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BZ 360: Bioinformatics and genomics


DSCI 510: Linux


DSCI 511: Python


DSCI 512: RNA-seq


Questions?

Tai Montgomery

http://www.colostate.edu

linux_schedule

Linux Fall 2018 Schedule

Topics Reading (TLCL) Assignments
Week 1:
Tuesday
August 21 (ERIN) 		Course introduction
The terminal
Navigating the file system 		Chapters 1, 2 Assignment 1
due Aug 28
Thursday
August 23 (ERIN) 		Options
Making & removing
Copying & moving
Wildcards
Working with files I
Getting help 		Chapter 3 (ls, less)
Chapters 4-5 		Assignment 2
due Aug 28
Enrichment 1
Week 2:
Tuesday
August 28 (ERIN) 		File formats
Genomic resources
Redirection
Working with files II
Pipes
More pipes 		Chapter 3 (file)
Chapter 6
Chapter 16 (wget)
Chapter 18 (gzip)
Chapter 20 (sort, uniq, cut)		 Assignment 3
due Sept 4
Thursday
August 30 (ERIN) 		Connecting to remote servers
Intro to supercomputing
Using summit
Parallel Processing
Best practices 		Chapter 16 (ssh)
Summit Guide 		Assignment 4
due Sept 6
Enrichment 2
Week 3:
Tuesday
September 4 (DK) 		Introduction to Scripting 🙋
Basic Scripting 🙆
Arguments, Intro to Flow Control 🙎		 Chapters 16, 18 Assignment 5
due Sept 11
Thursday
September 6 (DK) 		Loops and More Conditionals 🙉
Sed and grep 🙊
Substitutions and regular expressions 🙈
 Chapter 19, 24 Assignment 6
due Sept 11
Week 4:
Tuesday
September 11 (DK) 		Example Bioinformatics Pipeline 😅
Using regular expressions to find sequence motifs 😥
Downloading, installing, and running Bioinformatics software on Summit 😝		 Chapter 27-29
Thursday
September 13 (EN + DK) 		Conclusions and future directions
FINAL EXAM See Assignments
linux_schedule.txt · Last modified: 2018/09/10 15:20 by david

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