Lead Engineer Agentic Lab Automation & AI Orchestration

Lilly Group; San Diego (CA); On-site; USD 87,000 - 222,000; Full time

Benefits offered by this job

401(k)

Pension

Vacation benefits

Medical, dental, vision benefits

Flexible benefits

Life insurance

Well-being benefits

Job summary

Lilly is seeking a highly skilled engineer to advance Frontier AI by connecting agentic workflows to physical lab systems. You will prototype and productionize integrations with robotic platforms, analytical instruments, and data pipelines, working with chemists, biologists, and automation engineers to accelerate molecule discovery tasks.

The role emphasizes hands-on development, rapid prototyping, and deploying intelligent systems that enable autonomous experiments in the lab, aligning with

Qualifications

• PhD or MS + 2 yrs / BS + 5 yrs in engineering with wet-lab automation experience.
• Demonstrated experience with laboratory automation systems and LIMS engineering.
• Direct experience integrating software control and/or AI systems with lab automation platforms (liquid handlers, analytical instruments, robotic workflows).
• Strong experience with containerization (Docker) and Kubernetes-based orchestration in production environments.
• Experience building scalable and production-level Python applications using Redis, FastAPI, Flask/Streamlit, pytest, etc.

Responsibilities

• Build multi-agent systems with orchestration, state management, error recovery, and tool integration.
• Prototype and iterate agent planning strategies, memory systems, and human-in-the-loop patterns.
• Design architectures interfacing with lab automation platforms for closed-loop execution.
• Partner with engineers and scientists to transition prototypes into reliable lab operations.
• Deploy containerized services using Docker and Kubernetes with GitOps/CI/CD.

Skills

Lab automation

LIMS engineering

Docker

Kubernetes

Python stack

Education

PhD or MS + 2 yrs / BS + 5 yrs in engineering/robotics

Tools

Liquid handlers

Analytical instruments

Robotic workflows

Job description

Lilly is seeking a highly skilled engineer to advance Frontier AI by connecting agentic workflows to physical lab systems. You will prototype and productionize integrations with robotic platforms, analytical instruments, and data pipelines, working with chemists, biologists, and automation engineers to accelerate molecule discovery tasks.

The role emphasizes hands-on development, rapid prototyping, and deploying intelligent systems that enable autonomous experiments in the lab, aligning with