Location: Seattle, Washington
Type: Full Time
|The Department of Laboratory Medicine and Pathology serves as a regional resource for clinical laboratory services required for patient care, research and educational programs in laboratory medicine and pathology. The department now employs 900 people who work at the award-winning University of Washington Medical Center (ranked among the top medical centers in the United States as rated by U.S. News & World Report), Harborview Medical Center (the region's only Level I Trauma center, known for innovations and excellence in trauma care and its centers of emphasis: Trauma, Burn, Neurosciences, AIDS/STD CARER, and mentally- and medically- vulnerable populations.), and many other clinical and research facilities in the area. 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 and natural beauty. |
Our LABORATORY MEDICINE AND PATHOLOGY DEPARTMENT has an outstanding full-time position for a BIOINFORMATICS SOFTWARE ENGINEER. The person in this position will support bioinformatics for the clinical next-generation sequencing assays in Virology. The selected candidate will support bioinformatics for the clinical next-generation sequencing assays in Virology. The selected candidate will perform analysis and development work in a state-of-the art clinical laboratory, working closely with M.D./Ph.D. faculty members.
Develop next-generation sequencing data analysis pipelines, preferably developing user-friendly interfaces for running those pipelines, and manage the storage and organization of next-generation sequencing data using both commercial and open source software.
Support of routine data management to support clinical next-generation sequencing assays (i.e., data transfer, analysis, storage, and retrieval).
Administration of scientific computing infrastructure.
Maintenance of software pipelines for data analysis (i.e., maintaining our customized environment, software, and infrastructure for performing analyses).
Design and construction of database tools for managing historical results and interpretive data (such as a database categorizing genomic polymorphisms).
Design and construction of web-based decision support tools providing interpretive information for health care providers.
Develop software that integrates next generation sequencing data with an existing database that tracks molecular microbiology clinical workflow.
Develop software that integrates next generation sequencing data with publicly available databases such the NCBI Genbank (NT/NR databases), taxonomy, and Short Read Archive.
Analysis (sequence database search, alignment, assembly, taxonomic classification, SNP analysis), visualization, and reporting of biological sequence data.
BS in Computer Science, Engineering, Bioinformatics, Physics, Applied Math or a related discipline
Extensive professional experience in software design and/or development or Bioinformatics
At least four years of relevant experience.
Demonstrated programming skills, particularly in Python, R, and sql databases.
Skills with LINUX/UNIX system administration.
Experience with manipulation and analysis of high volume biological data.
Experience with commonly used software tools for biological sequence analysis.
Basic understanding of molecular biological concepts.
Excellent spoken and written communication and documentation skills.
Experience in development of or contribution to open source projects
Experience in collaborative software development (use of version control software, writing and following software specifications, participation in code review)
Knowledge of next-generation sequencing principles
Knowledge of basic molecular biology, virology, clinical genetics, and clinical microbiology.
Wet-bench experience performing PCR and sequencing-based assays
Experience with molecular diagnostics
CONDITIONS OF EMPLOYMENT
It will be necessary to work in other departmental locations in order to meet patient service requirements, especially at Harborview Medical Center. In addition, less frequent work effort will be required at other UW School of Medicine locations (e.g., South Lake Union) and Seattle-area healthcare institutions.
Will be considered essential staff and as such will be required to report to work when scheduled despite inclement weather.
Must be able to meet with all shifts on a regular basis