Lab Automation Engineer Jobs (NOW HIRING)

Job Summary:
Eli Lilly and Company is a global healthcare leader headquartered in Indianapolis, Indiana. They are seeking an Advisor Lab Automation Software Engineer to help build intelligent systems that connect software, data, and physical lab automation in antibody discovery, focusing on integrating AI capabilities into laboratory workflows.
Responsibilities:
• Lead the design and implementation of reliable software integrations between orchestration layers and physical lab systems including liquid handlers, plate readers, robotic workstations, and analytical instruments
• Own and evolve the translation layer between high-level workflow logic and low-level instrument control
• Partner with automation engineers and biologists to ensure integrations are robust, maintainable, and production-ready
• Deploy and maintain containerized services using Docker and Kubernetes with GitOps and CI/CD practices
• Integrate cloud-based orchestration frameworks with laboratory control systems and LIMS infrastructure
• Build scalable, production-grade Python applications and data pipelines that connect experimental readouts with downstream analysis tools
• Collaborate with the team to explore and prototype how AI-driven decision-making can be incorporated into existing automation workflows
• Contribute to the team's evolving approach to autonomous orchestration, bringing software engineering rigor to early-stage AI integration efforts
• Stay current with developments in LLM tooling and agent frameworks and help evaluate what is practically applicable to the lab environment
• Serve as a technical authority and mentor within the automation engineering team, helping to grow capability across software, integration, and emerging AI systems
• Influence the broader technical roadmap for autonomous discovery systems at the San Diego site
• Evaluate tools, frameworks, and vendor solutions for strategic fit with the team's long-term vision
Qualifications:
Required:
• Ph.D. in Computer Science, Software Engineering, Bioengineering, or related discipline with a minimum of 3 years of relevant industry experience, or
• M.S. in a related discipline with a minimum of 5 years of relevant industry experience, or
• B.S. in a related discipline with a minimum of 8 years of relevant industry experience
• Demonstrated experience integrating software systems with laboratory automation platforms is required across all levels.
Preferred:
• Strong Python development skills with proven experience building and maintaining production-level applications (FastAPI, Redis, Flask, pytest, etc.)
• Deep hands-on experience with Docker, Kubernetes, and CI/CD pipelines in production environments
• Experience with cloud-based orchestration frameworks such as Argo on Kubernetes
• Direct experience integrating software control systems with lab automation platforms (liquid handlers, analytical instruments, robotic workflows)
• Hands-on familiarity with common biologics discovery instrumentation — liquid handlers (Beckman, Hamilton, HighRes, etc.), micro-dispensers, plate readers, or integrated robotic workstations — is a strong plus
• Familiarity with scheduling and execution software used in integrated lab environments (Cellario, Green Button Go, Director, SAMI, VWorks, Genera, or similar)
• Experience with LIMS platforms, ELN systems, or laboratory data pipelines
• Curiosity about and some hands-on experience with LLMs, agent frameworks, or AI-driven workflow automation
• Familiarity with orchestration tools such as LangChain, LangGraph, or similar is a plus — deep expertise is not expected
• Demonstrated willingness to learn and experiment with new technologies as they emerge
• Proven ability to move fluidly between architectural thinking and hands-on engineering execution
• Strong collaboration skills — comfortable working across software, automation engineering, and biological science teams
• Genuine curiosity about biologics discovery and a desire to understand the science well enough to build systems that truly serve it
Company:
We're a medicine company turning science into healing to make life better for people around the world. Founded in 1876, the company is headquartered in Indianapolis, USA, with a team of 10001+ employees. The company is currently Late Stage.