Software Engineer III, Cloud Services - Brain Health

The mission of the Allen
Institute is 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.

The Allen Institute is launching a new accelerator on human brain health and disease. This initiative aims to dramatically accelerate our understanding of human brain structure and function, identify the molecular, cellular and circuit basis of disease progression, and pioneer new therapeutic strategies targeting vulnerable and affected cell types. Our mission focuses on taking a human-centric approach to understanding and treating disease, combining a large-scale open science discovery approach across multiple diseases, AI-based disease modeling, and translational programs in specific diseases to move from discovery to clinical application.

We aim to make transformational change in understanding and treating brain disorders, the biggest health challenge of our time.

We are seeking a Software Engineer III, Cloud Services with deep expertise in software engineering, cloud architecture, and security standards to drive the design, delivery, and operation of secure, scalable infrastructure supporting international, cross-institution collaborations and research in neurodegenerative diseases. This role requires both strategic vision and hands‑on execution to enable the storage, processing, and analysis of high-volume scientific data and the development of platforms that make these data accessible to international collaborators and the global research community.

As one of the first engineers on the Brain Health data and technology team, you will be responsible for contributing to our team’s vision, architecting and overseeing complex technical programs, and ensuring that cloud infrastructure is secure, reliable, compliant, and cost-effective. You will serve as a key technical partner to research and engineering teams, collaborate closely with engineers and solution architects from cloud providers, and represent the Institute in engagements with external vendors and collaborators.

The successful candidate will collaborate closely with system administrators, software engineers, neuroscientists, data scientists, and cross‑institutional partners to advance the Institute’s scientific mission.

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.

• Design and oversee implementation of secure, scalable, and compliant cloud‑based systems for scientific data processing
• Ensure adherence to regulatory and security standards (e.g., NIST SP 800‑171) where applicable
• Guide infrastructure optimization efforts, including performance tuning and cost management
• Represent the Allen Institute in technical discussions with external vendors (e.g., cloud providers) and scientific partners
• Collaborate effectively with engineers and architects from cloud providers and other vendors and partners
• Build and maintain strong relationships with internal stakeholders, including research teams, Central IT, and the Office of the CTO
• Translate complex technical concepts into clear, actionable insights for diverse audiences
• Collaborate with science teams to define requirements, scope, and priorities
• Identify risks, dependencies, and trade‑offs, and proactively drive mitigation strategies
• Oversee production readiness, monitoring, and incident response processes
• Ensure reliability and maintainability of deployed systems
• Foster effective communication across cross‑functional…