Software Engineer II – Scientific Instrumentation and Process Engineering

Software Engineer II – 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 Software Engineer II to build, test, and support software for automated scientific instruments and hardware-integrated systems. Working with guidance from senior engineers, this person will implement well-defined features and components spanning user interfaces, data collection and transfer, infrastructure automation, DevOps, testing, documentation, and hardware-integrated workflows. The Software Engineer II will collaborate with scientists, hardware engineers, systems engineers, and software engineers to translate defined scientific and operational needs into dependable software for laboratory instrumentation. This role is designed for a growing professional who can handle a broadening range of assignments with increasing independence, adapt to changing priorities, and contribute practical improvements within established architecture and technical direction.

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

• Develop, test, and maintain well-defined software features and components for automated scientific instrumentation and laboratory automation platforms under established architecture and technical direction
• Implement user interfaces, data collection and transfer workflows, infrastructure automation, and supporting services needed for reliable laboratory operation
• Contribute to modular designs, device interfaces, data flows, and hardware-abstraction layers while following patterns defined by senior engineers
• Integrate software with assigned robotics, motion-control, imaging, sensor, actuator, and data-acquisition components using documented interfaces and requirements
• Write and maintain unit, integration, and automated tests; participate in CI/CD, release, deployment, telemetry, logging, and system-monitoring practices
• Support system integration, verification, troubleshooting, and laboratory operation from prototype components through integrated platform testing
• Collaborate with scientists, hardware and systems engineers, software engineers, and end users to clarify defined workflows, resolve issues, and adapt implementation as priorities evolve
• Participate in design and code reviews, maintain clear technical documentation, and propose practical improvements to team processes and software quality
• Use modern software and AI-assisted development tools responsibly in accordance with team standards

*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 3 year of professional software engineering experience developing, testing, and maintaining software applications or services
• 2 years of experience with robotics, motion planning or control, machine vision, image processing, and precision automation
• Professional experience developing software in Python, C++, C#, or a comparable language
• Experience implementing well-defined features or components within an existing software architecture
• Experience with source control, code review, automated testing, debugging, and technical documentation
• Ability to work collaboratively across disciplines, respond to changing priorities, and complete assigned work with increasing independence

Preferred Education and Experience

• Experience developing software for scientific instrumentation, laboratory automation, robotics, industrial systems, or other hardware-integrated environments
• Experience integrating software with cameras, motion systems, sensors, actuators, data-acquisition devices, or device APIs
• Experience with safety critical software development and testing
• Experience with design for maintenance and support of a software product
• Experience with CI/CD, infrastructure automation, deployment, telemetry, logging, or system health monitoring
• Experience developing user interfaces and data collection, management, or transfer workflows
• Exposure to interprocess communication, event-driven systems, state machines, hardware abstraction, machine vision, or image processing
• Experience supporting integration, verification, troubleshooting, or operation of prototype or production systems
• Experience using AI-assisted engineering tools responsibly for 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 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.

Travel

• No travel is required

Additional Comments

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

Annualized Salary Range

• $121,450 - $151,800 *

* 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