Week 1 - A New Beginning

I'm here for another summer of CMOP research! I'm looking foward to learning and producing some useful research!

Monday, 06/09/14:
    I, and other CMOPers started the day with Vanessa Green orienting us for this CMOP internship. We saw the some of the OHSU campus, had Tai for lunch, and met with our P.I.s and front line mentors. Life in this internship is tremendously different than last years. Being in the city is raising some interesting challenges for us, but it seems that we are dealing with them quite nicely. I’m already enjoying this new batch of interns and I’m looking forward to having a great summer with them! These last couple of days, I’ve been briefly catching up with CMOP staff and I’m so glad and blessed to see them once again. It’s like I hadn’t left.
    I finally got to meet Dr. Karen Watanabe, and we started going into our project. I’m dealing with ovarian development in mice and attempting to produce a working model in CompuCell3D that represents 1-time or an entire 22 days of ovarian development. She also forwarded to me some relevant background documents regarding our project. I gotta say that this project sounds very interesting and Karen has been a very person with whom to speak.
    Near the end of the day, Amy Johnson let me know that I didn’t have to work in the basement of the building; so that’s quite nice! LOL I was moved to one of the 3rd floor labs, so I’ll be close to Karen. That will help me out a lot. While getting situated at my new desk in the lab, I met Riku and Youmbo who are my desk neighbors. They seem like pretty nice guys.

Tuesday, 06/10/14:
    I started the day by downloading CompuCell3D and Cell Designer. “CompuCell3D is an open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms. It uses Cellular Potts Model to model cell behavior” (http://www.compucell3d.org/). “CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks” (http://www.celldesigner.org/). Then, I had lunch with Krissy Remple, Sheree Watson, and others from CMOP at the weekly farmer’s marker here on campus. Shortly after, I had a meeting with Karen, and met matt McPike at noon. During that time, she allowed me to look through a book that had some relevant information. Eventually, I started looking into the CompuCell3D tutorials.
    I went the CompuCell3D website and clicked onto the tutorials link. When there, it demonstrated how to run a 2D simulation (http://www.compucell3d.org/Tutorials?action=AttachFile&do=get&target=cc3...). I was successful replicating the simulation. This application worked with my command prompt to allow me to build a simple CompuCell simulation from scratch (https://www.youtube.com/watch?v=J7cDWJv5t80). While there, I was able to see the code for a simulation. This simulation used Python and XML. This is pretty cool!

Wednesday, 06/11/14:
    I started my morning by having a meeting with Karen about where I’m at in project and discussing more about where to focus. Next, I began reading into the Python Scripting Manual to CompuCell3D, then looked up on some background on Python online, and read some more in my articles to the biological aspects of ovarian development in mice.

Thursday, 06/12/14:
    I continued reading about CompuCell3D and background reading on ovarian development in mice. In the afternoon, I attended a workshop about micro aggressions (http://www.ohsu.edu/xd/about/vision/center-for-diversity-inclusion/diver...) in society. Microaggression is a concept about certain interactions among people of differing backgrounds that can be seen as small actions of non-physical aggression. For example, someone may say, “He‘s pretty smart for a minority.” Many times good intentioned expressions are seen as unintended derogatory opinions of a person or people from a different background.

Friday, 06/13/14:
    I had a meeting with Karen regarding where to focus on CompuCell3D and the background readings. I continued reading about CompuCell3D.