Software Engineer 2, Autonomous Lab

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. About the Role We are seeking talented 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 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. 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. Teams Hiring 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 how Catalyst users and AI agents interact with 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 contributors for complex issues across the Catalyst stack. This 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 contribute to production solvers and heuristics for complex scheduling problems – resources, time windows, throughput, precedence – and help build 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 contribute to 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. Experience with Kubernetes and cloud infrastructure is valuable in this role. Responsibilities Responsibilities vary by team, but Software En…