SOFTWARE ENGINEER – University of Washington – Seattle, WA

The University of Washington (UW) is proud to be one of the nation’s premier educational and research institutions. Our people are the most important asset in our pursuit of achieving excellence in education, research, and community service. Our staff not only enjoys outstanding benefits and professional growth opportunities, but also an environment noted for diversity, community involvement, intellectual excitement, artistic pursuits, and natural beauty.

The Department of Electrical Engineering at the University of Washington is a nationally ranked education and research program. Located on the main Seattle campus of the University of Washington, UW Electrical Engineering currently supports greater than 750 undergraduate and graduate students and over 50 active research faculty. EE’s annual expenditures reach approximately $19 million and its external funding is close to $25 million. The Department has several key areas of research: communications/networking, electromagnetics/remote sensing, big data, integrated systems/circuits/VLSI, nanotech and photonics, power and energy, speech/image/video processing and systems/controls and robotics. Supporting over 470 undergraduate, 300 graduate and 100 professional students in their educational efforts, the Department has proven to be a leader in both education and research areas, as well as effectively leveraging intellectual and entrepreneurial engagement at all stages of research.

The UW BIOFAB ( is a semi-automated, human in the loop, molecular biology lab in the cloud service. The BIOFAB is controlled by the Aquarium software (, which was designed in-house to control every aspect of the lab. The BIOFAB allows users to design experimental workflows, which technicians execute. Users can attach upstream design tools, and send data to downstream analysis software. The key innovation in our approach is our use of people to perform many of the steps in the workflows, making the system flexible and reconfigurable. The Aquarium software compiles experimental workflows into very specific steps presented at touch screen monitors throughout the lab, instructing technicians to retrieve samples, perform various operations on them, place them in instruments to produce data, and so on. Presently, the BIOFAB system includes an extensive workflow language, a backchaining workflow generator, an API for 3rd party upstream design algorithms, and an API for downstream data access. We currently run hundreds of experiments a week for about ten research labs at UW, the Hutch, and Caltech as well as several industry partners in Seattle and the Bay Area.

We have an outstanding opportunity for a lead Software Engineer to help transform the current software into a highly robust, capable, and extensible cloud based application with possibly thousands of users across multiple universities. This effort will include implementing data security, user and organization privacy, a unified user experience, integrated machine learning, dynamic documentation, and the development of standards for representing biological workflows. The lead developer will work with a highly interdisciplinary team of about 20 engineers, biologists, and lab technicians who are building the world’s first modular, cloud-based, programmable laboratory.


-Design and implement software for release that is robust, usable, and scalable. Evaluate and select appropriate technologies to support requirements at all levels, including but not limited to dev ops, server backend, databases, and user interfaces.

-Lead a small team of software developers including professional staff, researchers, and students.

-Work alongside domain experts to ensure the validity of algorithmically generated biological workflows.

-Organize the release and distribution of the Aquarium software and workflows to make them available to researchers around the country.

-Maintain and update existing software after its release to the public. Interact with users and respond to their feedback.

-Rapidly develop prototypes of new features or other applications for evaluation during projects’ early brainstorm phases.

-Interact with researchers, lab managers, and technicians at UW and at collaborating institutions to assess and advance the usability of the software.

-Gather and analyze usage data, including running statistical analyses, and creating data visualizations.

-Assist in creation of figures, text, and videos for publications and dissemination.

-Travel to and participate in meetings organized by our government funders.


Bachelor’s Degree in Computer Science or related field and 7+ years of experience in software engineering (not necessarily in biotech). Includes at least 7 years of research management or software development management experience.

Additional requirements:

-Demonstrated ability to release quality products on schedule.

-Must have excellent communication and documentation skills.

-Demonstrated ability to work both in an interdisciplinary team and independently.

-Fast turnaround times and ability to work in a fast-paced, dynamic environment.

-Ability to multitask and work with multiple teams simultaneously.

-Has experience working with and managing a team.

-Has implemented and deployed complex, full stack applications.

-Is an expert in MySQL, Ruby on Rails, and Javascript (preferably AngularJS).

-Has developed software in a test-driven environment.

-Has experience with DevOps and AWS based cloud applications.

-Is willing to learn new skills.

Equivalent education/experience will substitute for all minimum qualifications except when there are legal requirements, such as a license/certification/registration.


– Journal or conference publications.

– Prior work experience in an academic research setting.

– Passion for biotechnology.

– Experience in cloud based software.

– Strong math skills.

– JSON experience.

– Proficiency in Docker, Capistrano, Python, UNIX.

– Mobile phone development experience.

– Has implemented machine learning and statistical inference algorithms.

– Has managed open source, community based projects on github.

– Has managed an agile development process to respond to users, feature requests, and bug reports.

– Has produced thorough written and video-based documentation.


Appointment to this position is contingent upon obtaining satisfactory results from a criminal background check

Application Process:

The application process for UW positions may include completion of a variety of online assessments to obtain additional information that will be used in the evaluation process. These assessments may include Work Authorization, Criminal Conviction History, Cover Letter and/or others. Any assessments that you need to complete will appear on your screen as soon as you select “Apply to this position”. Once you begin an assessment, it must be completed at that time; if you do not complete the assessment you will be prompted to do so the next time you access your “My Jobs” page. If you select to take it later, it will appear on your “My Jobs” page to take when you are ready. Please note that your application will not be reviewed, and you will not be considered for this position until all required assessments have been completed.

The University of Washington is a leader in environmental stewardship & sustainability , and committed to becoming climate neutral.

The University of Washington is an equal opportunity, affirmative action employer.
To request disability accommodation in the application process, contact the Disability Services Office at 206-543-6450 / 206-543-6452 (tty) or [email protected] .

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