Project Title: Genetic Simulators: Useful Tool or Scam?
BASIS Advisor: Carrie May
Internship Location: Work from Home, hosted by Georgetown University
Onsite Mentor: Matthew Hamilton
Have you wonder if the simulators you use in Biology class are accurate, or just outputs random numbers? These simulators are written using programing languages such as python or C++, how they work is by accepting input variables and then yielding output data, graphics, or relationships between variables. They are used in fields from high school education to graduate research, yet some of them are over 20 years old! With many different topics—genetic drift, linkage disequilibrium, and estimating reproduction rates—being simulated in population genetics, I want to test if these simulators are accurate. My virtual mentor site, Georgetown University, as well as many other universities, has many published simulators that I can draw samples simulations on. After learning more about the composition of these simulators, I will also program one by myself. Then I will investigate publications by institutions and environmental agencies to gather real world data about population genetics for two or three species in specific locations. The final step is to compare these data with the results of the chosen genetic simulations and the one written by me. The simulations should yield results within statistical random error range compared to the real-life data, if not, it will prove that simulators like this need revision and correction so researchers using them won’t be misled, and students and teachers could use them in class and lab with confidence.
Hi guys, this is apparently the end of the blog series, for those of you who read all my blogs since the first week, I thank you and it is an honor :). The past week I was keep on coding and doing the research on the effectiveness of simulations on representing real life data. […]
Hi guys, how’s everyone doing? Last week’s blog explores the effectiveness of genetic simulations in school teaching, but arguably a more important usage of these simulations in in lab research. This week, in addition to keep working on my own program simulation about clonal plants, I found a awesome research showing the effectiveness of genetic […]
Hi guys! How’s everything going? Last week I ranted about many drawbacks and limitations about simulations, I got so negative because I complained about my programing process, which was not very easy. But that doesn’t mean that there aren’t many positives about these stingy programs, in fact, according to my research, in addition to their […]
Hi guys, what’s up? In the past week I kept on debuging the code while researching on the pros and cons of computer simulations for my final research article. Here are some of my thoughts: There are always limitations and drawbacks of genetic simulations comparing to empirical data in representing scenarios in real life. In […]
What’s popping y’all?! Welcome back to my blog. In this week I’m going to reflect on my findings and results up to this point. Last week I talked about grids used to represent genetic information within a population. Now we finally have some output by the program that can visually better illustrate that point: in […]
Hi guys, welcome back to my blog! I hope all of you had a great Spring break! In the past 2 weeks I finished the transcription of the MATLAB program into python. I also started outlining and writing my final paper, which will discuss the effectiveness of population genetic simulations. Today I want to mainly […]
Hello guys! As I said in last week’s blog, I’m gonna talk more about the biology parts of the internship in this week. The salt marsh plants that we are simulating (above) could reproduce in various different ways: Clonal, aka vegetative, in which no sexual reproduction occurs and the genotype of the “parent” is […]
In this week I meet with the fellow students in Dr. Hamilton’s lab and we had a discussion on the ABC method mentioned last week. The following chart is an example of a population’s genotype probability at various loci. I feel more fortunate than every that I did not sleep too much in Mr. Loomis’s […]
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. […]