Research - Laboratory/Non-Laboratory, Staff/Administrative
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The Department of Genome Sciences (GS) is part of the University of Washington School of Medicine (UW SoM) and 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. GS 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. The department has 47 training, teaching, and research faculty.
We have an outstanding opportunity for a Core Developer, Bioinformatics at 75% FTE. The position will play an important role in the development of Percolator, a machine learning engine for analyzing high-throughput mass spectrometry proteomics data. This position requires the ability to design and maintain software testing infrastructure, knowledge of (or willingness to learn about) the analysis of tandem mass spectrometry data in the life sciences, and the ability to collaborate with a small team of developers on a shared codebase. Skills and knowledge needed for this position include programming skills in C++, and familiarity with relevant supporting tools (cmake, Cucumber, git).
The Noble lab at the University of Washington operates at the interface between machine learning on the one hand and genomics and proteomics on the other. The Percolator project is one of a wide variety of parallel projects going on in the lab, and to which the Core Developer will be exposed. Percolator is maintained collaboratively with the Science for Life Laboratory in Sweden, and the project will accordingly involve collaboration and regular interaction with team members in Sweden. Percolator is used by thousands of users around the world, so providing to this userbase robust, stable, and usable software is paramount.
Software development – testing (50%)
•Design and implement an automated testing system for Percolator, aiming to achieve >80% code coverage. •Couple the testing suite with the Percolator build system to ensure ongoing testing.
Software development – new functionality (40%)
•Collaborate with other team members to add new functionality to Percolator, in particular, to allow Percolator to operate on newer “data-independent acquisition” data sets.
•Assist other team members in responding to user queries. •Thrive in a fast-paced work environment that requires independent self-direction with an aptitude for team collaboration and open communication. •Provide support in writing manuscripts, abstracts and presentations. •Present analysis findings at group meetings and national conferences, if necessary. •Other duties may be assigned.
Dimensions and Impact to the University
This position will play an important role in supporting a public-facing software tool, Percolator, that was originally developed at the University of Washington. Ongoing collaborations with labs at the UW and elsewhere will be impacted by improvements to the tool, in terms of speed, robustness, and features.
The Core Developer position is expected to respond immediately to questions from investigators and teammates, and provide expert technical support for users.
•Bachelor’s degree in bioinformatics, computer sciences or related field, or equivalent experience. •3 years computer programming experience •Strong knowledge of basic principles of software engineering and development. •Experience working with C++ and Linux. •Ability to work with computational tools such as cmake, git, and Cucumber. •Ability to manage projects and solve problems independently. •Excellent collaborator with interdisciplinary teams. •Strong written and oral communication skills.
Equivalent education/experience will substitute for all minimum qualifications except when there are legal requirements, such as a license/certification/registration.
•Masters or Ph.D., or foreign equivalent, in bioinformatics, computer sciences, or related field •Knowledge of proteomics, and in particular tandem mass spectrometry.
As a UW employee, you will enjoy generous benefits and work/life programs. For a complete description of our benefits for this position, please visit our website, click here.
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