Coding with Stuart Castaneda, a PINC Mentor

Meet Stuart Castaneda! He is a PINC Mentor and graduate student at San Francisco State University. His current research delves into the HIV-1 subtype B’s different mutation classes and their fitness costs. Stuart utilizes coding to analyze this data! To read more about Stuart, his research and career outlook, as well as what he does as a PINC mentor, please check out his interview below.

  1. How did you get into coding?  

I was curious on how coding could be applied to various biological questions. More specifically I wanted to know how scientist design systems and models to analyze biological data. I learned about the PINC program through a colleague and thought the program would be a perfect fit to solving my questions about coding. I believe my first programming language I was introduced to was Python. After the first class I established a great foundation with the basics and was able to transfer the experience to learn new computer program languages.

  1. How did learning coding skills impact your career/career goals?

After learning how to code, I knew that I would always want a component of coding during my research career. My current research requires coding to analyze and estimate fitness costs of different mutation classes in HIV-1 subtype B. Coding makes this process of analyzing large datasets fast, and reproducible. A great skill I learned during PINC is to annotate my code. This allows others to understand what my code does step by step.

  1. What do you do as a PINC mentor?

As a PINC mentor I try to get to know my mentees and help them with any problems they find during the course. These problems can range from homework to understanding concepts covered in class. So far, I’ve only helped in the first class that all PINC scholars take, CSC 306. In this class scholars are introduced to Python, a computer language that I was first introduced to, and learn the basics of coding. I believe having a mentor in this first class is a great necessity, since this is their first step into the coding world.

  1. What do you like about being a mentor? 

My favorite part about being a mentor is helping my mentees understand computer science concepts. It allows me to think of analogies and visual aids that could explain these concepts that they are having trouble with.

For example, my favorite concept to explain to students is how for loops work. Imagine you’re driving on the road and you are directed into a racetrack. This racetrack will be our “for” loop. As you drive around the racetrack you notice a sign on the jumbotron saying “If you want to exit do 100 laps”. This is your conditional statement that must be met in order to exit the racetrack. The screen keeps track of the number of laps you’ve done and always compares it to 100. As you do your 100th lap the screen says “Exit” and one of the gates lead you back on to the road.

  1. Do you have any advice for students wanting to join the PINC program? 

Don’t be intimidated by learning a new computer language. Learning to code can be daunting at first, but if you have the time and determination, anyone can learn. 

  1. What do you think are the benefits of being a part of the PINC program, both as a mentor and a mentee?

There are several benefits that I received as a mentee in the PINC program. As a mentee I was guided by my mentor on how to approach concepts and problems. Our program coordinators hosted networking events, and professional panels. My favorite experience as a mentee was working as a team with my fellow colleagues. Just like programming professionals, we were tasked to work on a year-long project and had actual deadlines to finish our product. As a mentor I have the opportunity to pass down what I learned to my mentees. This experience as a mentor has given me translational skills to teach future colleagues.

  1. What are your next steps?

My next step is to finish my research project, and graduate with my master’s in science from SFSU. My current project deals with analyzing sequence data of HIV-1 subtype B. I plan to prove that CpG creating mutations are costly to HIV-1 subtype B. This class of mutation has been shown in previous studies to be costly in one region of HIV. My project hypothesizes that these mutations are costly throughout the genome. I plan to begin my PhD in Bioinformatics, at the University of Michigan later this year!

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