Bioinformatics - Level 1 - Module 2 - Session 1 - Kelly Zhang


Technical Area:

  • Installing several necessary packages in R
  • Working with RShiny, RStudio, and RStudio Cloud
  • Familiarizing myself with the GEO database and understanding how to view extracted data


  • RStudio, R, RShiny
  • WinRAR
  • R Packages: affy, affyPLM, simpleaffy, etc.
  • Bioconductor
  • Github

Soft Skills:

  • Time/Task Management - I’m still figuring out how to juggle being my lab internship with the STEM-Away tasks and my project management lead duties. I was able to get all the necessary things done but I will create an hourly schedule for myself next week so that I can stay on top of everything.
  • Project Management - I created a Google Spreadsheet detailing the Bioinformatics Pathway for my team. I’ve also been updating our team’s Trello and Google Calendar.
  • Leadership - I worked with our Project Leads on setting up the Github, making sure we covered everything during meeting agendas. I also make sure to post important information so that our team has all the tools they need to be successful.
  • Collaboration - I worked with Shravya last week on our Journal presentation and I am working with Leila this week on our module 3 deliverables.

Achievement Highlights (3):

  • Ivan and I played around with our Github repository. I was able to get a handle on creating branches, forking the repository, pulling and pushing changes, refreshing my fork, etc. I also familiarized myself with working with Github Desktop and Github via the Windows Command Prompt.
  • I successfully unzipped and opened the GEO datasets in RStudio. I have a Windows machine, so this was a bit of a challenge for me initially.
  • I kept constant communication with the other leads (from my own team and other BI teams) to coordinate the R Shiny project and to help guide and mentor my team members.

Difficulties Completing Tasks:

  • Since I installed R v4.1.0 initially, I had some trouble with further package installations. With Sam’s help, I reverted to R v4.0.5.
  • I kept getting a “path not writable” error when I tried installing the packages but I was able to work through this.
  • Completing batch corrections on multiple GEO datasets - I have not yet been able to do this but I’d like to figure it out