- Bucknell University Class of 2018
- Computer Engineering Major
Log 0: Orientation Day - 5/31
Today we met the REU program coordinators and our project mentors. We also got a tour of the labs we will be working in.
I spoke with my faculty mentor, Dr. Serdar Bozdag, about the different projects that he is currently working on. He is involved in the field of Bioinformatics, which I am very interested in but have very little experience with. During the first couple weeks of the program I will probably be reading a lot of background information on molecular biology. I will likely be working on developing a ranked list of transcription that most affect the expression of certain genes using a computational model.
Log 1: 5/31
Today I met with a PhD student, Duc, who is also working with Dr. Bozdag. He helped me
- Download R and RStudio onto my laptop
- Start a tutorial for learning R
R is the primary programming language used in the field of bioinformatics, so it is important for me to be familiar with it. It is a very high level language, so I don't think it will take long at all to learn.
Today the other REU students and I also got a tour of the library and learned how to search the library catalog and the many online databases that the library subscribes to. This information will be helpful when we go to search for published papers related to our current summer research. I checked out four books from the library, Gene Transcription, RNA Motifs and Regulatory Elements, R Programming for Bioinformatics, and Bioinformatics for Biomedical Science and Clinical Applications. I am hoping that these books will help me gain the background knowledge necessary to begin my research project.
Log 2: 6/01
- Continued working on the R tutorial for most of the day
- Listened to a lecture by Dr. Factor on good research practices
Log 3: 6/02
- Finished the R tutorial
- Began reading background information
Today I began reading through the books I checked out on Wednesday. Dr. Bozdag also sent me a pdf of a book chapter called "Molecular Biology for Computer Scientists" for me to read through. I am currently about a third of the way through taking notes on the pdf, and refreshing my memory on all the concepts I learned in my high school biology course. My mentor and I also developed a list of specific goals and milestones for the rest of the summer. This list can be found on my user page.
Log 4: 6/03 and 6/04
- Continued reading through background information
- Reformatted wiki page
- Goals and Milestones are now easily accessible from the 2017 projects list
Log 5: 6/05
- Continued reading though "Molecular Biology for Computer Scientists"
Log 6: 6/06
- Completed ethics training with other REU students
- Finished reading "Molecular Biology for Computer Scientists"
- Met with Dr. Bozdag and Duc to discuss more details of the project and goals for the next few weeks
Basically I will be conducting a literature search over the next week or so. Duc has sent me some initial papers to read, as well as a tutorial for some of the main R libraries used for RNA sequencing in bioinformatics.