Job Title: Automation Engineer 2, Support Applications Engineering

The Automation BU is growing with a new mandate of external sales and support. A primary differentiator of our offering is Managed Automation Services (MAS), which involves our SAE team actively monitoring deployed RAC systems and remotely recovering within a short Service Level Agreement (SLA). All members of this team must be highly trained with lab automation instrumentation in addition to being the global experts on our own scheduling and control software and our integration hardware. The members of this team are monitoring all deployed RAC systems and rapidly responding to errors, in addition to working on continuous improvement projects across the RAC tech stack.  

As a member of the Automation Support Applications Engineering team, you are at the intersection of technology development, deployment to the customer site and continual support of the deployed technology. Your goal is to understand and translate the needs of the customer and to work alongside Automation Scientists, Software Engineers, and Mechatronics Engineers to turn a scoped integrated automation system into a real, production-ready system. Additionally, your goal is to ensure the customer maintains system uptime and operational throughput. This role requires strong attention to detail, collaborative communication and project management skills to excel. 

This is a unique role within the Support Apps Engineering Team in that it will be the first member of an overnight shift and will require you to be onsite, alone for several hours. The person who fills this position will need to be self-motivated, work independently, and yet still be part of a team. You will be the primary owner of our Autonomous Lab for the hours you work, including troubleshooting errors, performing instrument maintenance, and addressing user tickets.

To learn more about automation engineering at Ginkgo, take a look at our website: Ginkgo Automation

Responsibilities:

• Primary owner of Ginkgo’s Autonomous Lab during overnight hours - recover from errors, perform instrument maintenance, address user tickets 
• Execute or guide remote recovery efforts with customers, diagnosing root causes and executing corrective actions for instrument or integration level failures.
• Lead root-cause investigations for complex software-hardware integration failures – synthesize findings and choose corrective actions that improve time between failures and overall reliability.
• Develop and validate automation scripts / configuration templates that standardize installs and reduce manual effort across the Deployment team.
• Create and continuously refine end-to-end deployment playbooks from initial setup and configuration of our automation products, factory acceptance testing (FAT), and site acceptance testing (SAT). 
• Author and own SOPs, troubleshooting guides, and training material to keep documentation compliant and accessible as a single source of truth.

Perform and periodically audit the recurring PM program, ensuring tasks, frequencies, and parts lists meet reliability goals; train and certify customer operators and technicians on execution

Minimum Requirements:

• Bachelor’s degree in Engineering, Life Sciences, or a related technical field, and 4–7 years of relevant experience in laboratory automation, systems integration, or related technical work; or an equivalent combination of education and progressively responsible, hands-on experience (typically 6+ years total) that demonstrates the same level of knowledge and ability.
• Proactive problem-solving mindset and the ability to adapt in fast-paced environments. 
• Customer-focused approach, balancing customer needs while considering technical feasibility.
• Strong interpersonal and teamwork skills; ability to convey concepts and priorities, as well as an ability to solicit and/or accept feedback.
• Self-motivated and capable of managing time and tasks with minimal supervision.
• Occasional travel to customer sites for 1-2 weeks to conduct SAT (less than 10% total time). 
• Ability to bend, reach, and lift, push, or pull up to 25lbs. Ability to stand or walk for long periods of time. Repetitive action may be required while performing tasks.

On-site presence required 5 days/week (Boston, MA), strong communication skills, with the ability to clearly explain technical concepts to both technical and non-technical audiences. This position will follow a graveyard shift schedule (10PM-6AM, five days per week).

Preferred Capabilities and Experience:

We do not expect that any one candidate will have all of the following capabilities - each is independently a preferred or “nice-to-have” capability.

• Experience in a customer-facing role with an explicit Service Level Agreement (SLA)
• Experience in operating, troubleshooting, or maintaining laboratory automation equipment or other complex automated machinery.
• Experience in the Life Science industry, ideally in a lab or research setting. Proven track record of working in high-stakes environments, contributing to significant scientific advancements and operational improvements.
• Experience in workflow/process scheduling software or interacting with multi-device systems. Expertise in managing complex workflows and integrating multiple devices to optimize laboratory processes and enhance productivity.

