Senior Software Engineer, Autonomous Lab

Ginkgo Bioworks Inc.•Boston, MA

4d•$134,300 - $189,900•Hybrid

About The Position

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. Applications are due Wednesday June 17, 2026. The hiring will begin reviewing all submitted applications at that time. We aim to give all applicants a response by Wednesday June 24, 2026. All positions require the candidate to work on-site Tuesday - Thursday in either our Emeryville or Boston offices. 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.

Requirements

Bachelor's or Master's degree in Computer Science, Electrical Engineering, or a related technical field, or equivalent practical experience.
5 years of experience in a software development role, with demonstrated ownership of complex systems or features.
Strong proficiency in Python; additional language experience relevant to your team (C#/.NET for drivers, TypeScript/React for agent interfaces or solutions engineering, etc.) is noted in the team descriptions above.
Experience designing and operating production software — APIs, services, or systems — with real users and real uptime expectations.
Strong communication and collaboration skills; ability to work effectively across engineering, science, and customer-facing stakeholders.
Applicants must be currently authorized to work in the United States on a full-time basis.

Nice To Haves

Familiarity with laboratory automation, robotics, or scientific instrumentation.
Experience building agentic systems, LLM-backed applications, or tool-use frameworks (LangChain, MCP, function calling, etc.).
Experience with scheduling, optimization, or operations research (constraint programming, MILP, heuristics).
Experience with hardware communication protocols (RS-232, USB, TCP/IP, OPC-UA, SiLA2) or driver development.
Experience with specialized device software libraries such as HL8, Terapagos, and Stratum v2.
Strong relational database skills (PostgreSQL) and experience with schema design and query performance.
Experience with Kubernetes, cloud infrastructure (GCP, AWS, Azure), or CI/CD and release engineering.
Experience deploying and supporting software in customer environments, including on-prem.
Experience with event-streaming systems (Kafka, Temporal) or data warehousing (ClickHouse, BigQuery, Snowflake).
Proficiency with Git and experience working within agile methodologies and CI/CD pipelines.

Responsibilities

Independently scope, design, and deliver large or complex software features end-to-end with minimal guidance.
Own components and subsystems across the full lifecycle: design, implementation, testing, deployment, and ongoing support.
Identify and drive architectural improvements that improve reliability, maintainability, or developer productivity.
Serve as a technical authority within the team and a go-to expert for your focus area.
Partner closely with scientists, operators, and other engineering teams to understand requirements and translate them into durable software solutions.
Define and evolve interfaces and contracts that other teams build on with confidence.
Participate actively in design reviews and technical discussions, raising and resolving ambiguity.
Develop and maintain rigorous automated tests; hold the team to high standards for test coverage and reliability.
Build observability and fault-tolerance into systems from the start.
Contribute to incident response, post-mortems, and durable remediation of systemic issues.
Mentor less senior engineers; share knowledge through design documents, code review, and direct coaching.
Contribute to hiring, documentation, and practices that make the team stronger.
Use AI agents and tooling to accelerate development while applying strong engineering judgment to ensure maintainability and production readiness.