Associate Director Automation Engineering

Leveraging an automated production platform, JAX’s iPSC repository is projected to become the largest in the world by 2030 by expanding to several thousand lines and enabling next-generation applications in disease modeling and drug discovery. The new Cellular Models production facility will be housed at The Jackson Laboratory for Genomic Medicine facility in Farmington, CT. The Associate Director, Automation Engineering, will oversee the automated systems and serve as the front-line manager for the technologists, ensuring workflow coordination and technical troubleshooting. The role guides the design, implementation, and maintenance of automated instruments, workcells, custom hardware, and robotics solutions that support complex workflows. It combines hands-on engineering (mechanical and electrical), method development, troubleshooting, and operational support with leadership, mentorship, and cross-functional planning. The role collaborates closely with partners across engineering, scientific, data, and project management functions to ensure the platform remains reliable, scalable, and technologically advanced.

For this role, we are seeking candidates who can train for approximately one month at our New York City location and then work full time at our Farmington, CT office.

Key Responsibilities & Essential Functions

• Lead, mentor, and develop the Cell Models team; provide technical direction, delegation, and ongoing coaching. Define best practices for method development, troubleshooting, maintenance, and system upgrades. Establish engineering standards for documentation, validation, safety, and change control.

• Coordinate team priorities and cross-functional communication with Software, Biology, and Platform Architecture teams. Oversee the design, development, and integration of automated instrumentation, robotic systems, and custom hardware across the Global Stem Cell Array. Work closely with biologists to translate manual workflows into automated processes with appropriate controls, liquid classes, calibrations, and failure modes.

• Develop and validate liquid-handling methods across diverse platforms (e.g., Hamilton STAR/VANTAGE, Agilent Bravo, Dynamic Devices Lynx, integrated workcells). Work with related teams to ensure seamless interoperability between automation hardware, instrument control software, LIMS, and data systems. Create custom software utilities (scripts, macros, dashboards, drivers) to support instrument control, monitoring, and workflow automation.

• Design and fabricate mechanical components, fixtures, adapters, and prototypes using CAD, 3D printing, CNC machining, or rapid prototyping methods. Integrate sensors, microcontrollers, actuators, or third-party devices into existing automation platforms. Conduct feasibility assessments, POCs, and platform evaluations for new technologies or robotic solutions. Maintain an engineering-first approach to reliability, ergonomics, and scalability.

• Serve as the highest-level resource for diagnosing and resolving complex system issues—mechanical, electrical, pneumatic, software, or workflow-related. Partner with Software Engineering to integrate instrument behavior with LIMS, orchestration layers, and monitoring pipelines. Collaborate with the Platform Architect to ensure alignment between hardware architecture, data structures, workflows, and interoperable subsystems. Communicate engineering insights and system performance trends to leadership and stakeholders.

• Develop and maintain a comprehensive preventative maintenance and repair program for all automated systems. Ensure systems meet internal quality standards, safety regulations, and research/manufacturing expectations. Train operators and junior engineers on troubleshooting, maintenance, and method debugging.

• Evaluate emerging automation platforms, robotics frameworks, and advanced instrumentation for adoption into the Array ecosystem. Identify opportunities for throughput increases, process simplification, and reductions in human intervention. Help lead technology transfer across sites and support scaling strategies for future automation expansions. Maintain deep familiarity with state-of-the-art tools in lab automation, robotics, machine vision, and process engineering.

Knowledge, Skills, and Abilities

• BS Degree required, Master’s Degree preferred

• 5+ years of hands-on experience developing, maintaining, and troubleshooting automated laboratory systems (liquid handlers, robotics, plate movers, incubators, imaging systems, etc.). Excellent troubleshooting ability across mechanical, electrical, and software layers.

• 3+ years of supervisory experience

• Demonstrated experience leading automation engineering teams or technical projects. Clear communication skills across technical and scientific teams.

• Expertise with one or more automation platforms (Hamilton STAR/VANTAGE, Agilent Bravo, Dynamic Devices Lynx, or similar).

• Strong understanding of mechanical assemblies, robotics, motion control, pneumatics, and hardware integration. Proficiency with one or more programming languages used in automation (Python, C#, C/C++, MATLAB, scripting languages).

• Experience with CAD, rapid prototyping (3D printing), or CNC machining.

• Experience integrating instrumentation via vendor APIs, serial communication, TCP/IP, SiLA2, or custom drivers. Familiarity with LIMS, SQL databases, data pipelines, and workflow metadata structures.

• Comfortable operating in a fast-paced R&D environment with evolving priorities. Highly organized, self-directed, and effective at managing multiple parallel projects.

Pay Range for this opening is $113,718 - $190,388 based on total years of related experience

About JAX:

The Jackson Laboratory is an independent, nonprofit biomedical research institution with a National Cancer Institute-designated Cancer Center and nearly 3,000 employees in locations across the United States (Maine, Connecticut, California), Japan and China. Its mission is to discover precise genomic solutions for disease and empower the global biomedical community in the shared quest to improve human health.

Founded in 1929, JAX applies over nine decades of expertise in genetics to increase understanding of human disease, advancing treatments and cures for cancer, neurological and immune disorders, diabetes, aging and heart disease. It models and interprets genomic complexity, integrates basic research with clinical application, educates current and future scientists, and provides critical data, tools and services to the global biomedical community. For more information, please visit www.jax.org​​​​​​​.

EEO Statement:

The Jackson Laboratory provides equal employment opportunities to all employees and applicants for employment in all job classifications without regard to race, color, religion, age, mental disability, physical disability, medical condition, gender, sexual orientation, genetic information, ancestry, marital status, national origin, veteran status, and other classifications protected by applicable state and local non-discrimination laws.