Software Engineer | GenomeWeb

Software Engineer

University of Washington - Genome Sciences Department
Job Location
Seattle, WA
Job Description

The Department of GENOME Sciences at the University of Washington has an outstanding opportunity for a Software Engineer in the Northwest Genomics Center. Core responsibilities include the following:

Software development
=> Develop software and scripts designed to analyze genetic data or facilitate genetic data production.
=> Include but not limited to development of genetic analysis algorithms, sequencing pipeline scripts, webpages, databases and other tools.

Requirements gathering
=> Interact with the management and the technical staff to gather requirements for the specific needs of the software to be designed in terms of overall function, fit with the process in the lab, and the need for reporting and analysis by managers.
=> Familiarize and understand the broad strategic objectives of the NWGC.
=> Attend GENOME Sciences and University meetings, retreats, status updates, orientations and planning days when necessary.

The successful candidate will play an important role in the design and development of research-related, custom software used in a high-throughput, second-generation DNA sequencing Laboratory. He/she must have the ability to dissect and analyze complex research questions using a multitude of programming languages that interact with existing software architecture. The person in this role must be highly organized, committed, and have the ability to work alone and in complex teams.

As a UW employee, you will enjoy generous benefits and work/life programs.


Bachelor of Science degree in computer science, engineering, or related field and a minimum 4 years of experience working in scientific computing environment to include: LINUX, UNIX, Windows; implementing scientific algorithm and software testing methodologies.

Additional Requirements:
=> Must be skilled in designing, developing and maintaining relational databases.
=> Must have demonstrated experience in the life-cycle of software development from requirements gathering through production and release.
=> Publication record demonstrating success at building software to support scientific research
=> Knowledge of laboratory information systems (LIMS) design and implementation.
=> Must be able to work with Java Servlets and scripting languages.

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

=> Knowledge of biology, genetics, genomics, and/or DNA sequencing
=> Experience working with generalized database design schemata
=> Experience with other programming and scripting languages (i.e. Perl, Python, Java, and R)
=> Experience with management of high-throughput data
=> Experience managing bioinformatics and IT groups
=> Experience developing LIMS (laboratory information systems) in a high-throughput environment
=> Analytical and troubleshooting skills for wet-bench laboratory protocols.
=> Knowledge of next-generation (Illumina) DNA sequencing chemistry.
=> Knowledge of next-generation sequencing protocols and analysis packages (GATK, SamTools, etc).

Condition of Employment:
Appointment to this position is contingent upon obtaining satisfactory results from a criminal background check.

How to Apply

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 Workforce 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.

About Our Organization

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 GENOME Sciences is comprised of 27 labs addressing leading edge questions in biology and medicine by developing and applying genetic, genomic and computational approaches taking advantage of genomic information now available for a host of species. The Department of GENOME Sciences is making major contributions in the application of GENOME science to understand the fundamentals of biology and to improve human health and well-being.

GENOME Sciences is a collaborative department supported by very different academic disciplines. We work with a multitude of Program Investigators (PIs) in departments both on the UW campus as well as worldwide. The department has gone through significant expansion since its beginning in 2001 with annual grant expenditures doubling between FY08 and FY10 and federal awarding in FY10 of $44M. The department has 41 core training, teaching, and research faculty.

The Northwest Genomics Center (NWGC) is involved in various research programs that require the processing of over thousands of samples per year, and has a focus on the identification of DNA variants in human populations. The NWGC also provides service to the University and other local labs as a cost center. The Software Engineer will develop and implement new software, algorithms and scripts for the analysis of genetic data for the NWGC.

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