Week 8: Fine Tuning Code, Scaling, and Scientific and Technical Writing

Monday, 07/28/14:
    This was a superb meeting with Karen today! After using CellDraw to create the establishment of the domain for the 6 - ~45 PrePGC mitosis to occur, I had trouble running it and was confused about making the non-rectangular (candy cane-like looking surface for the hindgut) surface a cell type. By establishing this surface as so, I thought that it would perform mitosis as well during the simulation; and that’s what happened. After Karen made some incredibly helpful suggestions toward creating a piff file from my CellDraw image and changing the parameters of that same file, and changing the dimensions in my XML code, we got the simulation to run but the candy cane-like surface divided. None the less, Karen was pleased to see the simulation to run closer to what she had suggested. She soon after proposed that I adjust the code so as to make larger cells and reduce the number of steps from occurring.

Tuesday, 07/29/14:
    I had a meeting with Karen and we discussed about how I was doing and what to do next. We ran what was now less steps, but not larger cells. After thinking about the sizing issue, it seemed to be unnecessary for what we needed. Later, Karen suggested that I find out about the cell types available in CompuCell3D, creating boundaries and walls, to keep in mind of the Monte Carlo Steps in one of the PowerPoints I have, how to define a boundary that doesn’t change, and to read about Angiogenesis in the CC3D Manual. I’ve kept some notes about an extra cellular matrix to create the hindgut for our PrePGCs to develop.

Wednesday, 07/29/14:
    I worked on the suggestions Karen presented fro mthe day before and I read through some of the pdfs for help.

Thursday, 07/31/14:
     I presented to Karen what progress I had made after our last meeting. Then, we spoke for quite some time while analyzing documentation and code to understand why we were seeing the hindgut cells dividing. After some time, she decided to leave the hindgut as it was because even thought the hindgut seemed to divide it didn’t change its shape nor allow the PrePGC to infiltrate. This allowed me to make the candy cane-like shape for the hindgut.

Friday, 08/01/14:
    Today, we had a workshop that was run by Jackie Wirz, Ph.D. She works in the library and has her doctorate in biochemistry. Her discussion was on scientific and technical writing. She gave two hours of information and fit it into one hour. She spoke about data, in that it’s complex, about discovery, does not speak for itself, we need to manage it, and it can mean differently to different people. She also mentioned that data is not static, it has a timeline, that there is a difference of what people think about data as opposed to what actually happens. Also, she spoke about how not to go crazy by organizing data in a useful manner, by having a useful data filing convention to follow.
    She also discussed ethics where the institution owns the data. She stated that metadata is data and describes it. Describing it will make our data understandable. In addition, she mentioned workflow analysis tools, and data publishing and sharing. A note was made about communication in scientific writing is important, and that there are four constraints: 1) audience, 2) format (journal, report, thesis, etc.), 3) mechanics (Oxford comma, technical writing practices, and to not stress to much about this), and 4) politics (culture norms). She then mentioned about subjects and action words in our sentences. For example, we can put subjects in verbs, keep subjects near verbs, to write things explicitly, put new information last, use positive voice judiciously, make paragraphs match, and to make sentences clear and concise.
    Later, I had my daily meeting with Karen. She suggested that I make my simulation closer to scale. So, I need to find out how small these cells are and to use graphing paper to help with my scaling. This scaling will help me to make my pixels in my simulation to be closer to reality. She then told me about some poster guidelines for my final presentation.