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Week 1: 5/29

  • Attended lab orientation and library orientation
  • Created wiki user page
  • Researched and practiced different methods of clustering genes on RStudio to determine the best suited method
  • Met with my PhD student mentor for the project, Ziynet, and Dr. Bozdag: discussed papers

Week 2: 6/4

  • RStudio on desktop kept freezing so requested for an account on the server
  • Read related papers to see what clustering methods other studies used while waiting for code to run
  • Read proposal for project
  • Read papers similar to the project's topic
  • Explored and read about different R clustering packages
  • Completed the three RCR training modules

Week 3: 6/11

  • Read articles and webpages about clustering in R while waiting for clustering code to run
  • Finished practicing clustering on RStudio
  • Met with Ziynet and Dr. Bozdag: discussed possible papers to support the pipeline
  • Read a paper related to the project's topic
  • Met with Ziynet: I discussed the paper I read and she told me to practice coexpression and correlation in RStudio
  • Began researching and practicing how to calculate coexpression of genes on RStudio

Week 4: 6/18

  • Finished writing the practice code for determining coexpressed genes
  • Met with Ziynet and Dr. Bozdag: discussed possible pipelines for the project
  • Read two papers related to the project's topic
  • Met with Ziynet: I discussed the two papers I read
  • Began researching how to determine the correlation between two different genomic datatypes
  • Began writing the practice code for determining correlation between mRNA and miRNA

Week 5: 6/25

  • Made the mini presentation on Monday & Tuesday
  • Wrote and practiced how to present the mini presentation
  • Presented on Thursday
  • Downloaded and tidied miRNA and transcription factor (TF) datasets of miRNA/TFs and their target genes
  • Created functions for both datasets to input miRNA/TF and output their target gene, and vice versa

Week 6: 7/2

  • Tidied the same miRNA and TF datasets again; had to convert gene IDs to gene names
  • Continued working on the correlation practice code
  • Read three papers related to determining coexpression of genes
  • Tidied a different miRNA dataset
  • Created a classification function that predicts cancer subtype based on gene expression dataset

Week 7: 7/9

Week 8: 7/16

Week 9: 7/23

Week 10: 7/30