Dir/Sr. Dir - Lab Automation Engineer, Discovery Oncology

Eli Lilly and Company • Us, NY

1d • Onsite

About The Position

We're looking for a Director (Principal) Lab Automation Engineer to lead the design, architecture, and software/usability layer of the automated systems that power our NY lab's discovery pipeline. As the senior-most individual contributor on automation, you'll work with the AVP to set technical direction and architecture, partner closely with scientists, software engineers, and platform leaders to translate scientific workflows into reliable, scalable automation — and you'll also get hands-on building the software, tools, and interfaces that make that automation genuinely easy for scientists to use day to day. This is a role for someone who's as comfortable in a scientist's workflow discussion as they are in a systems design review or writing the code themselves — someone who wants to help set the technical direction for automation and build the tools that make it usable. This position reports to the AVP-Automation, Discovery Oncology and will be onsite in NYC.

Requirements

• Bachelor's or advanced degree in Engineering, Robotics, Computer Science, Biology, or related field with 10+ years of hands-on experience in laboratory automation, robotics integration, or a closely related engineering discipline, including experience providing technical mentorship to other engineers
• You enjoy working with both scientists and engineers, and can move fluidly between a wet-lab workflow conversation and a systems architecture discussion
• You have a solid understanding of data processing pipelines and how automation systems fit into the broader flow of experimental data
• You've built tools — using standard programming or AI-assisted harnesses — that make lab automation easier to use, whether that's a UI layer, an instrument control abstraction, or automated data upload/ingestion
• You influence through technical credibility and clear communication, not formal authority
• You default to designing for the end user (the scientist at the bench) rather than just for the instrument or the codebase; you're a strong software engineer at heart, with enough working knowledge of physical systems to design good interfaces to them

Nice To Haves

• Working familiarity with liquid handling platforms (Tecan, Beckman Coulter/Labcyte, Agilent, Hamilton, etc) and automated imaging/detection systems
• Strong programming skills (Python, SQL, and/or C#) with demonstrated ability to build production-quality software, not just scripts; experience with scheduling/control software (e.g. Cellario, Momentum, VWorks, Green Button Go, or custom ACS)
• Demonstrated experience designing and qualifying the software/control layer of new automated systems from concept through production
• Experience designing user-facing tools (UIs, APIs, CLIs) for non-software-engineer end users
• Working knowledge of data processing pipelines and how lab systems integrate with downstream data infrastructure, including experience building or maintaining data pipelines that move data from instruments into analysis/storage infrastructure
• Experience building tooling (traditional or AI-assisted) that lowers the barrier for scientists and engineers to use, configure, or troubleshoot automation
• Strong cross-functional collaboration skills; able to communicate technical trade-offs to non-technical and senior audiences
• Experience partnering on vendor relationships or providing input on project resourcing and trade-offs
• Experience applying LLMs/AI agents to instrument control, troubleshooting, or lab software workflows
• Experience with Cellario and Cellario integrations
• Some background in oncology, mammalian cell biology, or related scientific field
• Experience with driver design and implementation
• Experience with observability/monitoring tooling (dashboards, alerting, logging pipelines) applied to lab or industrial systems
• Understanding of PLCs, safety circuits, and power electronics

Responsibilities

• Set technical implementation and architecture for the software/control layer spanning liquid handling protocols and integrated hardware/software systems across the site
• Own future workcell design as the platform matures beyond its initial build-out, building on the architecture and standards established during early platform development
• Set technical standards and review designs across the automation team, provide hands-on technical mentorship to other engineers without owning their formal management and career development
• Partner with the AVP on requirements gathering and vendor evaluation for the most complex automated systems; own installation, validation, and ongoing performance optimization
• Lead root-cause investigations for the most complex hardware/software integration failures; drive corrective actions and systemic reliability improvements across the platform
• Serve as the primary technical bridge between software engineering, hardware/controls, data teams, and bench scientists to ensure automation and data systems integrate seamlessly
• Design and build user-facing tools — UIs, dashboards, CLIs, or AI-assisted interfaces — that let scientists configure, launch, monitor, and troubleshoot automated runs without needing to understand the underlying instrument control code
• Build and maintain data capture, upload, and validation pipelines that move experimental data cleanly from automated systems into downstream data processing pipelines and analysis tools
• Build monitoring, alerting, and self-diagnostic tooling that surfaces instrument and workflow errors clearly, so scientists and engineers can resolve issues faster and with less escalation
• Write and maintain automation scripts, APIs, and configuration templates that standardize how new workflows get deployed onto existing hardware
• Advise on vendor relationships and evaluate new instrumentation, technologies, and partnerships to keep the automation platform state-of-the-art

Benefits

• company bonus (depending, in part, on company and individual performance)
• company-sponsored 401(k)
• pension
• vacation benefits
• 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)

What This Job Offers

• Job Type: Full-time
• Career Level: Senior