Workshop Description (Introductory Course)

Unix is a command-line-based platform that is a highly powerful and flexible tool for data management and analysis. First, this workshop introduces the basic concepts of UNIX operating system and shell scripting. We will explore essential hands-on skills to confidently use the command line interface on either a local (laptop) or a remote (hoffman2 cluster) computer running the Unix system. Next, this workshop covers how to navigate around the Unix file system from the command line and use a number of basic, common Unix commands. The course is supplemented with many hands-on examples. No prior knowledge of Unix or programming is required.

Workshop Topics

  • Learning the fundamentals of Unix
  • Understand the underlying philosophy of Unix and command line interface
  • Login and log out of a Hoffman2 Cluster (Unix file system)
  • Navigate through the Unix file system
  • Create and modify files using Unix editor
  • Copy, rename, delete files

Slides: Day 1

  • Use the productivity features of the Unix shell
  • Display files
  • Use tools for processing text files
  • Search plain-text data sets for lines matching a regular expression using grep
  • Edit files in non-interactive mode using sed

Slides: Day 2

  • Process tab delimited files using awk
  • Write simple shell scripts
  • Submit jobs via qsub on hoffman2

Slides: Day 3

Technical Requirements

  • Attendees are required to have a Hoffman2 account. To apply for an account, click here. UCLA participants who lack a faculty sponsor and non-UCLA participants may apply for a temporary Hoffman2 account, requesting sponsorship from Collaboratory Workshops.

Instructor

Dr. Shawn Cokus is an Associate Researcher in the Department of Molecular, Cell, and Developmental Biology. Dr. Cokus has been doing bioinformatics at UCLA since 2002, and his interests include methods for BS-Seq, RNA-Seq, Hi-C, and protein-protein interaction prediction. His recent work focuses on de novo genome assembly and annotation. Dr. Cokus earned a Ph.D. in Mathematics from the University of Washington.
Email: cokus@ucla.edu

Videos

Reviews

I really loved that she shared advice on the best way to learn about new commands/modules, which are often very inaccessible to beginners. Going forward I feel that I have a really strong foundation in UNIX command line, and working with bioinformatics data in general, that I can build upon. Perfect introduction course for those that want to learn bioinformatics!
It’s a great workshop. Highly recommend for whoever wants to learn -omics analysis without any programming background!

It was great! I have learned a lot!

I learned much more than when I tried to learn this on my own!

This has been a great experience, it was very easy to follow and the instructor was phenomenal! I learned a lot and I feel much more comfortable opening a terminal and learning how to work with it now.

Workshop Details

Prerequisites: None
Length: 3 days, 3 hrs per day
Level: Introductory
Location: Boyer 529
Seats Available: 28

Fall 2023 Dates

October 3, 4, and 5
1:30 PM – 4:30 PM

REGISTRATION IS CLOSED!

UCLA and Cedars-Sinai Affiliates: Click to Enroll
Non-UCLA Affiliates: Click to Enroll
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