Programming for Biology 2016: Gramene’s Continued Commitment to Enabling Science Through Education

By Michael Campbell

The programming for biology course at Cold Spring Harbor Laboratory has be equipping scientists to answer big data questions for 18 years. This year’s course started on October 10th and ran through October 25th.

The investigators at Gramene have seen the value and reaped the benefits of this course as students and as instructors/teaching assistants. This year was no exception. In support of Gramene’s commitment to education and outreach for enabling science, I worked two weeks of 14+ hour days as a teaching assistant for the course.

This is my second year as a teaching assistant for this course. Despite the long hours, I had a great experience last year and have been looking forward to doing it again ever since. Incredibly, students progress from little to no knowledge of the command line, Unix, or programing to writing scripts to address scientific questions untenable with their starting skill set. I was as amazed this year as I was last year at the rate in which the students progress. By the end of two weeks they were writing scripts using programming principles and skills that took me a year in the lab in graduate school to learn and develop.

For the students the course culminates in a small group project. The projects addressed variant prioritization, genome annotation, fusion transcript identification, and more. This is probably my favorite part of the course. The 1:30am nights aside, it is great to see the students teach each other and work together applying their newly developed skills. Top it off with a lobster dinner, and you can’t ask for much more in a course.

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