Advisor - Lab Automation Software Engineer, AI-Integration

100 Eli Lilly and Company; San Diego (CA); On-site; USD 141,000 - 207,000; Full time

Benefits offered by this job

401(k) plan

Pension

Vacation benefits

Medical, dental, vision coverage

Flexible benefits

Life insurance

Time off and leave

Well-being benefits

Job summary

Lilly’s Biologics Automation team in San Diego seeks an Advisor Lab Automation Software Engineer to bridge automation and digital tools in antibody discovery. You will own the software integration layer, deploy containerized services, and help weave AI into automation workflows.

You will lead design, implement robust lab-system integrations, and mentor the automation engineering team while exploring AI-driven decision-making and scalable data pipelines.

Qualifications

• PhD/MS/BS with strong software and lab automation integration experience.
• Experience integrating software with laboratory automation platforms.
• Production-grade Python and data pipelines experience.

Responsibilities

• Lead software integrations between orchestration layers and lab systems.
• Develop containerized services with Docker/Kubernetes and CI/CD.
• Prototype AI-driven automation and ensure robust, scalable solutions.
• Collaborate across software, automation engineering, and biology teams.

Skills

Python development

Docker

Kubernetes

CI/CD pipelines

AI integration

LangChain familiarity

Cloud orchestration

Team mentorship

Education

PhD in CS/Software Eng/Bioengineering

MS in related discipline

BS in related discipline

Tools

FastAPI

Redis

Flask

pytest

Argo on Kubernetes

GitOps

Job description

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.

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

Basic Qualifications

• Ph.D. in Computer Science, Software Engineering, Bioengineering, or related discipline with a minimum of 3 years of relevant industry experience
• M.S. in a related discipline with a minimum of 5 years of relevant industry experience
• 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 Skills & Attributes

Software Engineering & Infrastructure

• 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

Lab Automation & Integration

• 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

AI & Emerging Technologies

• 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

General

• 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

Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions. If you require accommodation to submit a resume for a position at Lilly, please complete the accommodation request form (https://careers.lilly.com/us/en/workplace-accommodation) for further assistance. Please note this is for individuals to request an accommodation as part of the application process and any other correspondence will not receive a response.

Lilly is proud to be an EEO Employer and does not discriminate on the basis of age, race, color, religion, gender identity, sex, gender expression, sexual orientation, genetic information, ancestry, national origin, protected veteran status, disability, or any other legally protected status.

Our employee resource groups (ERGs) offer strong support networks for their members and are open to all employees. Our current groups include: Africa, Middle East, Central Asia Network, Black Employees at Lilly, Chinese Culture Network, Japanese International Leadership Network (JILN), Lilly India Network, Organization of Latinx at Lilly (OLA), PRIDE (LGBTQ+ Allies), Veterans Leadership Network (VLN), Women's Initiative for Leading at Lilly (WILL), enAble (for people with disabilities).

Actual compensation will depend on a candidate's education, experience, skills, and geographic location. The anticipated wage for this position is $141,000 - $206,800. Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance).

Benefits

• 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
• well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities)

Lilly reserves the right to amend, modify, or terminate its compensation and benefit programs in its sole discretion and Lilly’s compensation practices and guidelines will apply regarding the details of any promotion or transfer of Lilly employees.

#WeAreLilly At Lilly we strive to ensure our employees are part of a team that cares about them and our shared purpose of making life better for those around the world. How do we do this? We continue to look for ways to include, innovate, accelerate and deliver while maintaining integrity, excellence and respect for people. We hope that you seek to join us on our journey as we create medicine and deliver improved outcomes for patients across the globe!