About the Role: We are seeking a highly motivated and skilled Senior Software Engineer to join our core engineering team to work on Catalyst, our software stack that runs our robotic lab systems. This is a critical, high-impact role responsible for the design, development, full integration testing, and field support of software drivers for our cutting-edge autonomous labs.

The ideal candidate possesses a strong background in programming reliable physical real-time systems in production environments. They must also excel at cross-functional collaboration, ensuring our drivers meet the exacting standards of the scientific community and providing rapid response to critical customer issues.

To learn more about automation engineering at Ginkgo, take a look at our website.

Responsibilities:

Driver Development & Implementation (70%)

• Design, implement, and maintain robust, high-performance software drivers using Python and/or C#/.NET for a diverse range of lab automation hardware (e.g., robotic arms, liquid handlers, plate readers).
• Deeply understand and implement various low-level hardware communication protocols, including RS-232, USB, and TCP/IP.
• Develop drivers with a focus on reliability.
• Contribute to the design of the device abstraction layer to create intuitive and robust interfaces for high-level application developers.
• Use and enable agentic software.

Integration & Validation (20%)

• Extensive testing with the rest of the Catalyst stack
• Collaborate closely with scientists and quality assurance teams to perform joint functional testing and validate driver performance against scientific requirements.
• Develop and maintain sophisticated automated unit and integration tests.
• Design and build hardware simulation environments to enable comprehensive driver testing and rapid iteration without relying on physical instrument access.
• Ensure the drivers include comprehensive error handling, logging, and fault-tolerance mechanisms to guarantee graceful recovery from communication timeouts and hardware failures.

Field Support & Diagnostics (10%)

• Act as a Tier 2 technical resource, providing rapid diagnosis and resolution to software and communication errors occurring at critical customer laboratory sites.
• Utilize remote diagnostic tools, system logs, and protocol analyzers to troubleshoot complex field issues quickly and effectively.
• Develop and document workarounds and permanent solutions to maintain high customer uptime.
• Proactively observing usage of our drivers and proposing improvements to the user experience/reliability

Minimum 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 a focus on hardware integration, embedded systems, or driver development.
• Extensive experience with Python.
• Strong communication and collaboration skills. 
• Familiarity with laboratory automation, robotics, or scientific instrumentation is highly beneficial.

Preferred Capabilities and Experience

We do not expect that any one candidate will have all of the following capabilities - each is independently a preferred or “nice-to-have” capability.

• Experience in a fast-moving, deep-tech company
• Experience or understanding of laboratory automation and lab automation user personas
• Strong understanding of Operating System fundamentals (threading, synchronization, memory management) and real-time constraints.
• Excellent communication, patience, and the ability to translate complex technical issues for non-software stakeholders (scientists, customers).
• Proficient with Git and experience working within agile methodologies and CI/CD pipelines.
• Advanced skills in debugging low-level code, including use of protocol sniffers, logic analyzers, and remote debugging tools.
• Experience with Windows, C#, COM.
• Experience with OPC-UA, SiLA2.
• Experience or background in a life science or chemistry laboratory

About the Role: Ginkgo Bioworks is constructing the world’s first "Total Autonomous Lab"—a facility where scientific work is requested by code and executed by robots, 24/7. We are looking for a Software Intern to help build the digital brain of this lab. You will work with Catalyst, our proprietary software stack that orchestrates fleets of Reconfigurable Automation Cells (RACs). This role is ideal for software engineers who want to apply their skills to physical systems or computational biologists who want to move beyond analysis into autonomous execution.

Responsibilities:

• Enable "Protocols as Code": Develop and refine Python-based protocols using the Catalyst Client to control liquid handlers, plate readers, and robotic arms.
• Build the AI Scientist: Assist in the development of Catalyst Agent, our LLM-based interface that allows scientists to launch experiments using natural language.
• Integrate Lab Data: Work on data pipelines that automatically harvest, structure, and upload experimental data from RACs into our data lake for AI model training.
• Develop Device Drivers: Help integrate new hardware instruments into the Catalyst ecosystem, writing the drivers that allow our software to "talk" to new lab tools.

