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Week 1: Getting Started

Mar 12, 2021

Hello all! I am Jiaming Zhang and welcome to my first blog!

My internship is about creating a simulation about population genetics with Professor Matthew Hamilton of Georgetown University. In this week I learned about the specific population we’re working on: Salt-marsh clonal plant population in New Jersey that could reproduce both sexually or asexually. My mentor provides me several articles to read and have an understanding on ways to simulate complex plant population, specifically we aim to use a process called “Approximate Bayesian Computation”, or “ABC”, in our final simulation.

He also send me a sample program about a simulation he wrote and therefore help me to get started in programming. In our meeting this Thursday, we discussed about the program and the articles, that is the first time I realized that coding terms like “for loop” could be so neatly correlated with biology terms like “allele frequency” and statistical terms like “spatial grid”. Since I am not familiar with complex programming, he wants me to write a simplified, “toy” version of that program in python (the ultimate goal is for a program in R, which I need to start learning now) and get more used to concepts mentioned in the articles and the sample program, and be prepared to discuss with him next week.

My research project is to examine the effectiveness and accuracy of simulators like this, so the internship would be a great start on letting me know how these simulations work and what are the potential drawbacks of them. I plan to use the salt marsh plant simulation as one of the examples used in my research. Of course I also need to find empirical data for it, which could be obtained by my colleagues in Prof. Hamilton’s lab, and then compare it with the result of the simulation to reach a solution.

Overall, I am slightly overwhelmed by the amount of things I don’t know at the start of the internship, but I am ready and excited to learn a bunch of useful things to prepare for my future college researches and works.

3 Replies to “Week 1: Getting Started”

  1. Dora X. says:

    Jiaming, your project sounds quite complicated and detailed, but will most definitely offer many new learning experiences for you. I am also doing a similar biology project where I need to learn how to code in R, so I understand how overwhelming everything is! I look forward to seeing your progress as you begin coding. Good luck!

  2. Peter L. says:

    Sounds great Jiaming! I completely understand the process of learning a new coding language, and I am sure that you will master it. Best of luck to your research, and looking forward to what you will do with the empirical data!

  3. Sean P. says:

    Wow Jiaming, your project sounds so complex and exciting at the same time! I find it fascinating that a programming language can be used to simulate population genetics! I can’t wait to hear what you find out. I will definitely stay tuned. Keep up the good work!

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