Automation Engineer

The Automation Engineer will serve as the technical lead for laboratory automation and workflow integration in support of functional cellular assays and high-content screening projects at the Single Cell Biology Laboratory (SCBL) within The Jackson Laboratory for Genomic Medicine (Farmington, CT). The SCBL is a core facility enabling the research community with advanced single-cell omics, spatial profiling, and high-content functional screening platforms. This role is central to the lab’s automation strategy and operational scalability, requiring strong expertise in liquid handling systems, robotic integration, and workflow orchestration across complex assay pipelines.

We are seeking a dynamic, committed, and enthusiastic individual who thrives in a fast-paced, collaborative research environment. You will partner closely with the Associate Scientist for Cellular Models to design, implement, and maintain automated workflows supporting 2D and 3D cell culture, organoids, co-culture systems, and iPSC-based models. You will be responsible for translating experimental workflows into robust, reproducible automated methods, optimizing instrument scheduling and integration, and ensuring seamless coordination between liquid handlers, incubators, imaging systems, and analytical platforms. Experience with high-content or high-throughput screening environments, laboratory robotics, scheduling software, and cross-platform integration is strongly preferred.

Strong communication skills and a collaborative spirit are essential. In this role, you will work closely with SCBL staffs to enhance throughput, reproducibility, and data quality, while contributing to the continuous development of innovative and scalable automation solutions within the SCBL.

Key Responsibilities

• Troubleshoot hardware and software issues across laboratory automation systems (liquid handlers, robotic arms, incubators, plate readers, centrifuges, etc.).

• Perform routine and preventative maintenance—including calibrations, alignments, PM cycles, and minor mechanical adjustments. Coordinate with vendors for repairs, service calls, upgrades, and preventive maintenance activities. Maintain logs, records, and documentation of repairs, calibrations, and system performance.

• Translate manual workflows into automated scripts with appropriate controls, tip strategies, error handling, and labware definitions. Conduct dry runs, wet tests, and QC checks; troubleshoot failed runs with both mechanical and software perspectives. Assist in scaling workflows for increased throughput or expanded use cases.

• Contribute to the design and fabrication of fixtures, adapters, plates, or mechanical components using CAD, 3D printing, or light machining. Assist in integrating sensors, peripherals, or custom hardware into existing automation platforms. Support mechanical prototyping and iterative design processes.

• Analyze data using commercial data analysis packages and effectively communicate results within a team environment.

• Evaluate new automation platforms, instruments, and emerging technologies; run feasibility tests where appropriate. Help implement and test API-based instrument interfaces or middleware components. Contribute to continuous improvement initiatives, such as reducing error rates, increasing throughput, improving reliability, or redesigning labware handling strategies.

• Provide feedback to biologists and software engineers to help refine workflows and user experiences. Draft and update SOPs, method documentation, and troubleshooting guides. Train operators and junior staff on equipment use, maintenance routines, and troubleshooting practices. Communicate results, observations, and system performance to cross-functional teams in a clear, data-driven manner. Work collaboratively in a multidisciplinary environment with scientists, software engineers, data scientists, and project managers.

Knowledge, Skills, and Abilities 

•Experience with Computer Assisted Design, 3D printing, and embedded systems OR microcontroller programming

•Experience with programming/software development is a strong advantage, and demonstrated hands-on experience programming robotic instruments/liquid handlers (Tecan, Biomek, Hamilton)

•Experience writing testable, well-structured, maintainable software or computer programs

•Lab environment experience, particularly with "bench science", e.g. experience using manual pipettes, particularly cell culture.

•Familiarity with laboratory test equipment (signal analyzer, digital multimeter)

Education Level Required / Preferred: Bachelor's Degree / Master's Degree

Experience Required / Preferred: 3 years / 4 years

Pay Range:  $65018 - $108857

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.