You are here
Week 4 - More Reading and Simulations, and The Bonneville Dam
Monday, 06/30/14:
Today, I combed through my PDFs to scourer answers of questions asked of me on Friday regarding the simulations. I had trouble finding the topic on coloring of cells, but I tested labels in the Cell Type Specification section of Twedit++. By doing so, I was able to speculate on the green and blue cells from the simulations. I determined that the green cells were always produced but can be labeled arbitrarily by the programmer established (i.e. “Condensing”). The blue cells were the secondary name (i.e. “Noncondensing”), and red cells were produced for the third name. This, of course, only worked if the programmer chose parameters that would allow for a functional simulation.
Eventually, I had my daily meeting with Karen and I informed her of my findings. I was able to get a clearer picture of what to do in the upcoming days. We spoke of calling Matt, one of Karen’s grad students, to help, and renaming the labels for the cells in the Cell Type Specification section. Instead of using “medium,” I can change that to “extra cellular matrix” or “matrix,” and Condensing to “extraembryonic mesoderms” or “Primordial Germ Cell (PGC) precursors.”
Later on, I began reading from “The Mammalian Ovary from Genesis to Revelation”.
Tuesday, 07/01/14:
Decided last minute to visit the Bonneville Dam with the internship cohort. I missed last years, but I’m glad that I went this year.
Wednesday, 07/02/14:
I began reading in the CellDraw_Manual_v.1.5.1.pdf and realized that this will help to initialize cells for simulation (pg. 4). I may need this in the near future. I learned that a “PIFF file, as read by CompuCell3D, is a collection of data points representing cell types, defining the starting conditions for running simulations” (CellDraw_Manual_v.1.5.1, pg 9). Also, “CellDraw has been designed to provide a graphical interface for generating initial conditions without having to manually type PIFF text files” (pg. 10).
Thursday, 07/03/14:
I continued to read through some of my pdfs to better understand the time intervals/steps in the simulations, the units of volume, how different variables are used in a simulation, and the ways to control and regulate cell division. I later had a meeting with Karen and she suggested focusing changing parameters, in a simulation I created, such as rectangular to hexagonal, renaming cell types (i.e. condensing to PGCs); and to fix the One Cell Mitosis simulation. We had a good talk as she helped me to be more at ease as far as what to take out of this internship.
