Principal Engineer, Agentic Lab Automation Systems

Biopharma Careers; Indianapolis, Northern (IN, KY); Hybrid; USD 87,000 - 222,000; Full time

Benefits offered by this job

401(k) plan

Pension

Vacation benefits

Medical, dental, vision coverage

Flexible benefits

Well-being programs

Job summary

Lilly is seeking an Engineer to build agent-based systems that accelerate molecule discovery through automated lab platforms and AI integration. You will prototype, productionize, and collaborate with chemists and automation engineers to deploy intelligent systems accelerating DMTA tasks.

The role requires hands-on work with agent workflows, lab automation, and cloud orchestration. It offers a competitive compensation package and broad benefits typical for a senior engineering position at Lilly.

Qualifications

• PhD or MS+2 yrs / BS+5 yrs equivalent in Engineering, Robotics, or CS with wet-lab automation experience.
• Experience with laboratory automation and LIMS engineering.
• Direct experience integrating software control/AI with lab automation platforms.
• Strong containerization and Kubernetes in production environments.
• Proficient in building scalable Python applications (Redis, FastAPI, Flask/Streamlit, pytest).

Responsibilities

• Build multi-agent systems with robust 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 (Hamilton, Tecan, Opentrons) for closed‑loop experiments.
• Deploy and maintain containerized services using Docker/Kubernetes with CI/CD.

Skills

Python development

Lab automation experience

Multi-agent systems design

CI/CD familiarity

Education

PhD in Chemical/Mechanical Engineering, Robotics, Computer Engineering

MS + 2 yrs / BS + 5 yrs equivalent experience

Tools

Docker

Kubernetes

LIMS

Redis

FastAPI

Flask/Streamlit

pytest

GitHub

Job description

Lilly is seeking an Engineer to build agent-based systems that accelerate molecule discovery through automated lab platforms and AI integration. You will prototype, productionize, and collaborate with chemists and automation engineers to deploy intelligent systems accelerating DMTA tasks.

The role requires hands-on work with agent workflows, lab automation, and cloud orchestration. It offers a competitive compensation package and broad benefits typical for a senior engineering position at Lilly.