Week 5 - Fine Tuning CompuCell3D and Prepping for Grad School

Monday, 07/07/14:
    I read from my CompuCell3D Reference Manual and Introduction to CompuCell pdfs to help me to make changes for my simulation. I also had a meeting with Karen about starting my simulation as a hexagonal image as opposed to square because hexagonal seem closer to a realistic start for cells.

Tuesday, 07/08/14:
    I had Professional Development Workshop #3 that was lead by Wendy Smythe and was about preparing for grad school and its funding. She spoke about curricula vitae vs. resumes, tips for funding graduate school, a checklist for evaluating the personal statement, developing the personal statement, writing tips, critiquing my statement, and types fellowships for graduate school. I also continued working with CompuCell3D to produce Karen’s suggested simulation.

Wednesday, 07/09/14
    I continued rewriting code so as to produce a cell mitosis that started with six cells. Now, I need to figure how to get them to 42 cells. I continued reading from my CompuCell3D Reference Manual and Introduction To CompuCell3D.

Thursday, 07/10/14
    I met with Karen about the simulations and we refocused. She suggested that produce a new folder for a working simulation to be our foundation module. I agree wit this because we don’t have to rely on CompuCell3D demos as out foundational code. I started this process and called it mouseOvarianDevelopment.

Friday, 07/11/14
    After some struggle with the simulations, I was able to produce something close to what Karen wanted. My simulation started with a hexagonal lattice, and six non-adjacent cells. Karen later decided to start with a square lattice because it was producing a strange simulation where cells were decreasing in size. That’s the opposite of what we want.! We also changed the steps to 1000, neighborhood order to 2, added surface parameters, and changed the contact of the cell from condensing to PrePGC. Based on the research available, the PrePGCs are what the cells are at this point of development. For this simulation, I borrowed most of the code that was useful for producing out stappableBasedMitosissimulation. Later, I attended a seminar on applying for graduate school and it’s funding, and discussed how to survive when there. This was a useful talk since I’m attending grad school in the fall at the University of Washington. Krissy Remple was the main speaker, with Ph.D. student discussed finding a researcher with whom I can work well, dealing with advisors, expectations for graduation, and learning a skill set in grad school.