System Design Engineer, Principal

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Current job opportunities are posted here as they become available.

The mission of the Allen Institute

to understand the principles that govern life, and to advance health. Our creative and multi-dimensional teams focus on answering some of the biggest questions in bioscience. We accelerate foundational research, catalyze bold ideas, develop tools and models, and openly share our science to make a broad, transformational impact on the world.

Allen Institute for Neural Dynamics is seeking a Principal System Design Engineer

to join the Scientific Instrumentation and Process Engineering (SIPE) team. In this critical role, the principal engineer will lead the design and integration of advanced scientific instruments, developing innovative and robust solutions that meet the complex demands of neuroscience research. Responsibilities include setting technical direction, mentoring senior engineers, and ensuring all design and execution processes meet the highest standards of excellence.

Candidates

for this role should possess extensive experience in systems engineering

with a proven background in integrating both hardware and software components. The ability to lead multidisciplinary teams is essential, as collaboration is a key aspect of the SIPE team’s approach. Mastery of system design principles is required, along with demonstrated leadership in technical innovation.

At the Allen Institute, we believe that science is for everyone – and should be open to everyone.

We are dedicated to combating biases and reducing barriers to STEM careers more broadly. We also believe that science is better when it includes different perspectives and voices. We strive to make the Allen Institute a place where everyone feels like they belong and are empowered to do their best work in a supportive environment. We are an equal opportunity employer and strongly encourage people from all backgrounds to apply for our open positions.

Essential Functions

• Spearhead the architecture, design, and integration of complex scientific instruments that combine robotics, imaging, automation, and control systems
• Serve as a pillar of technical leadership for SIPE initiatives, providing guidance to senior and mid-level engineers and overseeing collaborative development efforts that span both hardware and software domains
• Manage projects from concept through production, including feasibility studies, prototyping, and final rollout, while formulating comprehensive project plans to ensure timely delivery
• Collaborate with scientific stakeholders to capture system requirements, translate them into actionable team tasks, and remain engaged throughout prototyping and development
• Set and refine standards for engineering processes, including documentation, validation, source code management, issue tracking, deployment procedures, and observability
• Design, develop, evaluate, and implement equipment for control operations, data acquisition, and analysis workflows, ensuring reliable collection of large-scale datasets
• Leverage broad technical expertise and creativity to resolve complex challenges
• Champion organizational strategies that enhance innovation, open science, and operational efficiency

Note:

Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects management’s assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.

Required

Education and Experience

• Bachelor’s degree in mechanical, electrical, optical, or systems engineering, or related field; or equivalent combination of education and experience
• 7 years of progressive experience in system design engineering, including leadership of complex instrumentation projects
• Demonstrated success in delivering production-ready systems for scientific or medical instrumentation

Preferred Experience and Competencies

• Master’s degree or PhD in mechanical, electrical, optical, or systems engineering
• 15+ years of combined education and experience in multidisciplinary system design
• Multidisciplinary expertise:
  Demonstrated…