Classes 1 6 - mestato/EPP622_2024 GitHub Wiki
Class 1. Tuesday August 20 - Command Line I
- In person and recorded.
- Bioinformatics - what is it and where did it come from? Slides
- Lab:
- Apple - Terminal
- Windows - Mobaxterm - Use portable edition
- Get on Sphinx
- Software Carpentry
- Class Recording
- 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. Thursday August 22 - Command Line II
- In person and recorded.
- Slides: Computers and HPCs
- Lab:
- Navigating files and directories - Continued from Tuesday
- Working with files and directories
- Command to download data for command line lessons:
/home/your_utk_username
wget https://swcarpentry.github.io/shell-novice/data/shell-lesson-data.zip
- Reading, HPCs in Oak Ridge
- Class recording
Class 3. Tuesday August 27 - Command Line III
- In person and recorded.
- Lecture:
- AgBioData Lesson 1 - Intro to Biological Databases and Repositories
- Filesystem Practice
- Working with files and directories - continued from last time
- SWC 4 - Pipes and Filters
- Reading
- Bash-Cheat-Sheet
- Or find or make your own!
- Brandies and Hogg 2021 Ten simple rules for getting started with command-line bioinformatics
- Tang 2023 Embracing the command line: my unexpected career in computational biology
- Bash-Cheat-Sheet
- Class recording
Class 4. Thursday August 29 - Command Line IV
- In person and recorded.
- Sequence Alignment: Slides
- Lab: BLAST and Diamond
- 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 recording
Class 5. Tuesday September 3 - Command Line V
- In person and recorded.
- Test 1 distributed. (TEST 1 Due at midnight on September 10th.)
- Slides: Finish up BLAST algorithm
- Perhaps others can explain this better, try these vids:
- Deborah Thurtle-Schmidt global sequence alignment
- Professor Hendrix understanding sequence alignment algorithms
- Perhaps others can explain this better, try these vids:
- Sequence Alignment: Lab: BLAST and Diamond - finish from class 4
- SWC 4 - Pipes and Filters (finish from Class 3)
- SWC 5 - Loops
- Day 5 Class Recording
Class 6. Thursday September 5 - No new material.
- Optional work on Test 1 in class. TEST 1 Due at midnight on September 10th.
- Class recording part I
- Class recording part II