1.Account Set Up

1.1 Bioinfo Prep

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Objective: Set up Student Wiki Page, Journal, Insight! in the repo.

Time estimated: 1 h; taken 1 h;

Date started: 2023-1-12 ; completed: 2023-1-12

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Wiki

• Task: Wiki edit: name+page
• Create Wiki in my repo
• Use [[Journal]] to link subpages
• Add copy-right {{CC-BY}} in footnote

Journal

• Task: make Journal page with CC
• Document procedure+results

Insights!

• Task: make insight! page with CC
• Template: Context, insight, date

Plagiarism and academic integrity

• “Full Disclosure Policy”

• “inspired by…”,

• “based on…”,
• “according to …”,
• “following …”,
• “see also …”,
• etc. as appropriate.

• Task: model of the following three types of references
  • In reports, cite method footnotes ➕ APA style
  • In R code, # comment to cite StackOverflow with URL in code
  • cite this idea is from classmatte

Data Backup

• Backup with icloud, wiki, and OneDrive

Netiquette + Technical Questions

• Describe: title + enviornment + expected behavior/ target + error message + which line of code

Information Sources for Bioinformatics

• introductory notes on bioinformatics concepts + introductory notes on information sources for bioinformatics

💡Conclusion and outlook: Set up my Student Wiki and repo on github, started course journal. If I feel uncertain for anything that is not of my own, I will cite the original source with URL ➕ author (➕ context) in APA to avoid issues.

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1.2 R - Basics

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Objective: R basics

Time estimated: 1 h; taken 1 h;

Date started: 2023-1-12 ; completed: 2023-1-12

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R

• Task: Install R & RStudio

Docker

• Task: Install Docker

• pull BCB420 docker image

  docker pull risserlin/bcb420-base-image

• Run Docker in course folder, create image.

  cd /Users/wengjiaming/Documents/BCB420
  docker run -e PASSWORD=changeit --rm \
    -v "$(pwd)":/home/rstudio/projects -p 8787:8787 \
    risserlin/bcb420-base-image:winter2023

  Error, m1 mac cannot run RStudio server with docker, Solution: switched to intel mac.

RStudio

• 2.RBasics.rmd

  seqinr::words(3, c("A", "G", "C", "U"))
  # result: all 3 letter code with ATCG
  > [1] "AAA" "AAG" "AAC" "AAU" "AGA" "AGG" "AGC" "AGU" "ACA" "ACG" "ACC" "ACU" "AUA" "AUG" "AUC" "AUU" "GAA"
  [18] "GAG" "GAC" "GAU" "GGA" "GGG" "GGC" "GGU" "GCA" "GCG" "GCC" "GCU" "GUA" "GUG" "GUC" "GUU" "CAA" "CAG"
  [35] "CAC" "CAU" "CGA" "CGG" "CGC" "CGU" "CCA" "CCG" "CCC" "CCU" "CUA" "CUG" "CUC" "CUU" "UAA" "UAG" "UAC"
  [52] "UAU" "UGA" "UGG" "UGC" "UGU" "UCA" "UCG" "UCC" "UCU" "UUA" "UUG" "UUC" "UUU"
  
  # better way to install
  **if (! requireNamespace("seqinr", quietly=TRUE)) {
    install.packages("seqinr")
  }**
  
  # find packages
  **sos::findFn("moving average")**

• Git

• Set wd as the project directory.

  setwd("/home/rstudio/projects")
  
  # confirm by 
  list.files()

.Rprofile

• NOT save workspace

  rm(list=setdiff(ls(), "task_counter"))

💡 Conclusion and outlook: Downloaded and installed docker, created a new image and container from the bcb420 Dockerfile. Wish that the docker can be available for m1 macs soon.

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