Josh Ives, Computational Biology at CMU, Week 1

Hello everybody, this is Josh Ives. I just started my internship at Carnegie Mellon for Computational Biology.

This first week of my internship was a very exciting one as I got started on my Pinternship. I began this week having only a basic understanding of what computational biology even was and the intensive learning I’m undergoing has only shown me how much farther their is to explore in this field. I  was blown away. To put it “simply,” computational biology is using computers to analyze biological datasets, which modern data collection techniques have made too large for humans to understand on our own. Myself and approximately 3o other interns/students–who are highschoolers just like me–prepared DNA that we extracted from river water for sequencing. When highschoolers can do that, and even the simplest Genome has millions of base pairs the data quickly becomes overwhelming. Computational biology uses computers to help solve that problem

Speaking of sequencing DNA extracted from river water (one of the coolest sentences I have ever been able to say about myself) one of the highlights of the week was going out on a river boat to get that river water and then bringing it back to the lab the next day to add different chemicals to it and run it through a centrifuge about a million times under the watchful eye of Josh Kangas (or as we call him: mentor Josh). This prepares the DNA for sequencing and is the same process that professionals use. Doing this with Elliot (my lab partner) wearing cool purple lab coats and rubber gloves the entire time made me feel like a scientist of the highest caliber regardless of the truth of the matter. Unfortunately I wasn’t able to get any photos of this because touching your phone–which frequently touches your face and hands–in a microbiology lab where various bacteria, viruses, prions, etc… are cultivated  is very ill advised.

The remainder of my time learning was spent in a computer science lab where we learned the computational side of Comp-bio. This was fairly simple at the beginning, but very quickly ramped up and became a test of mental flexibility as Philip Compeau led us through the various techniques of analyzing gene sequences. Both Philip and mentor Josh are absolutely amazing people, professors and experts. One of the first things they did upon meeting us was insist we use their first names. Theirs is among the only classes I have ever been in that was promised to be fun that actually delivers in full. I truly cannot extoll their virtues enough.

As far as fun goes I have been fortunate to find a great group to hang out with (I was lucky enough to be surrounded by people my age) and we have done nothing but go on adventures and play great games since I got here. Of particular note was our visit to Phips which is the botanical gardens near CMU. They have incredible glass sculptures among incredible plants displayed in an incredible way. I’m fairly sure you all can figure out what word I most like to use to describe Phips. This, I was able to get photos of but they don’t do it justice so if any of you reading are ever in the Pittsburgh area, I highly recommend it.

Thank you so much for reading. I’m looking forward to a wonderful week two.