Scott Higgins, Weeks 7/8/9- New Project

Hey everyone! The next three weeks in my EXP experience take a really interesting turn. I had initially planned to be done with my EXP on July 29th, but in case you haven’t read my last blog post, I decided to extend it to further my understanding and get my hands on some more projects. I chatted with my post-doc Kayla on the 29th and she advised me to operate remotely and do things from home for two weeks, work on the coding course and the proposals, while her and the PI, Nick, craft a project for me to do with some of the knowledge I’ve picked up on coding. The lab uses this great interface called Slack to communicate with each other, there are group chats, individual direct messages, and you are also able to send snippets of code! So that’s what I did for that 7th week, continued editing and revising the medical documents and made sure that they were all ready to be sent off the IRB. I worked on my online coding course, which was really interesting, but a learning curve is definitely present in this situation. MATLAB and Python are quite different in terms of their dictionaries and how to perform different functions, so it is something that I was told to work through at my own pace. I briefly talked about the first proposal in the last post, but the two proposals really go hand in hand, with one being a more general primary step, and the second being more focused. The first proposal is for a new translational medicine center within the Columbia Presbyterian Hospital, in which the vast amount of data that our lab has (clinical, genomic, databases, etc.) in combination with coding algorithms will create personalized medical treatment with the lowest risk for adverse drug reaction (ADR) as possible, while also being the most efficient. The Tatonetti group has access to all of the patients data from the hospital in this standardized form known as the Electronic Health Record. Since I’m not board certified/18 I can’t access this, and the EHR to me is like a mythical creature. Everyone talks about it, how great it is, and all of the amazing things it does for them. Sadly I have never seen it! But it’s still interesting to learn about how each of the lab personnel manipulates and interprets these data sets, which I learn about during lab meeting each Wednesday
My mini-break soon came to a close, and I had a meeting scheduled with my post-doc and the PI, to discuss the rest of the summer. I was a little nervous, even though the PI is so nice and actually super cool. We all met and he legitimately took 45 minutes out of his schedule to walk through my next task. Since I am really a beginner in my coding ~career~, this was just for simulation purposes with a focus on developing skills and seeing where things could go. He explained what a binary chemical fingerprint is, which is a unique string of values (either 0s or 1s) that is specific to that chemical compound. You end up with this string after essentially going through a large checklist (355 characteristics) of chemical properties, and if the compound has that property, that codes for a one in that spot, and if not, a zero. 354 values later and you have your string. We thought it would be interesting to see how two different compounds that are similar in the sense that they have the same amount of ones, proportionally, yet not in the same spot, compare with each other. We went through the entire explanation of this, and how to calculate the similarity score by hand (called the Tanimoto coefficient), and then it was on me to code! That’s where I’m at now, working on this assignment. I have to first generate a random string of either 0s or 1s that is 355 values long, with 8% of those values being 1s. After doing this twice, I will compare them to produce the score. Long term, I would loop this function to keep comparing and comparing. Longer term, (aka if I had 4 more weeks), I could use real chemical compound fingerprints. Also, I found out that next week, on my last day, I will be the presenter at lab meeting! I am a tad nervous but I have always loved presenting so I will let you guys know how it goes. Stay tuned for the final installment!

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