Repository navigation
Module 1
Meg Staton edited this page Sep 9, 2026
·
1 revision
This module will last for 7 class periods. The grading will be as follows:
- 80% In person test, 10 minutes, see Test 1 Options
- 20% In class discussion participation
- Request an Isaac Account
- Go to the HPSC home page
- Click the button in the left-hand navigation that says "Request an ISAAC Account".
- On the following page, click the button that says "I have a UT NetID"
- Then follow the prompts to log in and claim your personal account.
- Introductions
- Join Slack
- Slides - Intro to Class
- Test 1 Options
- Get logged on (see above)
- Homework: Reading:
- Brandies and Hogg, 2021 Ten simple rules for getting started with command-line bioinformatics
- Gauthier, 2019. A brief history of bioinformatics
- Lustre file system - Limits and policies
- Discussion of reading, Class 2 Discussion Seeds
- Get data: shell-lesson-data.zip
- SWC 1
- SWC 2
- Homework:
- Finish/review SWC modules 1 and 2
- Complete Canvas Survey- abstract of your research, how bioinformatics is/will be important, and what skills you most want to learn
-
Test 1 sign up on canvas was a fail - lets try google sheets - New Test 1 Sign Up
-
Optional quality of life improvements:
- Change your prompt. After logging into isaac, in ~/.bashrc, to show full path add:
PS1='\w\$ ' - Log in slightly faster and no need to DUO as many times. One your terminal (before SSHing anywhere), add to .ssh/config
- Change your prompt. After logging into isaac, in ~/.bashrc, to show full path add:
Host sphinx
HostName sphinx.ag.utk.edu
User mstaton1
ControlMaster auto
ControlPath ~/.ssh/socket_%C
ControlPersist yes
Host isaac
HostName login.isaac.tennessee.edu
User mstaton1
ControlMaster auto
ControlPath ~/.ssh/socket_%C
ControlPersist yes
- Homework:
- Finish SWC module
- Read: Stephens et al. 2015. Big Data: Astronomical or Genomical?
- Teach yourself (WARNING AI generated content ahead) the basics of BLAST and DIAMOND
Papers:
- Altschul et al, 1990. Basic local alignment search tool. Key concepts: word-based seeding, high-scoring segment pairs (HSPs), and the statistical framework for E-values.
- Altschul et al, 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Key concepts: gapped alignments and the position-specific scoring matrix (PSSM) framework - PSI-BLAST
- Buchfink, Xie & Huson, 2015. Fast and sensitive protein alignment using DIAMOND Key concepts: double-indexing approach, speed gain
- Buchfink, Reuter & Drost, 2021. Sensitive protein alignments at tree-of-life scale using DIAMOND Key concepts: --very-sensitive and --ultra-sensitive modes match BLASTP sensitivity while achieving an 80× speedup, why algorithmic efficiency matters at genomic scale
- Discussion of reading, Class 4 Discussion Seeds
- VS Code Demo (Zane)
- Lab - BLAST and DIAMOND Lab
-
New Test 1 Sign Up - make sure you are signed up
-
No slides, straight to lab
-
Lab - BLAST and DIAMOND Lab
-
SWC 5 - Loops
-
Homework: Finish SWC module and reading:
- Noble 2009. A Quick Guide to Organizing Computational Biology Projects
- Sandve et al. 2013. Ten Simple Rules for Reproducible Computational Research
-
Helpful Links:
- VSCode Tutorials:
- VSCode in 100 seconds: https://www.youtube.com/watch?v=KMxo3T_MTvY
- VSCode Beginner's Tutorial: https://www.youtube.com/watch?v=ORrELERGIHs
- Windows Subsystem for Linux (WSL2) Tutorials:
- What Is The Windows Subsystem for Linux (WSL) For?!: https://www.youtube.com/watch?v=EAROgwvOV4s
- How to Install WSL2 on Windows 11: https://www.youtube.com/watch?v=JzSZhdptuTs
- VSCode Tutorials:
- Class 5 Discussion Seeds
- Option 1 Practice Test as a doc, Practice Test as pptx
- File: middle_earth_test1.zip
- Test 1 Option 2 Practice Test - TBD, stay after class
- SWC 6 - Bash Scripts
Test - See Sign Up Times
Test 1 Data Set: hitchhikers.zip