skip to content
Computational biology at CSU
User Tools
Log In
Site Tools
Search
Tools
Show pagesource
Old revisions
Backlinks
Recent Changes
Media Manager
Sitemap
Log In
>
Recent Changes
Media Manager
Sitemap
Trace:
•
linux_resources
Sidebar
BZ 360: Bioinformatics and genomics
home
syllabus
schedule
resources
data
DSCI 510: Linux
home
syllabus
schedule
assignments
resources
requirements
DSCI 511: Python
home
syllabus
schedule
assignments
problem sets
resources
scripts
sample data
DSCI 512: RNA-seq
home
syllabus
schedule
assignments
resources
requirements
Seminars and Workshops
upcoming seminars
upcoming workshops
Links
CSU NGS Core
Summit HPC
Questions?
Tai Montgomery
linux_resources
Table of Contents
Additional Resources
Hardware / Software Requirements
Summit Resources
Linux Resources
Textbook for the course
Beyond the basics
Linux cheat sheet
BONUS CONTENT
Best practices resources
Lesson Cheatsheets
Extra Course Content (from past courses)
Additional Resources
Hardware / Software Requirements
Click here to learn more about
Requirements
Summit Resources
Batch jobs an job scripting
FAQ (some are CU-centric)
Jupyterhub
Top level
Linux Resources
Textbook for the course
The Linux Command Line, 2nd ed
.
Beyond the basics
tmux
.
Linux cheat sheet
Linux cheat sheet
Useful shortcuts
The linux documentation project:
old-school and encyclopedic.
BONUS CONTENT
Nano tutorial
Best practices resources
Erin's Best Practices
Best Practices for Scientific Computing
A Quick Guide to Organizing Computational Biology Projects
Gene name errors are widespread in the scientific literature
Lesson Cheatsheets
200825_cheatsheet.docx
200827_cheatsheet.docx
200901_cheatsheet.docx
Extra Course Content (from past courses)
File formats - general
File formats - genomic
Connecting to remote servers
Permissions
Intro to supercomputing
Using summit
Parallel Processing
2018 scripting lectures (these include work on Summit)
Introduction to Scripting
Basic Scripting
Arguments, Intro to Flow Control
Assignment 5
Loops and More Conditionals
Sed and grep
Substitutions and regular expressions
Assignment 6
Example Bioinformatics Pipeline
Using regular expressions to find sequence motifs
Downloading, installing, and running Bioinformatics software on Summit
linux_resources.txt
· Last modified: 2021/06/01 15:05 (external edit)
Page Tools
Show pagesource
Old revisions
Backlinks
Back to top