Class 1 6

Class 1. Thursday, August 25 Command Line I (Online Only. Consider attending PRC).

Topics:

• Slides:

  • Syllabus, Slack - Video
  • History of Bioinformatics, Linux - Video, Slides

• Lab:

  • Get on Sphinx
  • Getting started with PowerShell (Windows users)
  • SWC 1 - Introducing the Shell (Allyson) - Video, Slides
  • SWC 2 - Navigating Files and Directories (Allyson) - Video
    • Command to download data for command line lessons (make sure you're in your home directory (/home/your_utk_username)): wget https://swcarpentry.github.io/shell-novice/data/shell-lesson-data.zip

• Reading:

  • A brief history of bioinformatics Gauthier et al 2019
  • How Margaret Dayhoff Brought Modern Computing to Biology - McNeill, Smithsonian 2019

• Book Recommendation: Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools Buffalo 2019

Class 2. Tuesday, August 30, Command Line II (In person.)

• Lab:
  • Slides: Computers and HPCs
• SWC 3 - Working With Files and Directories (Ryan)
• Class & Lab Recording
• Reading
  • Why do Bioinformaticians Avoid Using Windows?

Class 3. Thursday, September 1, Command Line III (Online Only. Football parking mess.)

• Lecture:
  • AgBioData Intro Slides & Video
  • AgBioData Lesson 1 - Intro to Biological Databases and Repositories Slides & Video
• SWC 4 - Pipes and Filters (Allyson) Video
• Reading
  • The 40 Most-Used Linux Commands You Should Know

Class 4. Tuesday, September 6, Command Line IV (In person.)

• Sequence Alignment: Slide & Video
• Lab: BLAST and Diamond (Ryan)
• Class and Lab Recording
• Additional reading for learning more if you are interested:
  • Buchfink et al. 2001 Sensitive protein alignments at tree-of-life scale using DIAMOND
  • Software Carpentry's Regular Expressions for Biologists
  • Diamond software & documentation

Class 5. Thursday, September 8, Command Line V (In person.)

• Slides: Data Management
• SWC 5 - Loops (Allyson)
• Class & Lab Recording

Class 6. Tuesday, September 13 (No class.)

Work on Test 1.