Senior Software Engineer – Scientific Instrumentation and Process Engineering

Senior Software Engineer – Scientific Instrumentation and Process Engineering

The Allen Institute accelerates science for a healthier world through large-scale research designed to answer some of the most complex questions in biology. Our multi-disciplinary teams generate foundational knowledge, tools, and data to understand how our brain, cells, and immune system work. We share our work openly so others can build on it, move faster, and ask bigger questions. We drive discovery forward and create new possibilities for improving human health.

We are searching for a Senior Software Engineer that will provide technical leadership and hands-on software development for complex automated systems in which software controls and coordinates hardware. This person will define software architecture, technical plans, development standards, and delivery roadmaps; lead integration across robotics, motion control, machine vision, data acquisition, telemetry, user interfaces, and electromechanical subsystems; establish reliable testing, CI/CD, deployment, and observability practices; and guide systems from early prototypes to maintainable, supportable platforms. The Senior Software Engineer will partner closely with scientists, hardware engineers, systems engineers, and other software engineers to translate scientific and operational workflows into robust, modular solutions that support a range of instrumentation and automation initiatives.

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

• Serve as software technical lead for complex automated and hardware-integrated systems, setting architecture, technical direction, development standards, and implementation roadmaps
• Design, develop, test, and maintain modular software for automated scientific instruments that integrate robotics, motion control, imaging, sensors, actuators, and data systems
• Define stable interfaces, interprocess communication patterns, data flows, and hardware-abstraction layers across complex electromechanical subsystems
• Translate scientific, operational, and system requirements into software specifications, technical plans, milestones, and executable work for the engineering team
• Define and oversee the strategy, standards, and technical direction for CI/CD, automated testing, simulation, release, deployment, telemetry, logging, and observability practices appropriate for reliable laboratory automation
• Lead integration, verification, and troubleshooting across software, robotics, machine vision, and instrument hardware from prototype through validated system operation
• Partner with scientists, hardware engineers, systems engineers, and end users to refine workflows and deliver safe, maintainable, and supportable solutions
• Provide technical guidance, design and code review, and mentorship to software engineers while promoting consistent engineering practices and documentation
• Own software and process technical learning loops aligned with the candidate's interest and skills or team needs
• Evaluate and apply modern software and AI-assisted development tools where they improve engineering velocity, quality, testing, documentation, and long-term maintainability

*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 computer science, software engineering, computer engineering, robotics, or a related technical field, or an equivalent combination of education and experience
• At least 5 years of professional software engineering experience, including technical leadership for complex systems or products
• Demonstrated experience architecting and delivering maintainable, modular software for automated, robotic, scientific, industrial, or other hardware-integrated systems
• Professional experience developing software in Python, C++, C#, or comparable languages used for instrument control and automation
• Demonstrated experience integrating software with hardware devices, including motion systems, cameras, sensors, actuators, data-acquisition devices, or related instrumentation
• Demonstrated experience with source control, code review, automated testing, continuous integration, release management, and technical documentation
• Demonstrated experience translating system and user requirements into software architecture, interfaces, implementation plans, and delivered functionality

Preferred Education and Experience

• Master’s degree in computer science, software engineering, robotics, or a related technical field
• 10+ years of professional software engineering experience, including experience with robotics, motion planning or control, machine vision, image processing, and precision automation
• Experience with distributed systems, interprocess communication, hardware abstraction, device APIs, and event-driven or state-machine architectures
• Experience with safety critical software and software architecture including leading qualification and reliability campaigns and operationalization, maintenance, and support of reliable systems
• Experience developing user interfaces, data acquisition and management workflows, telemetry, logging, and system health monitoring for scientific or industrial equipment
• Experience moving prototypes into reliable production or laboratory operation, including verification, validation, deployment, and sustainment
• Experience collaborating across scientific, software, electrical, mechanical, and systems engineering disciplines
• Experience mentoring engineers and influencing technical standards across a team
• Experience using AI-assisted engineering tools responsibly to accelerate development, testing, documentation, or maintenance

Work Environment

• Work is performed in office, software-development, engineering, and laboratory environments
• Regular onsite work with automated scientific instruments, robotics, imaging systems, and electromechanical prototypes
• Possible exposure to laboratory materials or chemical, biological, mechanical, electrical, or other hazards; use of required personal protective equipment and adherence to established safety procedures are expected

Physical Demands

• Occasional lifting up to 30 pounds
• Fine motor movements in fingers and hands to operate computers, instruments, and other office or laboratory equipment
• Occasional pushing or pulling of laboratory carts or equipment up to 50 pounds
• Occasional stooping, bending, crouching, and reaching while integrating or servicing equipment

Position Type/Expected Hours of Work

• This is a full-time, exempt position with standard business hours
• Occasional evening or weekend work may be required to support instrument integration, testing, deployment, or time-sensitive project milestones
• This role is currently working onsite and is expected to work onsite for the majority of working hours. The primary work location for this role is 615 Westlake Ave N., with the flexibility to work remotely on a limited basis.

Travel

• No travel is required

Additional Comments

• **Please note, this opportunity does not offer relocation assistance**
• **Please note, this opportunity does not offer work visa sponsorship**

Annualized Salary Range

$170,350 - $212,900 *

* 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.