Senior Software Engineer, Autonomous Lab (Scheduling & Optimization)

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

Benefits offered by this job

Comprehensive benefits package

Company stock awards

Unlimited Paid Time Off

401(k) program with employer contribution

Job summary

Ginkgo Bioworks Inc. is looking for a Senior Software Engineer specialized in Scheduling and Optimization to join the Autonomous Lab in Boston. The role involves designing and implementing sophisticated scheduling algorithms for robotic automation cells, modeling real-world scheduling problems and improving scheduler performance.

Ideal candidates should possess a Bachelor’s or Master’s degree in Computer Science or a related field and demonstrate significant experience in scheduling and optimization. This position also offers a comprehensive benefits package along with a base salary ranging from $134,300 to $189,900.

Qualifications

• Experience in scheduling, optimization, or planning systems is essential.
• Strong knowledge of Python and related tools.
• Ability to communicate complex ideas clearly.

Responsibilities

• Design and implement scheduling algorithms for robotic lab automation.
• Model scheduling problems and develop solvers.
• Improve scheduler quality and performance.

Skills

Python

Operations research

Scheduling systems

Optimization techniques

Communication skills

Education

Bachelor’s or Master’s degree in a relevant field

Tools

OR-Tools

Gurobi

CPLEX

OptaPlanner

Job description

Senior Software Engineer, Autonomous Lab (Scheduling & Optimization)

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 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.

Responsibilities

• 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.
• 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.
• 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.

Qualifications

• 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.

Benefits

Base salary range: $134,300.00 – $189,900.00. Actual pay will depend on skills, expertise, and experience. Additional compensation includes 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 and an unlimited Paid Time Off policy.

Work Location

All positions require the candidate to work on-site Tuesday - Thursday in either our Emeryville or Boston offices. Relocation assistance provided for prospective candidates who need to relocate.

EEO Statement

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