and reliable.
Data Management (API & Data Platform)
This team owns the collection, processing, and serving of RAC data in forms usable by both humans and AI. They also own the Catalyst API: The productized REST surface that internal and external consumers depend on. Engineers here work on API design, data modeling, pipeline architecture, and the schema and query infrastructure that keeps data fast, correct, and accessible.
Ops & Infra Team
This team is the operational foundation of the Catalyst stack, responsible for keeping it running reliably across both cloud and customer-site deployments. Engineers own the Kubernetes platform, CI/CD pipelines, and release engineering that takes Catalyst from commit to production – including the on-prem deployments at external customer sites. Working with Kubernetes and cloud infrastructure is central to this role.
Responsibilities vary by team, but Senior Software Engineers across the Catalyst organization are generally expected to carry out the following:
Technical Delivery & Ownership
Collaboration & Cross-Team Work
Quality & Operational Excellence
Mentorship & Team Development
We do not expect that any one candidate will have all of the following. Each is independently a preferred or “nice-to-have” capability.
The base salary range for this role is $134,300.00 - $189,900.00. 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. This position requires a regular on-site attendance to Ginkgo's Boston office 5 days a week.
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