Preferred Qualifications:

• No college degree necessary but some skills in coding or related areas required.
• Strong proficiency in Python; experience with hardware control or APIs is a plus.
• Enthusiasm for "Lab-in-the-Loop" technologies where AI models drive physical experimentation.
• Interest in biological data standards and laboratory automation.

About the Role: Ginkgo Bioworks is constructing the world’s first "Total Autonomous Lab"—a facility where scientific work is requested by code and executed by robots, 24/7. We are looking for a Software Intern to help build the digital brain of this lab. You will work with Catalyst, our proprietary software stack that orchestrates fleets of Reconfigurable Automation Cells (RACs). This role is ideal for software engineers who want to apply their skills to physical systems or computational biologists who want to move beyond analysis into autonomous execution.

Responsibilities:

• Enable "Protocols as Code": Develop and refine Python-based protocols using the Catalyst Client to control liquid handlers, plate readers, and robotic arms.
• Build the AI Scientist: Assist in the development of Catalyst Agent, our LLM-based interface that allows scientists to launch experiments using natural language.
• Integrate Lab Data: Work on data pipelines that automatically harvest, structure, and upload experimental data from RACs into our data lake for AI model training.
• Develop Device Drivers: Help integrate new hardware instruments into the Catalyst ecosystem, writing the drivers that allow our software to "talk" to new lab tools.

Preferred Qualifications:

• Recent graduate (BS/MS) or current student in Computer Science, Bioengineering, or a related STEM field.
• Strong proficiency in Python; experience with hardware control or APIs is a plus.
• Enthusiasm for "Lab-in-the-Loop" technologies where AI models drive physical experimentation.
• Interest in biological data standards and laboratory automation.

The role is based out of Ginkgo’s Boston, MA location and requires regular in-person attendance.

About the Role: Ginkgo Bioworks is deploying a massive fleet of Reconfigurable Automation Cells (RACs)—modular, mobile robotic units that snap together like LEGOs to form an autonomous lab. We are looking for an Automation Scientist Intern to be the hands-on force behind this fleet. You will learn how to load, operate, take down, and troubleshoot protocol runs on the most advanced lab automation hardware in the world, pushing our "Nebula" frontier lab towards autonomous operation.

Responsibilities:

• Master the RAC Platform: Learn to operate and maintain a system of Reconfigurable Automation Cells, designed to support a variety of molecular and cell biology scientific workflows. You will queue and submit programmatically-generated protocols, remote monitor for errors and conduct remote and on-site error recovery, with the support of our Apex Support team. Over time, you will advance to modifying or writing new protocols for our RAC Automation system.
• Learn Biology: You will prepare and onboard reagents and consumables for upcoming molecular and cell biology scientific workflows, execute and monitor such workflows, and take down and offboard used plates from completed workflows.  In the process, you will learn how to carefully handle and prepare reagents and consumables for workflows, do basic monitoring and error recovery of runs and safely dispose of used plates from completed workflows.

Preferred Qualifications:

• No college degree necessary but some skills in coding, biology or computational biology required. 
• "Automation-forward" mindset: you love working with lab automation and making robotic systems run smoother.
• Willingness to do whatever it takes to ensure that existing and new scientific workflows run successfully on our RAC automation system.

Bonus (not required):

• Interest in communications, marketing, social media, and/or short form video

About the Role: Ginkgo Bioworks is deploying a massive fleet of Reconfigurable Automation Cells (RACs)—modular, mobile robotic units that snap together like LEGOs to form an autonomous lab. We are looking for an Automation Scientist Intern to be the hands-on force behind this fleet. You will learn how to load, operate, take down, and troubleshoot protocol runs on the most advanced lab automation hardware in the world, pushing our "Nebula" frontier lab towards autonomous operation.

Responsibilities:

• Master the RAC Platform: Learn to operate and maintain a system of Reconfigurable Automation Cells, designed to support a variety of molecular and cell biology scientific workflows. You will queue and submit programmatically-generated protocols, remote monitor for errors and conduct remote and on-site error recovery, with the support of our Apex Support team. Over time, you will advance to modifying or writing new protocols for our RAC Automation system.
• Learn Biology: You will prepare and onboard reagents and consumables for upcoming molecular and cell biology scientific workflows, execute and monitor such workflows, and take down and offboard used plates from completed workflows.  In the process, you will learn how to carefully handle and prepare reagents and consumables for workflows, do basic monitoring and error recovery of runs and safely dispose of used plates from completed workflows.

