Research opportunity in scientific computing
The Noble lab in the Department of Genome Sciences develops machine learning and statistical methods for interpreting complex genomic and proteomic data sets. We currently have openings for undergraduate CSE students interested in helping to improve our existing Crux software for tandem mass spectrometry analysis.
- Optimization. The Crux command “tide-index” fragments a given database of protein sequences into constituent parts (called peptides) using a predefined set of rules. The program as currently implemented uses more memory than it needs to and is somewhat slow. This research involves speeding up and reducing the memory footprint of this code.
- User interface design. The Crux software is currently implemented as a series of commands, implemented in a single binary and compiled under Linux, MacOS and native Windows. A graphical user interface, implemented in an appropriate cross-platform language, would facilitate use of the toolkit by biologists. This research involves designing, implementing and testing the user interface.
Students interested in signing up for research credits for either of these projects should contact Bill Noble (wnoble@uw.edu).