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

Lilly•New York, NY

3d•$180,000 - $297,000•Onsite

About The Position

Lilly is seeking a Director (Principal) Lab Automation Engineer to lead the design, architecture, and software/usability layer of automated systems supporting the Discovery Oncology laboratory in New York City. This senior individual-contributor role partners with the AVP to set technical direction and architecture, translating scientific workflows into reliable, scalable automation. The engineer will collaborate with scientists, software engineers, and platform leaders while also building software, tools, and interfaces that make automation accessible to scientists in their daily work. The position reports to the AVP-Automation, Discovery Oncology and is onsite five days per week in New York, NY. The role sets technical implementation and architecture for software and controls spanning liquid-handling protocols and integrated hardware/software systems. It shapes future workcell design, establishes technical standards, reviews designs, and provides hands-on technical mentorship without formal people-management responsibilities. The engineer also partners on requirements and vendor evaluations, leads installation, validation, optimization, and complex root-cause investigations, and serves as a technical bridge among software, hardware/controls, data teams, and bench scientists. The position involves building scientist-facing interfaces and tools, data capture and ingestion pipelines, monitoring and diagnostic tooling, automation scripts, APIs, and configuration templates. It also advises on vendor relationships and new instrumentation, technologies, and partnerships. Lilly describes the work as full-time and offers a compensation range of $180,000–$297,000, with eligibility for a company bonus and a comprehensive benefits program.

Requirements

Bachelor's or advanced degree in Engineering, Robotics, Computer Science, Biology, or a related field.
10+ years of hands-on experience in laboratory automation, robotics integration, or a closely related engineering discipline.
Experience providing technical mentorship to other engineers.
Strong software engineering capability and working knowledge of physical systems sufficient to design effective interfaces to them.
Ability to collaborate with scientists and engineers and move between wet-lab workflow discussions and systems architecture discussions.
Understanding of data processing pipelines and how automation systems fit into experimental data flows.
Experience building tools that make lab automation easier to use, such as user interfaces, instrument-control abstractions, or automated data upload/ingestion.
Ability to influence through technical credibility and clear communication, without formal authority.
Ability to design for end users, particularly scientists working at the bench.

Nice To Haves

Working familiarity with liquid-handling platforms such as Tecan, Beckman Coulter/Labcyte, Agilent, or Hamilton, and automated imaging/detection systems.
Strong programming skills in Python, SQL, and/or C#, with demonstrated ability to build production-quality software.
Experience with scheduling/control software such as Cellario, Momentum, VWorks, Green Button Go, or custom ACS.
Experience designing and qualifying the software/control layer of new automated systems from concept through production.
Experience designing user-facing tools such as UIs, APIs, or CLIs for non-software-engineer end users.
Working knowledge of data processing pipelines and laboratory-system integration with downstream data infrastructure, including experience building or maintaining data pipelines from instruments to analysis or storage infrastructure.
Experience building traditional or AI-assisted tooling that makes automation easier to use, configure, or troubleshoot.
Strong cross-functional collaboration and ability 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 or AI agents to instrument control, troubleshooting, or laboratory software workflows.
Experience with Cellario and Cellario integrations.
Some background in oncology, mammalian cell biology, or a related scientific field.
Experience with driver design and implementation.
Experience with observability or monitoring tooling, such as dashboards, alerting, and logging pipelines, applied to laboratory or industrial systems.
Understanding of PLCs, safety circuits, and power electronics.

Responsibilities

Set technical implementation and architecture for the software/control layer across liquid-handling protocols and integrated hardware/software systems at the site.
Own future workcell design as the platform matures, building on architecture and standards established during early platform development.
Set technical standards, review designs, and provide hands-on technical mentorship to other engineers without owning their formal management or career development.
Partner with the AVP on requirements gathering and vendor evaluation for complex automated systems; own installation, validation, and ongoing performance optimization.
Lead root-cause investigations into complex hardware/software integration failures and drive corrective actions and systemic reliability improvements.
Serve as the primary technical bridge among software engineering, hardware/controls, data teams, and bench scientists to ensure automation and data systems integrate effectively.
Design and build user-facing tools—including UIs, dashboards, CLIs, or AI-assisted interfaces—that enable scientists to configure, launch, monitor, and troubleshoot automated runs.
Build and maintain data capture, upload, and validation pipelines that move experimental data from automated systems into downstream processing and analysis tools.
Build monitoring, alerting, and self-diagnostic tooling to surface instrument and workflow errors and speed issue resolution.
Write and maintain automation scripts, APIs, and configuration templates that standardize deployment of new workflows onto existing hardware.
Advise on vendor relationships and evaluate new instrumentation, technologies, and partnerships to maintain a state-of-the-art automation platform.

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, including 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, including an employee assistance program, fitness benefits, and employee clubs and activities.
Employee resource groups that are open to all employees.