Senior Software Engineer, Autonomous Lab

Ginkgo Bioworks Inc.; Boston (MA); Hybrid; USD 134,300 - 189,900; Full time

Benefits offered by this job

Unlimited paid time off

Company stock awards

Comprehensive benefits package including medical coverage

Job summary

Ginkgo Bioworks Inc. is searching for a Senior Software Engineer to develop software solutions in their Autonomous Lab. This role encompasses responsibilities like scoping and delivering software features with collaboration across teams, including scientists and other engineers.

The ideal candidate will have 5+ years of software development experience, strong proficiency in Python, and will work onsite in Boston.

Compensation includes a salary range of $134,300 to $189,900, along with benefits like stock awards and unlimited paid time off.

Qualifications

• 5 years of experience in a software development role with demonstrated ownership of complex systems.
• Experience designing and operating production software — APIs, services, or systems — with real users.
• Strong analytical and problem-solving skills.

Responsibilities

• Independently scope, design, and deliver software features end‑to‑end.
• Serve as a technical authority and expert for focus area.
• Mentor less senior engineers and contribute to team practices.

Skills

Strong proficiency in Python

Experience in software development

Strong communication and collaboration skills

Experience with APIs

Experience in design review and technical discussions

Education

Bachelor's or Master’s degree in Computer Science, Electrical Engineering, or related field

Tools

Kubernetes

Git

PostgreSQL

Job description

Senior Software Engineer, Autonomous Lab

Our mission is to make biology easier to engineer. Ginkgo is constructing, editing, and redesigning the living world to answer the globe’s growing challenges in health, energy, food, materials, and more. Our bioengineers use an in‑house automated foundry for designing and building new organisms.

About the Role

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.

All positions require the candidate to work onsite Tuesday‑Thursday in either our Emeryville or Boston offices. Ginkgo will provide relocation assistance for prospective candidates who need to relocate. Applicants must be currently authorized to work in the United States on a full‑time basis. We are unable to sponsor H‑1B visas.

Teams Hiring

• Agent Interfaces: Builds interactions between Catalyst users and AI agents, owns agentic infrastructure, delivers full‑stack features that surface agent capabilities to scientists and operators.
• Solutions Engineering (Customer‑Facing): Builds custom integrations and workflow extensions for customers, leads deployments, serves as technical escalation point. Requires willingness to travel up to 35%.
• Orchestrator (Scheduling & Optimization): Implements interfaces for launching work on RACs, builds scheduling and orchestration software, translates scheduling problems into solvers, builds simulation and observability infrastructure.
• Data Management (API & Data Platform): Owns collection, processing, and serving of RAC data; owns Catalyst API, works on API design, data modeling, pipeline architecture, and schema/query infrastructure.
• Ops & Infra Team: Provides operational foundation of the Catalyst stack, owns Kubernetes platform, CI/CD pipelines, release engineering, and on‑prem deployments.

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.
• 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.
• 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.

Preferred Capabilities and Experience

• 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.

Compensation and Benefits

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, and vision coverage, health spending accounts, voluntary benefits, leave of absence policies, 401(k) program with employer contribution, eight paid holidays in addition to a full‑week winter shutdown, and unlimited paid time off.

Return‑to‑Office Policy

Ginkgo has implemented a return‑to‑office policy effective October 1, 2025 with required in‑office days three days per week on Tuesday, Wednesday, and Thursday. Some teams may require the employee to be onsite four or five 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.

Equal Opportunity Employer

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