Track: Bioinformatics
Undergrad: University of Oregon, Eugene, OR - Computer Science and Biology
Internship: Oregon Health and Science University
Current Job Title: PhD Student in Computer Science, University of Oxford and Principal Engineer, Omics Data Automation, Inc.
How did you find yourself at Oregon? What about the program attracted you?
I heard about the program from a friend in a lab I was working in at UO. The most attractive thing about the program was that I could get real world experience, which a lot of master’s programs lack.
What was the intensive summer like for you?
The summer intensive was a lot of fun for me. I was able to sharpen my coding/computational skills as applied to the biological realm, while at the same time learning how to talk to people of all disciplines about how to approach problems. There was never a dull moment in the summer. If we weren’t in class, then the whole group was in the lab helping each other with assignments and projects. Since all the work in the course was very hands on, I learned way more than I would from just taking a normal lecture course.
Where was your internship?
My internship was at the Computational Biology department at Oregon Health and Science University (OHSU).
What was your internship like? What are you responsible for? What is a typical day like?
For my internship, I worked on a collaborative project with OHSU and Intel called the Collaborative Cancer Cloud (CCC), which is a federated platform meant to facilitate data, workflow, and analysis sharing among cancer researchers all over the world. I was responsible for working on a large team of 30 engineers to do both software development with and work as a research consultant to the Intel engineers. I worked on countless problems: designed and implemented use cases for the platform, developed and dockerized workflows, wrote analysis scripts, implemented and deployed data management systems, implemented data standard APIs (GA4GH) on top of a database specifically designed for efficient querying of large scale variant data, built web applications to visualize biological data, gave demos of our products, etc. My typical day consisted of a combination of all of those tasks.
Do you feel the program prepared you for the internship? In what ways?
I feel the program definitely prepared me for my internship. I learned about all of the important data types and common analysis techniques of a bioinformatician, which came in very handy when developing use cases and thinking about what sorts of visualization tools researchers would want to use. I learned how to quickly research and think creatively about problems, as well as how to communicate effectively to colleagues.
How did your internship prepare you for your current position/career path?
My internship has given me a great look into how technology can be used to advance the field of bioinformatics, as well as how to work with a team of talented people of mixed backgrounds to solve complex problems in the field.
Do you have any advice for prospective students?
Enjoy the summer and take advantage of your peers as much as possible. Every person in the program has something special you can learn from them. You will not only get an education and real world experience, but you will meet so many great people who are going through the same intensive summer as you.