Preferred Qualifications:

• No college degree necessary but some skills in coding, biology or computational biology required. 
• "Automation-forward" mindset: you love working with lab automation and making robotic systems run smoother.
• Willingness to do whatever it takes to ensure that existing and new scientific workflows run successfully on our RAC automation system.

Bonus (not required):

• Interest in communications, marketing, social media, and/or short form video

About Ginkgo Datapoints: Ginkgo Datapoints, a newly established business unit within Ginkgo Bioworks, is poised to usher in the coming era of AI-backed biotechnology breakthroughs. By leveraging Ginkgo's state-of-the-art automation and digital infrastructure, Datapoints aims to address the growing demand for high-quality, large-scale biological datasets essential for training AI models in drug discovery and development. Unlock AI to unlock biology.

Position Overview:
We are seeking a Scientist to join our High Throughput Screening (HTS) wet-lab team at Ginkgo Datapoints. This role is ideal for someone passionate about lab automation, assay development, high-throughput screening, and process optimization, eager to onboard assays onto workcells and increase throughput.

Key Responsibilities

• Execute primary screens and downstream plate reader assays on automated systems with minimal supervision.
• Perform rigorous quality control of screening results, monitoring assay robustness (e.g., Z’ and CVs) to ensure all data is accurately posted to electronic notebooks and uploaded to databases.
• Test, maintain, and troubleshoot robotic platforms and liquid handlers, including the Echo, Hamilton, and Lynx, to ensure peak performance and minimal downtime.
• Maintain impeccable lab records while supporting routine laboratory maintenance and safe lab practices.
• Partner with science teams to develop, optimize, and adapt biochemical and cell-based assays into 384- and 1536-well formats.
• Collaborate with bench scientists to transition manual assays onto fully automated screening systems and robotic workcells.
• Proactively identify and implement process improvements to increase throughput and drive overall screening efficiency.

Desired Experience and Capabilities

• BS or MS in Molecular Biology, Biochemistry, Cell Biology, Pharmacology, or a related field with at least 3 years of industry experience in HTS or automation.
• Hands-on proficiency operating and troubleshooting common HTS equipment such as the Echo, Prime/Lynx/Hamilton, EL406/Tempest/Combi liquid handlers, and Pherastar readers.
• Proven ability to diagnose and resolve hardware or software issues on automated platforms.
• Experience with automated scheduling software (Cellario) and LIMS/database environments is highly preferred.
• Familiarity with high-content imaging platforms or compound management workflows is a significant plus.
• Demonstrated ability to work in a fast-paced, dynamic culture with a strong sense of urgency and focus on high-quality deliverables.
• Effective communication skills to ensure alignment across cross-functional project teams and external stakeholders.

Why Join Ginkgo Datapoints?

• Work at the cutting edge of AI/ML and automation in drug discovery.
• Contribute to biologically relevant high-throughput screening efforts.
• Join a passionate team dedicated to scientific innovation.
• Competitive compensation and benefits.

Here at Ginkgo, we are aiming to modernize ADME by bringing our experience in high-throughput screening to the in vitro small molecule drug pipeline. We are re-imagining ADME at scale, and we are seeking a visionary and technically adept High-Throughput ADME Scientist to help us build and execute this next-generation platform. This role is critical in accelerating our drug discovery pipeline by providing timely and high-quality in vitro ADME (Absorption, Distribution, Metabolism, and Excretion) data to guide lead optimization.

The ideal candidate will possess deep technical expertise in developing, validating, and implementing a variety of high-throughput ADME assays.

Key Responsibilities

Assay Development & Implementation

• Design, develop, optimize, and validate a wide array of high-throughput in vitro ADME assays (e.g., solubility, MDCK permeability, plasma protein binding, microsomal stability, hepatocyte stability, and CYP inhibition/induction).
• Automation and Screening: Experience working with automated liquid handlers such as Hamilton, Lynx, Bravo, and Formulatrix.

