• Name: Kyle Lee (Sang Hyuk Lee)
• Email: sanglee81@berkeley.edu
• homepage: Kyle Lee's cozy mini homepage (don't block the pop ups at this time ha)
• Interests:
  • BioMEMS
  • Computational Biology
  • Bike
  • Snowboarding

BioE 131 HW1

1. HW1 Using Wiki
2. HW4 RNA logic
3. HW5 Sequence Alignment Lab
4. Extra Credit: Ronald Breaker talk
5. HW7 Info. content
6. Extra Credit: Broken Telephone Tree
7. Final Prj:Retrovirus
   1. JBROWSE.ORG
   2. Tutorial for editting ConfigFile from Kamran's wiki
   3. It was my first semester to have ubuntu on my laptop as an OS. I spent a lot of time trying to become familiar with it. Installing Jbrowse on my laptop was not an easy task. I kept getting a weird error message saying that "DB_File can't locate @INC" whenever I ran jbrowse at home. For some unknown reason, I found out that jbrowse works fine on campus but not at my house. Andrew did the research for our retrovirus, Daniel provided us the templates for our website, and Kamran helped me set up the jbrowse on my labtop. Thanks you all. They explained what they learned about the assigned project in detail without complaining. With their help, I was able to set up one of the bovine viruses in jbrowse. My assigned genomes(Bovine IV) are simple compared to others. After converting the genome information from genbank files, the gff files showed that each genome has few tracks. I analyzed the genome with blast in order to look for other genomes that share great similarities with it(M32690). Researches performed on published papers on the same subject will further develop this website. Better practice of converting the jbrowse friendly gff files, retrieved from genbank, will also improve the efficiency of website. Not only was this class interesting, but I also acquired a lot of knowledge on databases and perl coding. Through this class, I was introduced to different fields of bioengineering. I have gained such a valuable experience, and I am sure these skills I learned will help me in the future.