Week 3: On Track

Mar 26, 2021

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.

A field of salt marsh plants in coastal plains, with some empty spots representing dead plants in the previous generation


The salt marsh plants that we are simulating (above) could reproduce in various different ways:

  1. Clonal, aka vegetative, in which no sexual reproduction occurs and the genotype of the “parent” is inherited in the progeny (offspring). Only need to make sure there is one “parent” plant able to clone at that area to produce progenies.
  2. Outcrossing, the type of sexual reproduction that requires 2 parent, both parent pass genetic information to offspring.
  3. Selfing, the type of sexual reproduction that requires only 1 parent, whose genetic information will pass to offspring.

In the simulation, we imagine a field of plants and their generations, each generation has some plant dies at random chance, leaving their spots vacant. At those vacant spots there will grow new plants using one of the three methods above. The plants’ genotypes and their relative locations in the field are recorded. The idea is that if a section of field is empty with no other plant adjacent to it, there will be no chance for it to regrow, at least not from the center, since refilling it requires reproduction starting from the edge of the area.

The simulation program mentioned above that I am working on was originally in a format of MATLAB, a subordinate of the Mathematica language. It was written by my mentor and I am transcribing it into python, which is a quite different language. I transcribed 5/17 functions of it in the past week, I am trying to finish transcribing it in the next 2 weeks (hopefully I can get some work done over the spring break). This simulation program will be crucial for the next step, which involves the R language and even more statistical programming, so I am looking forward to see that (unsarcastically).

Anyways, have a nice spring break and see you in 2 weeks!

One Reply to “Week 3: On Track”

  1. Dora X. says:

    This sounds great! It’s really nice that you’re learning the biology aspect of your project along with the computer science applications. You’ve made good progress so keep up the good work with transcribing!

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