Principal Software Engineer – Allen Institute for Brain Science

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 mission of the Allen Institute for Brain Science is to accelerate the understanding of how the human brain works in health and disease. Using a big science approach, we generate useful public resources, drive technological and analytical advances, and discover fundamental brain properties through the integration of experiments, modeling, and theory.

The Allen Institute for Brain Science is at a pivotal moment in the evolution of the Brain Knowledge Platform (BKP) that supports our mission to accelerate neuroscience discovery. With contributions from a growing number of organizations, BKP has become a foundational system for structuring, integrating, and leveraging vast, diverse brain datasets.

We are seeking a Principal Software Engineer to lead the next phase of BKP’s technical development. This individual will play a critical role in architecting a scalable, AI-enabled platform that supports multimodal data, powers scientific tools, and integrates state-of-the-art AI models.

This is a unique opportunity to apply cutting-edge software, data, and AI engineering in a mission-driven environment—helping to unlock the brain’s complexity and catalyze new therapies and insights for human health.

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

Platform Architecture & Scalability

• Design and evolve the Brain Knowledge Platform’s technical architecture to support scalability, performance, and interoperability across diverse neuroscience data modalities (transcriptomic, imaging, connectomics, etc.)
• Lead system-level architecture decisions that enable modularity, extensibility, and integration with external platforms across the BRAIN Initiative and global neuroscience community
• Establish data and service standards that promote long-term maintainability and cloud-native scalability

AI Integration & Scientific Impact

• Guide integration of AI capabilities into the knowledge platform to support intelligent search, hypothesis generation, and cross-modal reasoning
• Ensure the infrastructure supports real-time, data-grounded interactions between AI models and scientific workflows
• Evaluate and adopt emerging technologies (LLMs, vector databases, multimodal embeddings) to accelerate discovery and translational outcomes

Tooling Evolution & Product Leadership

• Contribute to the modernization of flagship neuroscience tools like ABC Atlas and MapMyCells, aligning them with new AI-native architectures and evolving user needs
• Maintain a balance between innovation and operational reliability to ensure ongoing research support and platform usability
• Work closely with product, data, and science teams to prioritize technical decisions that align with strategic goals

Cross-functional Integration & Thought Leadership

• Serve as a technical integrator across multiple teams to ensure architectural alignment and reduce redundancy
• Provide mentorship, code review, and architectural guidance to engineers across the platform
• Represent the Allen Institute in collaborations with external partners, industry experts, and open science consortia

*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 in computer science or related field (or equivalent combination of degree and experience)
• Minimum of 7 years of experience in software engineering, including significant work on large-scale, distributed systems and data platforms
• Proven leadership in architecting cloud-native platforms supporting high-throughput, heterogeneous data
• Deep expertise in designing and deploying AI/ML systems, particularly involving multimodal models or LLMs
• Strong knowledge of modern backend technologies (e.g., Python, Go, Kubernetes, gRPC, Spark, cloud services like AWS or Azure)
• Demonstrated success in leading cross-functional technical initiatives from concept to production
• Familiarity with the entire software tool chain, including source code management (git), build systems, debuggers, linkers, and profiling tools

Preferred Education and Experience

• PhD degree in computer science or related field
• 8 - 11+ years of experience in software engineering, including significant work on large-scale, distributed systems and data platforms
• Experience with scientific data platforms in life sciences, neuroscience, or healthcare
• Experience integrating foundation models (e.g., GPT, CLIP, or domain-specific LLMs) into production data systems
• Excellent communication skills and the ability to collaborate effectively with scientists, engineers, and partners
• Familiarity with FAIR data principles and open science platforms

Physical Demands

• Fine motor movements in fingers/hands to operate computers and other office equipment

Position Type/Expected Hours of Work

• This role is currently able to work both remotely and onsite in a hybrid work environment. We are a Washington State employer, and the primary work location for all Allen Institute employees is 615 Westlake Ave N.; any remote work must be performed in Washington State.

Additional Comments

• **Please note, this opportunity does not sponsor work visas **
• **Please note, this opportunity does not offer relocation assistance**

Annualized Salary Range

$180,350 - $236,650 *

* Final salary depends on the required education for the role, experience, level of skills relevant to the role, and work location, where applicable.

Benefits

Employees (and their families) are eligible to enroll in benefits per eligibility rules outlined in the Allen Institute’s Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute’s 401k plan. Paid time off is also available as outlined in the Allen Institutes Benefits Guide. Details on the Allen Institute’s benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits.

It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities