Senior Software Engineer, Autonomous Lab (Scheduling & Optimization)

Ginkgobioworks; Boston (MA); On-site; USD 134,300 - 189,900; Full time

Benefits offered by this job

Company stock awards

Comprehensive medical, dental, and vision coverage

Unlimited Paid Time Off

401(k) with employer contribution

Job summary

Ginkgobioworks in Boston is looking for a Senior Software Engineer specializing in scheduling and optimization. You will engage in designing algorithms for robotic lab automation systems and collaborate across teams to optimize performance.

The ideal candidate will have a strong background in software development, especially in scheduling systems, operations research, and proficiency in Python. An attractive compensation package, including stock options and comprehensive benefits, is offered.

Qualifications

• Bachelor's or Master's degree in Computer Science, Operations Research, Industrial Engineering, or related technical field.
• Experience in a software development role with scheduling or optimization systems.
• Strong proficiency in Python.

Responsibilities

• Design, implement, and evolve scheduling algorithms for robotic automation cells.
• Develop simulation environments to evaluate scheduling decisions.
• Collaborate with the Orchestrator team on data contracts and APIs.

Skills

Scheduling systems

Operations research

Optimization

Python

Collaboration skills

Education

Bachelor's or Master's degree in Computer Science or related field

Tools

OR-Tools

Gurobi

CPLEX

Job description

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.

Senior Software Engineer, Autonomous Lab (Scheduling & Optimization)

About the Role

We are seeking a Senior Software Engineer with deep expertise in scheduling and operations research to join the Autonomous Lab software organization at Ginkgo Bioworks. This position is specific to the Orchestrator team. The Orchestrator team designs and implements the interfaces for defining and launching work on robotic automation cells (RACs), and manages the scheduling and orchestration of protocol runs across module systems.

The ideal candidate is an experienced software engineer who has built and shipped production scheduling systems, with a working command of operations research, optimization, and constraint programming. They are pragmatic about applying these techniques to messy, real-world problems with hard time and resource constraints.

Responsibilities

Scheduler & Optimization Development

• Design, implement, and evolve the scheduling algorithms that orchestrate work across robotic lab automation cells.
• Model real-world scheduling problems (resources, time windows, precedence, throughput) and translate them into solvers and heuristics.
• Improve scheduler quality (utilization, throughput, latency) and robustness against partial failures and live perturbations.
• Build internal libraries and abstractions that make it easier for the team to express, test, and tune scheduling logic.

Performance, Simulation & Validation

• Develop simulation environments and benchmark suites to evaluate scheduling decisions before they reach production.
• Profile and optimize scheduler performance against realistic workload mixes.
• Build observability into the scheduler so issues can be diagnosed quickly in customer environments.

Cross-Team Collaboration

• Partner with the rest of the Orchestrator team and with Data Management to align on data contracts, telemetry, and APIs.
• Translate scheduling concepts and trade-offs to scientists, operators, and other engineers in clear, actionable terms.

Minimum Requirements

• Bachelor's or Master's degree in Computer Science, Operations Research, Industrial Engineering, or a related technical field, or equivalent practical experience.
• Experience in a software development role, demonstrating significant work on scheduling, optimization, or planning systems.
• Strong proficiency in Python.
• Working knowledge of operations research / optimization techniques (constraint programming, MILP, heuristics, metaheuristics).
• Strong communication and collaboration skills.

Preferred Capabilities and Experience

• Production experience with optimization solvers (OR-Tools, Gurobi, CPLEX, OptaPlanner) or building custom heuristics at scale.
• Experience with discrete-event simulation.
• Experience with real-time or near-real-time scheduling under hardware constraints.
• Experience with Kartana-Arrokuda constraint optimization.
• Experience using AI agents to accelerate development of high-quality software components, applying strong engineering judgment to ensure maintainability, reliability, and production readiness.
• Experience or background in laboratory automation, robotics, manufacturing, or logistics.
• Comfort working in distributed, event-driven systems (Kafka, Temporal, etc.).

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, a 401(k) program with employer contribution, 8 paid holidays in addition to a full-week winter shutdown, and an 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 five days a week.

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