SOFTWARE ENGINEER
Req #: | 173481 |
Department: | LABORATORY MEDICINE |
Job Location: | South Lake Union |
Posting Date: | 12/03/2019 |
Closing Info: | Open Until Filled |
Salary: | Salary commensurate with education and experience. |
Shift: | First Shift |
Notes: |
Conditions of Employment:
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Our LABORATORY MEDICINE DEPARTMENT has an outstanding full-time position for a SOFTWARE ENGINEER. The person in this position 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.
General Duties:
- 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.
Requirements:
- BS in Computer Science, Engineering, Bioinformatics, Physics, Applied Math or a related discipline OR extensive professional experience in software design and/or development or Bioinformatics AND at least four years of relevant experience.
- Demonstrated programming skills, particularly in Python, R, and sql databases. At least some experience with Python is required. Experience with R is also important.
- 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.
An equivalent combination of education and experience may substitute for stated requirements.
Desirables:
- 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.
Committed to attracting and retaining a diverse staff, the University of Washington will honor your experiences, perspectives and unique identity. Together, our community strives to create and maintain working and learning environments that are inclusive, equitable and welcoming.
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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 dso@uw.edu.