Senior Software Engineer - Lab Automation

Roche • South San Francisco, CA

2d • $142,500 - $264,700

About The Position

The Senior Software Engineer – Lab Automation will connect software architecture, frontier AI models, and physical laboratory instrumentation to help build autonomous, self-healing laboratories for lights-out drug discovery. The role is part of the Computational Sciences Center of Excellence and Data and Digital Catalyst team, which are developing foundational platforms that combine AI models, physical telemetry, and multi-vendor robotics to run complex science unattended.

The engineer will architect hardware abstraction layers, instrument integration frameworks, and orchestration engines so diverse lab automation platforms can operate reliably, recover from errors, and support continuous operation. The role involves designing and troubleshooting high-throughput lab workflows, integrating hardware and software systems, maintaining a real-time digital representation of laboratory resources, and translating scientific protocols into production-grade technical architectures in collaboration with multidisciplinary teams.

Requirements

• At least 5 years of software engineering and physical hardware integration experience, or an equivalent advanced degree with a proven industrial automation track record.
• Proficiency in Python or C# for building modular software architectures, integration frameworks, and distributed services.
• Strong software engineering fundamentals, including system design, automated testing, version control, CI/CD, debugging, and production operations.
• Effective use of AI-assisted software engineering practices, including providing context, decomposing problems, directing agents, reviewing their work, and validating results; deep understanding of limitations of AI-generated code.
• Hands-on experience programming commercial liquid-handling platforms and integrating robotic arms or manipulators into unified automated workcells.
• Experience designing workflow orchestration and scheduling systems that manage shared resources, dynamic dependencies, and execution priorities.
• Skill using APIs and SDKs such as REST, gRPC, and vendor interfaces to interact with laboratory software ecosystems.
• Practical rapid-prototyping design experience, including CAD, 3D printing, CNC milling, or laser cutting for custom fixtures and hardware adaptations.
• Familiarity with molecular biology, biochemistry, or wet-lab workflows to translate scientific requirements into engineering deliverables.
• Clear communication and ability to collaborate across research scientists, software developers, and automation engineers.

Nice To Haves

• Experience creating and evaluating AI agents used within applications, including designing robust evaluations to measure agent performance and reliability.
• Experience integrating computer vision models such as OpenCV, YOLO, or SAM for automated error recovery, deck inspection, and anomaly detection.
• Hands-on background in training, evaluating, or adopting AI/ML models, including reinforcement learning or imitation learning for robotics.
• Knowledge of sensors, microcontrollers, embedded communication protocols, and task-and-motion planning.
• Familiarity with cloud infrastructure, containerized deployment, and digital twin simulation workflows.

Responsibilities

• Design, program, and troubleshoot high-throughput laboratory workflows to ensure robust assay execution on physical hardware.
• Build orchestration systems, hardware abstraction layers, and instrument drivers that manage retries, shared-resource contention, and unattended 24/7 operation.
• Implement telemetry, logging, metrics, and alerting across hardware and software to diagnose failures and resolve root causes using software hooks or vision models.
• Build and maintain an accurate real-time digital representation of the lab, including sample tracking, instrument state, and reagent availability, with bidirectional integration into LIMS and ELNs.
• Manage hardware requirements, site constraints, communication protocols, and workcell integration from mechanical layout and prototyping through production deployment.
• Collaborate with software engineers, automation scientists, and hardware engineers to translate scientific protocols into production-grade technical architectures.

Benefits

• A discretionary annual bonus may be available based on individual and Company performance.
• The position qualifies for company benefits detailed at the provided link.

What This Job Offers

• Job Type: Full-time
• Career Level: Senior
• Education Level: No Education Listed