Data Analysis & Reporting

• Develop and perform mass spectrometry (LC-MS/MS, acoustic ejection mass spectrometry, or similar) analysis of samples from ADME assays. Responsibilities will include method development and troubleshooting.
• Ensure proper sample preparation and management for high-throughput analysis.
• Analyze, interpret, and report complex ADME data, including calculating key pharmacokinetic parameters.
• Present results and provide expert recommendations to medicinal chemists and project teams to inform go/no-go decisions.

Quality & Compliance

• Maintain detailed and accurate laboratory records, SOPs, and electronic notebooks.
• Ensure all laboratory activities comply with internal quality standards and safety regulations.

Minimum Qualifications

• Education: Ph.D. in Pharmaceutical Sciences, Pharmacology, Analytical Chemistry, or a related field with 2+ years of relevant industry experience, or a Master's degree with 5+ years of industry experience.
• Technical Expertise:
  • Extensive, hands-on experience with LC-MS or acoustic MS particularly in a high-throughput setting.
  • Proven track record in developing and running automated in vitro ADME assays using state-of-the-art laboratory automation.
  • Strong theoretical and practical knowledge of drug metabolism pathways and DMPK.
  • Familiarity with common ADME prediction software and data visualization tools.

 Preferred Skills

• Experience using lab automation.
• Programmatic coding experience (e.g., Python, R, or similar).
• Data visualization (Spotfire, Python, R, or similar).
• Experience handling clinical samples.
• Familiarity with working in a CRO (Contract Research Organization) environment or managing CRO relationships.
• Proficiency with electronic laboratory data capture systems (e.g., LIMS, ELN).

Position Summary

We are seeking a Lead Scientist to drive the evolution of Ginkgo’s automated antibody production and developability platforms. This role is pivotal in bridging complex antibody engineering, specifically bi- and multi-specific formats, with Ginkgo’s RAC (Reconfigurable Automation Cart) systems. The ideal candidate is a technical expert in antibody transfection, purification, and characterization who thrives on translating manual workflows into robust, automated pipelines.

Key Responsibilities

• Lead method development and execution of antibody production and characterization on Ginkgo’s autonomous robotic labs using the RAC (reconfigurable automation cell) systems.
• Optimize high-throughput transfection and purification protocols for complex modalities, including bi-specifics and multi-specifics, at various scales (96 wp, 24 wp, 6 wp), ensuring high purity and correct assembly.
• Execute and automate standard developability suites (thermal stability, aggregation, polyreactivity, etc), binding assay (BLI, SPR) and functional assays (cell-based) to support rapid "Design-Build-Test" cycles.
• Serve as the project lead for customer projects focused on antibody production and developability characterization.
• Mentor junior scientists and contribute to scientific strategy and innovation.
• Author technical reports, SOPs, and present findings to internal leadership and external customers

Required Qualifications

• Ph.D. in Chemical Engineering, Bioengineering, Molecular Biology, or a related field with 2+ years of industry/academic experience in antibody production and characterization (or M.S. with 6+ years of industry/academic experience).
• Direct experience with the production and purification of complex antibody formats (e.g., bi-specifics, VHH-Fcs). Experience with Protein A/G/L, IEX, and SEC, specifically in a high-throughput or automated context.
• Demonstrated proficiency in antibody binding (SPR, BLI) and developability (DSF, DLS, SEC, HIC, AC-SINS, Polyreactivity, etc.) assays
• Demonstrated proficiency in using automated liquid handlers such as the Lynx, Bravo, TECAN, Hamilton

Preferred Qualifications

• Prior experience onboarding assays onto robotic platforms (e.g., translating a manual SEC-MALS or ELISA to a liquid handler).
• Experience with mass spectrometry (LC-MS) for confirming chain pairing in multi-specific formats.
• Familiarity with Python or scheduling software for automation.

