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The purpose of this site is to provide a resource for students and instructors participating in the course.
Syllabus Version 2 - Two students had conflicts with December 5th, so we'll have the last day of presentations on Dec 11th.
Final Project Instructions - Posted 11/14/18, the full instructions are here for sure
- Video of in class project instructions
- Wednesday, August 22nd, 2018 - Introduction/ACF Registration
- Monday, August 27, 2018 - Shell I
- Wednesday, August 29, 2018 - Shell II
- Wednesday, September 5, 2018 - Shell IV
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Monday, September 10, 2018 - BLAST
- This video is essentially useless as the screen share quits about 10 minutes in, and you can't see the slides or the terminal. :( Video
- Wednesday, September 12, 2018 - Shell V - No class meeting, ACF Down, see materials
- Monday, September 17, 2018 - Shell Test - see assigned times
- Wednesday, September 19, 2018 - DNASeq I
- Monday, September 24, 2018 - DNASeq II
- Wednesday, September 26, 2018 - DNASeq III
- Monday, October 1, 2018 - DNASeq IV
- Wednesday, October 3, 2018 - DNASeq V
- Monday, October 8, 2018 - TEST 1
- Wednesday, October 10, 2018 - Python Intro & Python I Practical
- Monday, October 15, 2018 - Python II
- Wednesday, October 17, 2018 - Python III
- Monday, October 22, 2018 - Python IV
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Wednesday, October 24, 2018 - RNASeq I
Video of lecture Fixed link- Video of lecture Maybe fixed for real this time?
- Video of lab
- RNASeq I Qsub script - if you need to generate the files from the lab
- Instruction of alignment visualization by IGV
- Monday, October 29, 2018 - RNASeq II
- Wednesday, October 31, 2018 - RNASeq III
- Monday, November 5, 2018 - Guest Lecture - Project Proposal Due!
- Wednesday, November 7, 2018 - Guest Lecture
- Monday, November 12, 2018 - Test 2
- Wednesday, November 14, 2018 - Work on Project - See above for project instructions
- Monday, November 19, 2018 - Work on Project
- Wednesday, November 21, 2018 - Work on Project - No in class meeting
- Monday, November 26, 2018 - Work on Project
- Wednesday, November 28, 2018 - Project Presentations
- Monday, December 3, 2018 - Project Presentations
- Wednesday, December 11, 2018 - Project Presentations
Log in to ACF:
ssh yourusername@duo.acf.tennessee.edu
Create a handy shortcut for logging in so you don't have to type as much
Qsub to the Debug Queue (the third version!):
qsub -I -A ACF-UTK0085 -q debug -l walltime=1:00:00,nodes=1:ppn=1,naccesspolicy=singleaccount
After qsub, if you have problems with line wrappings, try
resize
Class directory on ACF:
/lustre/haven/courses/EPP622-2018Fa
Your folder in the class directory on ACF:
/lustre/haven/courses/EPP622-2018Fa/yourusername
You don't have to buy a book for this course, but these are great resources.
Attendance at OIT or ACF training for a topic related to the course. Get the instructor to email me that you attended. 5 points added to a test grade. See OIT Schedule of Training
- R Basics, Thursday, 09/06/18 9:00am - 12:00pm
- R for Machine Learning, Tuesday, 09/25/18, 9:00am - 11:00am
- UT BRC Workshop: Microbial Genomes Atlas (MiGA) Web-server and Metagenome-Annotated Genomes (MAGs), Thursday, 10/4/18, 1:00pm - 5:00pm
- Introduction to Python, Thursday, 11/15/18, 12:40pm - 2:40pm
For other trainings, send them to the instructor for approval and to be added to the list.
- Wednesday November 28th, 2:30-4:30
- Monday December 3rd, 2:30-4:30
- Tuesday December 11th, 2:45-4:45