Staff Software Engineer –Lab Automation

Work Schedule

Environmental Conditions

Job Description

LOCATION: This is a fully onsite position based at our Pleasanton, CA site. Unfortunately, relocation assistance is NOT provided. Priority will be given to LOCAL candidates currently residing in the Bay Area.

• Must be able to pass a comprehensive background check, which includes a drug screen.

As a Staff Software Engineer specializing in laboratory automation and AI-enabled solutions, you will provide technical leadership in designing, developing, and supporting software that connects scientific instruments, automation platforms, and laboratory workflows. 

This role will contribute to the software ecosystem supporting sample preparation and casework workflows. You will collaborate with engineering, product management, applications, service, and customer-facing teams to address technical and customer needs while improving the reliability, scalability, and maintainability of existing solutions. 

Key Responsibilities 

• Provide technical leadership and architectural direction for instrument-control software, graphical user interfaces, laboratory automation, workflow orchestration, and connected instrumentation. 

• Design and develop automation frameworks that orchestrate instruments, robotics, devices, and software services into reliable end-to-end laboratory workflows, including sequencing, instrument-state management, synchronization, exception handling, and fault recovery. 

• Design, integrate, and deploy AI-enabled capabilities for intelligent troubleshooting, workflow and protocol assistance, knowledge retrieval, run-data interpretation, anomaly detection, and context-aware automation. Ensure these solutions include appropriate evaluation, testing, monitoring, security, data protection, traceability, human oversight, and clearly defined safety and control boundaries. 

• Diagnose complex issues involving application software, instrument communication, hardware, firmware, scripts, operational data, and laboratory workflows. 

• Translate scientific, customer, system, and business requirements into reliable, scalable, and maintainable technical solutions. 

• Define reusable instrument and device abstractions, APIs, data models, and communication patterns that support interoperability and orchestration across instrument platforms. 

• Collaborate effectively with cross-functional and geographically distributed engineering, product, applications, service, and customer-facing teams. 

• Help define and execute the long-term technical roadmap for connected instruments, intelligent instrument-control software, and interoperable laboratory automation, including increasingly autonomous workflows. 

Minimum Qualifications 

• Bachelor’s degree with at least 5 years, or Master’s degree with at least 3 years, of professional software development experience in Computer Science, Computer Engineering, Automation Engineering, or a related technical field. 

• Advanced proficiency in Python and TypeScript, with demonstrated experience designing and delivering production-quality software systems; experience with Java is preferred. 

• Experience developing, integrating, and supporting software for scientific instruments, laboratory automation, robotics, medical devices, or other hardware-controlled systems, including instrument-control applications, graphical user interfaces, simulators, engineering utilities, diagnostic tools, scripts, protocols, or automated workflows. 

• Experience integrating instruments, automation systems, embedded controllers, sensors, robotics, or firmware using vendor SDKs, REST APIs, messaging systems, serial communication, or comparable technologies. 

• Strong understanding of software architecture, object-oriented or modular design, design patterns, data structures, APIs, data models, and hardware abstraction. 

• Experience with asynchronous programming, multithreading, event-driven design, instrument-state management, synchronization, exception handling, and fault recovery. 

• Experience applying AI technologies or AI-assisted development tools to scientific instrumentation, laboratory automation, or engineering use cases, including deployment in local, edge, offline, or resource-constrained environments. 

• Experience working within Agile or Scrum development methodologies and familiarity with regulated product development practices, including documentation, requirements traceability, cybersecurity, risk management, verification, validation, and design controls. 

Compensation and Benefits

This position may also be eligible to receive a variable annual bonus based on company, team, and/or individual performance results in accordance with company policy. We offer a comprehensive Total Rewards package that our U.S. colleagues and their families can count on, which includes:

• A choice of national medical and dental plans, and a national vision plan, including health incentive programs

• Employee assistance and family support programs, including commuter benefits and tuition reimbursement

• At least 120 hours paid time off (PTO), 10 paid holidays annually, paid parental leave (3 weeks for bonding and 8 weeks for caregiver leave), accident and life insurance, and short- and long-term disability in accordance with company policy

• Retirement and savings programs, such as our competitive 401(k) U.S. retirement savings plan

• Employees’ Stock Purchase Plan (ESPP) offers eligible colleagues the opportunity to purchase company stock at a discount

For more information on our benefits, please visit: https://jobs.thermofisher.com/global/en/total-rewards