Total compensation for this role is market driven, with a starting salary of $100k+, as well as company stock awards.  Base pay is ultimately determined based on a candidate's skills, expertise, and experience.  We also offer a comprehensive benefits package including medical, dental & vision coverage, health spending accounts, voluntary benefits, leave of absence policies, Employee Assistance Program, 401(k) program with employer contribution, 8 paid holidays in addition to a full-week winter shutdown and unlimited Paid Time Off policy.

Ginkgo has implemented a return to office policy effective October 1, 2025 with required in-office days 3x per week on Tuesday, Wednesday, Thursday.  Some teams may require to be onsite 4-5 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.

This role strongly prefers candidates located in the Boston area with the ability to regularly commute to our Seaport headquarters.

Due to the nature of this role, candidates should expect to support U.S. Government customers. Candidates must have the ability to obtain and maintain a U.S. security clearance per business requirements. In connection therewith, candidates must be willing to undergo a background investigation and meet eligibility requirements. Clearance sponsorship will be available.

Candidates who currently hold an active or recently inactive U.S. Government security clearance are encouraged to apply.

Ginkgo Biosecurity is building next-generation biosecurity infrastructure to help governments and partners detect, attribute, and deter biological threats. Our mission extends across public health, national security, and global defense, ensuring nations can rapidly identify dangerous pathogens, understand where threats originate, and respond with confidence.

We are seeking a Senior Full-Stack Software Engineer to join the Biosecurity engineering team. This role is ideal for someone who thrives in cross-disciplinary environments and is excited to build production software that directly supports biosecurity, epidemiology, and biological data workflows. We are looking for an engineer who is not only a technical expert but also a forward-thinker who embraces AI-augmented development and maintains a 'deploy-with-confidence' culture through rigorous CI/CD and automated testing

You will work across the stack—from backend services and data pipelines to user-facing web applications—building reliable, scalable systems that turn complex biological data into actionable insights.

Responsibilities

• Develop high-performance full-stack applications that translate complex biological data and operational needs into intuitive software using Python and modern JavaScript frameworks
• Champion an AI-first mindset, leveraging generative AI tools and LLM-based assistants to accelerate feature development, optimize code quality, and automate routine engineering tasks
• Collaborate with cross-functional domain experts to architect and operate on biological datasets (genomic, diagnostic, or epidemiological), ensuring that surveillance workflows maintain high standards for data integrity, provenance, and security.
• Influence the technical roadmap and long-term evolution of the Biosecurity platform, identifying and mitigating technical debt and architectural bottlenecks before they impact delivery.
• Design and implement robust CI/CD pipelines where automated unit, integration, and security testing are treated as mandatory gates for every code deployment.
• Drive engineering excellence by leading technical design reviews and providing critical feedback on software modularity, while upholding rigorous standards for documentation, observability, and long-term maintainability
• Support production systems by monitoring performance, troubleshooting issues, and continuously improving reliability, including on-call support and triage in off hours

Minimum Requirements

• 6-8+ years of professional software engineering experience, with significant full-stack development work, including ownership of complex systems and cross-team technical initiatives.
• Strong proficiency in Python for backend development (our primary programming language).
• Experience building and consuming APIs (REST and/or GraphQL).
• Experience developing modern web frontends using JavaScript/TypeScript and frameworks such as React.
• Demonstrated ability to integrate AI-assisted development tools (e.g., GitHub Copilot, Cursor, or similar) into daily workflows to increase productivity and code reliability
• Proven experience collaborating  domain experts (scientific, operations, product, etc) to translate complex biological data (genomic, diagnostic, or epidemiological) into robust software solutions and actionable insights
• Solid grounding in software engineering fundamentals: data structures, system design, version control, and modern CI/CD patterns for automated testing and deployment

Preferred Capabilities and Experience

• Prior experience in bioinformatics, computational biology, public health, or a related domain.
• Familiarity with cloud infrastructure (e.g., AWS) and containerized environments (Docker, Kubernetes).
• Experience with data pipelines, workflow orchestration, or analytics platforms.
• Exposure to regulated or sensitive-data environments (e.g., HIPAA, public health data).
• Demonstrate high levels of ownership and independent execution
• Comfort working in fast-moving, ambiguous problem spaces where requirements evolve
• Flexibility and willingness to work on the highest priority needs of the business