The Noble Lab in the UW Department of Genome Sciences is recruiting undergraduate CSE majors to carry out research in computational genomics and proteomics. No background in biology is necessary to take part in these projects.
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Annotating big genomic data sets. As part of the National Institutes of Health ENCODE Consortium, we have developed a software analysis pipeline called Segway for automatically annotating the human genome on the basis of large collections of diverse high-throughput sequencing assays. The Consortium has recently completed a third round of experiments, and we are embarking on a new annotation effort based on this new data. The undergraduate would assist in this annotation process. Knowledge of Python is a plus, but not required.
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Differential measurement of 3D genome structure. The UW Center for Nuclear Organization and Function aims to characterize the 3D conformation of DNA in the nucleus of human cells. This project involves implementation and validation of a tool for making sense of Hi-C data, which measures DNA 3D conformation. Ideally, the candidate should be familiar with Python and the Unix environment. Some coursework in statistics is helpful but not essential.
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Software for mass spectrometry analysis. The Crux mass spectrometry toolkit helps scientists analyze and interpret large protein mass spectrometry data sets. The software is command line driven, written in C++ and compiled under Linux, MacOS and native Windows. We need help maintaining the software by responding to user requests and adding new features. Longer term projects may involve improving memory usage, adding new statistical methods, or adding a GUI to the software. Candidates should be familiar with programming in C++.
Each of these research projects will initially be done for research credits. In future quarters, students who perform well may opt to convert to a paid research assistant position. If you are interested in one or more of these projects, please send a resume and transcript to Dawn Counts (dawnc@uw.edu).
The CSE Security Lab looking for an undergraduate to help develop and maintain Confidante, an encrypted email client that makes sending PGP encrypted email easy by using Keybase (https://keybase.io) for automatic key management.
Confidante is built with modern web technologies including React, Electron, and Node.js. This is a great opportunity to learn how to write web apps, improve your JavaScript, and contribute to ongoing research in the security lab.
For more information about Confidante, please contact franzi@cs.washington.edu.
We’re looking for someone for approximately 10-20 hours a week to:
– Help maintain Confidante (fix bugs, respond to user feedback)
– Add new functionality to Confidante (e.g., improving the user interface, adding encrypted drafts)
– Port Confidante to other platforms (desktop, mobile)
We’re looking for someone who has:
– Familiarity with or willingness to learn JavaScript and modern web technologies
– Strong communications skills
– (Bonus points but not required) Experience with Electron or React Native
If you are interested in this position, please send a copy of your resume, a copy of your unofficial transcript, and a paragraph describing your relevant experiences and interests to Franzi Roesner <franzi@cs.washington.edu>
We at the UW’s Clinical Informatics Research Group (http://cirg.washington.edu) are looking for graduate and undergraduate students interested in hourly or RA positions in software development. This is a great opportunity for students to gain experience with open-source software engineering and health informatics. Our group designs, develops, and administers clinical, global, population, and consumer health information systems for both research and usual care.
Requirements:
· Demonstrated development experience with PHP or Python, and database experience with PostgreSQL or MySQL.
· Comfort working with Linux systems at the command line.
· 10-20 hours / week.
Desired experience:
· Python Flask, CakePHP.
· HTML5, CSS, Javascript.
· Development of consumption of RESTful APIs.
· Mobile dev.
· Health informatics.
For more information, please contact either Justin McReynolds (mcjustin@uw.edu) or Dr. Bill Lober (lober@uw.edu). Note that we’re also looking for UI/UX developers (see http://tiny.cc/CIRG-Dev-