Advisor - Lab Automation Software Engineer, AI-Integration

Eli Lilly and Company•San Diego, CA

10d•$141,000 - $206,800

About The Position

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease, and give back to our communities through philanthropy and volunteerism. We give our best effort to our work, and we put people first. We’re looking for people who are determined to make life better for people around the world. The Biologics Automation and High-throughput Technologies Group at the Lilly Biotechnology Center in San Diego is seeking an Advisor Lab Automation Software Engineer to help build the intelligent systems that connect software, data, and physical lab automation in antibody discovery. Our team is working toward a vision of closed-loop autonomous discovery — where robotic platforms, lab digitalization, and AI-driven orchestration work together to accelerate how biologics are found and developed. In this role, you will own the software integration layer between our automation infrastructure and the digital tools that drive it, while helping to shape how emerging AI capabilities get woven into that foundation over time. If you're a seasoned software and integration engineer who is excited about what AI might do for laboratory science, we want to hear from you. 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 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 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 that connect experimental readouts with downstream analysis tools AI & Intelligent Automation · 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 Technical Leadership · 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 What Success Looks Like · Lab automation systems are reliably connected, well-instrumented, and generating clean data that flows seamlessly into digital workflows · The team's software architecture evolves from early-stage integrations toward scalable, production-grade infrastructure · AI capabilities are thoughtfully and pragmatically incorporated into automation workflows as the field matures · Your technical leadership accelerates the capability growth of the broader automation engineering team

Requirements

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.

Nice To Haves

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

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

Benefits

Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance).
In addition, Lilly offers a comprehensive benefit program to eligible employees, including eligibility to participate in a company-sponsored 401(k); pension; vacation benefits; eligibility for medical, dental, vision and prescription drug benefits; flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts); life insurance and death benefits; certain time off and leave of absence benefits; and well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities).

Stand Out From the Crowd

Upload your resume and get instant feedback on how well it matches this job.

Upload and Match Resume