Senior Lab Automation Engineer — In Vitro Pharmacology

100 Eli Lilly and Company; Indianapolis (IN); On-site; USD 131,000 - 211,000; Full time

Job summary

Eli Lilly and Company in Indianapolis is seeking a senior automation engineer to design, deploy, and support laboratory automation for in vitro pharmacology and chemistry workflows. You will work closely with scientific users to understand needs, ensure reliable operation, and drive adoption of automation across pipeline processes.

The role emphasizes hands-on bench proximity, system integration, and building robust automated workflows with a focus on reproducibility and scalability.

Qualifications

• Bachelor's degree in engineering, computer science, biological sciences, or related field with 5+ years of hands-on laboratory automation experience.
• Experience with Hamilton automation and lab workflow integration.
• Experience automating in vitro pharmacology and chemistry workflows.
• Experience collaborating with scientific users to gather requirements and support adoption.
• Proficiency in scripting or programming for automation.
• Experience with ELN/LIMS integration (Benchling).

Responsibilities

• Build, program, deploy, and maintain laboratory automation systems for in vitro pharmacology, chemistry, and related pipeline workflows.
• Develop and validate automated methods, translating scientific protocols into robust, reproducible automated processes.
• Partner directly with scientific users to gather requirements and deliver automation solutions that meet their needs.
• Deploy and support automation systems tailored to specific pipeline processes and throughput needs.
• Provide ongoing support for deployed systems, responding to user needs and keeping automation running reliably day to day.
• Develop clear documentation, quick-reference guides, and ongoing support resources for teams.
• Plan and deliver hands-on training to local end users on new instrumentation, automated methods, and protocols.
• Resolve hardware, software, and integration issues to keep systems running reliably.
• Strengthen data reproducibility across automated processes through sound standards, controls, and qualification practices.
• Integrate automation with scheduling and lab orchestration software and with ELN/LIMS platforms such as Benchling.
• Apply LLM-based coding tools and agentic assistants to accelerate method development, scripting, and systems integration.
• Contribute to generation of large-scale, structured datasets for AI/ML applications.
• Build effective working relationships across scientific and engineering teams to ensure automation solutions fit real-world use

Skills

Lab automation

Scripting/Programming

Scientist collaboration

LLM tooling

Education

Bachelor's degree in engineering/CS/biological sciences

Tools

Hamilton automation ecosystem

Echo acoustic dispenser

Tecan instruments

Benchling ELN/LIMS

Lab schedulers/orchestration

Job description

Eli Lilly and Company in Indianapolis is seeking a senior automation engineer to design, deploy, and support laboratory automation for in vitro pharmacology and chemistry workflows. You will work closely with scientific users to understand needs, ensure reliable operation, and drive adoption of automation across pipeline processes.

The role emphasizes hands-on bench proximity, system integration, and building robust automated workflows with a focus on reproducibility and scalability.