Advisor - Lab Automation Software Engineer, AI-Integration
Eli Lilly and Company
August 23, 2026
On-site
San Diego, CA
IT
In This Role, You Will Have The Opportunity To
Lab Automation Integration
- Lead the design and implementation of reliable software integrations between orchestration layers and physical lab systems (liquid handlers, plate readers, robotic workstations, 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.
Platform & Infrastructure
- 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 connecting experimental readouts with downstream analysis tools.
AI & Intelligent Automation
- Explore and prototype how AI-driven decision-making can be incorporated into automation workflows.
- Contribute to autonomous orchestration approaches by bringing software engineering rigor to early-stage AI integration.
- Evaluate LLM tooling and agent frameworks for practical applicability to the lab environment.
Technical Leadership
- Serve as a technical authority and mentor within the automation engineering team.
- Influence the technical roadmap for autonomous discovery systems at the San Diego site.
- Evaluate tools, frameworks, and vendor solutions for strategic fit.
Basic Qualifications
- Ph.D. with 3+ years relevant industry experience, or M.S. with 5+ years, or B.S. with 8+ years.
- Demonstrated experience integrating software systems with laboratory automation platforms.
Preferred Skills & Attributes
- Python (e.g., FastAPI, Redis, Flask, pytest) and production application development.
- Docker/Kubernetes and CI/CD in production.
- Cloud orchestration (e.g., Argo on Kubernetes).
- Integration experience with lab automation platforms and biologics instrumentation.
- Familiarity with lab scheduling/execution tools; LIMS/ELN/lab data pipelines.
- Some hands-on experience with LLMs/agent frameworks/AI workflow automation (LangChain/LangGraph a plus).
- Collaboration across software, automation engineering, and biological science teams; curiosity about biologics discovery.
Benefits (if eligible)
- 401(k) (company-sponsored), pension, vacation; medical/dental/vision/prescription; flexible benefits; life insurance; time off/leave; well-being benefits (EAP, fitness, clubs).
Application Instructions
- If you require accommodation to submit a resume, complete the workplace accommodation request form: https://careers.lilly.com/us/en/workplace-accommodation
Lab Automation Integration
- Lead the design and implementation of reliable software integrations between orchestration layers and physical lab systems (liquid handlers, plate readers, robotic workstations, 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.
Platform & Infrastructure
- 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 connecting experimental readouts with downstream analysis tools.
AI & Intelligent Automation
- Explore and prototype how AI-driven decision-making can be incorporated into automation workflows.
- Contribute to autonomous orchestration approaches by bringing software engineering rigor to early-stage AI integration.
- Evaluate LLM tooling and agent frameworks for practical applicability to the lab environment.
Technical Leadership
- Serve as a technical authority and mentor within the automation engineering team.
- Influence the technical roadmap for autonomous discovery systems at the San Diego site.
- Evaluate tools, frameworks, and vendor solutions for strategic fit.
Basic Qualifications
- Ph.D. with 3+ years relevant industry experience, or M.S. with 5+ years, or B.S. with 8+ years.
- Demonstrated experience integrating software systems with laboratory automation platforms.
Preferred Skills & Attributes
- Python (e.g., FastAPI, Redis, Flask, pytest) and production application development.
- Docker/Kubernetes and CI/CD in production.
- Cloud orchestration (e.g., Argo on Kubernetes).
- Integration experience with lab automation platforms and biologics instrumentation.
- Familiarity with lab scheduling/execution tools; LIMS/ELN/lab data pipelines.
- Some hands-on experience with LLMs/agent frameworks/AI workflow automation (LangChain/LangGraph a plus).
- Collaboration across software, automation engineering, and biological science teams; curiosity about biologics discovery.
Benefits (if eligible)
- 401(k) (company-sponsored), pension, vacation; medical/dental/vision/prescription; flexible benefits; life insurance; time off/leave; well-being benefits (EAP, fitness, clubs).
Application Instructions
- If you require accommodation to submit a resume, complete the workplace accommodation request form: https://careers.lilly.com/us/en/workplace-accommodation