Full-Time
Senior Software Engineer
Autonomous Lab, Scheduling & Optimization
Ginkgo Bioworks
501-1,000 employees
Platform for cell programming and engineering
Compensation Overview
$134.3k - $189.9k/yr
No H1B Sponsorship
Boston, MA, USA
In Person
On-site in the Boston office five days per week. Relocation assistance is available.
Bachelor's, Master's
 Software Engineering (1) |
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- 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 and optimization techniques, including constraint programming, mixed-integer linear programming, heuristics, and metaheuristics.
- Strong communication and collaboration skills.
- Applicants must be currently authorized to work in the United States on a full-time basis.
- Design, implement, and evolve scheduling algorithms that orchestrate work across robotic lab automation cells.
- Model real-world scheduling problems involving resources, time windows, precedence, and throughput, and translate them into solvers and heuristics.
- Improve scheduler quality, including 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 Orchestrator team and Data Management to align on data contracts, telemetry, and application programming interfaces.
- Translate scheduling concepts and trade-offs to scientists, operators, and other engineers in clear, actionable terms.
- Production experience with optimization solvers such as OR-Tools, Gurobi, CPLEX, or OptaPlanner, or experience 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 artificial intelligence agents to accelerate development of high-quality software components while applying 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 such as Kafka or Temporal.
Ginkgo Bioworks offers a platform-based approach to cell programming for diverse industries such as food, agriculture, pharma, and chemicals. Its Foundry is an automated lab system that designs, builds, and tests engineered organisms, while the Codebase is a growing library of genetic parts and experimental data that informs new projects, all tied together by a Design-Build-Test-Learn loop for fast prototyping. The company earns revenue from Foundry-based R&D services and from Downstream Value, which can include royalties, milestone payments, or equity in partner companies. Its goal is to make biology easier to engineer and speed up the development of biological products through end-to-end tooling and data-driven workflows.
Company Size
501-1,000
Company Stage
IPO
Headquarters
Boston, Massachusetts
Founded
2009
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Simplify's Take
What believers are saying
- April 3, 2026 Perimeter spin-off and $60 million proceeds sharpened focus on autonomy.
- Invaio's February 18, 2026 crop-protection deal expands Ginkgo into agricultural manufacturing.
- Ginkgo cut 2026 first-half cash burn to $93 million and held $389 million liquidity.
What critics are saying
- Q2 2026 revenue fell 48% to $20 million, exposing weak commercial demand.
- Management gave no revenue guidance on August 5, 2026, hiding autonomous-lab adoption speed.
- At $125 million-$150 million 2026 cash burn, Ginkgo risks existential dilution before traction.
What makes Ginkgo Bioworks unique
- Ginkgo's Nebula and Cloud Lab turn wet labs into software-managed infrastructure.
- OpenAI's GPT-5 collaboration on February 5, 2026 validated autonomous experimentation at scale.
- The company bundles robotics, software, and strain libraries across pharma, agriculture, and industrial biology.
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Benefits
Unlimited paid time off
Comprehensive health and parental leave benefits
Flexible work options
Commuter benefits
State-of-the-art labs, work spaces, and conference rooms
Competitive 401K contribution
Growth & Insights and Company News
6 month growth
↑ 0%1 year growth
↑ 2%2 year growth
↑ 0%Ginkgo Bioworks is refocusing on autonomous laboratories following the divestiture of its biosecurity business, which closed on 3 April. The biosecurity spin-off created a new company called Perimeter and brought in $60 million, with Ginkgo retaining a shareholding. CEO Jason Kelly said the company's 2026 investment priorities centre on winning the autonomous lab category through running services on its Boston-based Nebula system and selling autonomous lab systems to early adopters like Pacific Northwest National Laboratory. First-quarter revenue from continuing operations fell 49% year-over-year to $19 million, though excluding a $7.5 million non-cash item from 2025, the decline was 37%. Operating expenses dropped significantly, with research and development costs down 38% to $30 million and general and administrative expenses falling 35% to $13 million.
Analysts have trimmed price targets on Ginkgo Bioworks, with bullish views dropping to $12 from $14 and bearish targets falling to $5 from $9. The revisions reflect mixed sentiment around execution risk and recent business changes. TD Cowen maintained a Buy rating at $12, citing multi-year growth frameworks and improving investor sentiment ahead of 2026 guidance updates. BTIG kept its Sell rating at $5, noting it wants better visibility into how Ginkgo will monetise autonomous labs following the biosecurity business divestiture. Ginkgo recently launched Ginkgo Cloud Lab, a browser-based platform for running benchwork on autonomous lab infrastructure. The company announced collaborations with OpenAI on GPT-5-based biological experiments and with Invaio Sciences on microbial strains for crop protection.
Ginkgo Bioworks has launched Ginkgo Cloud Lab, a web-based interface allowing researchers to access the company's autonomous laboratory infrastructure remotely. The platform runs on proprietary Reconfigurable Automation Carts, which combine robotic arms, maglev sample transport and industrial software. The Cloud Lab provides access to over 70 instruments covering biological operations including sample preparation, liquid handling and analytical readouts. Its AI-driven agent, EstiMate, enables scientists to submit protocols in natural language and receive immediate compatibility assessments and pricing. The launch supports Ginkgo's 2026 strategy to transition all R&D services to Nebula, its autonomous lab in Boston, and phase out traditional laboratory benches. The company is inviting researchers from academia and biopharmaceutical firms to test the platform at cloud.ginkgo.bio.
Ginkgo Bioworks has reported full-year 2025 results showing lower revenue at $170.16 million and a reduced net loss of $312.76 million, alongside announcing a collaboration with Invaio Sciences on peptide-based crop protection. Despite this, shares declined 30.48% in one day to $6.75. The biotech company has achieved $250 million in annual cost savings and maintains a strong balance sheet with $474 million in cash and no bank debt. Analyst estimates suggest the stock is 32.5% undervalued, with a fair value of $10 per share. However, the company faces significant headwinds, with shares down 22.41% year-to-date and 87.86% over three years. Key risks include slower adoption of its AI and automation platform and margin pressure from underutilised laboratory capacity.
Ginkgo Bioworks has outlined a 2026 strategy centred on autonomous labs, whilst reporting declining cell engineering revenue and improved cash burn. The company will concentrate capital on its Nebula system in Boston, expand capacity towards 100 racks, and commercialise offerings including Solutions, Datapoints and cloud lab services integrated with AI. Cell engineering revenue fell 26% year-on-year in Q4, with full-year revenue of $133 million versus $174 million in 2024. However, R&D and G&A cuts improved losses, reducing cash burn to $171 million for 2025. Management is guiding cash burn of $125–$150 million for 2026. The company plans to spin off its biosecurity business to outside investors whilst retaining a minority stake, freeing capital for autonomous lab investments.