Workshop Description

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.

Day 1

  • 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

Video: https://www.youtube.com/watch?v=liC5uM8czyo
Slides: https://github.com/QCB-Collaboratory/W1.UNIX.command.line/blob/master/workshop.slides/day1_Unix.pdf

Day 2

  • Use the productivity features of the Unix shell
  • Create and modify files using Unix editor
  • Copy, rename, and display files
  • Search plain-text data sets for lines matching a regular expression using grep

Slides: https://github.com/QCB-Collaboratory/W1.UNIX.command.line/blob/master/workshop.slides/day2_Unix.pdf

Video: https://www.youtube.com/watch?v=xHu7qI1gDPA

Day 3

  • Use tools for processing text files
  • Edit files in non-interactive mode using sed
  • Process tab delimited files using awk
  • Write simple shell scripts
  • Submit jobs via qsub on hoffman2

Slides: https://github.com/QCB-Collaboratory/W1.UNIX.command.line/blob/master/workshop.slides/day3_Unix.pdf
Video: https://www.youtube.com/watch?v=PHmfgIuOMFQ

Workshop Materials

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.
  • We strongly encourage attendees to bring a laptop capable of accessing UCLA’s WiFi.

Instructor

Dr. Peter Scott is a postdoctoral researcher in the laboratory of Dr. Brad Shaffer. He received his PhD in Ecology and Evolutionary Biology from the University of Alabama. Peter’s primary research interests lie in applying genomic methods to understand species limits and diversification, hybrid zone dynamics, and landscape and conservation genomics in reptiles and amphibians. Additionally, he is interested in investigating how to best apply and adapt modern genomic methods to non-model systems that are representative of difficult evolutionary questions (e.g. resolving relationships in recent, rapid radiations), or that push the limits of these technologies (e.g. organisms with very large genomes). Email: pscott17@ucla.edu

Videos

Introduction to Unix, Part 1 of 3. Taught by Dr. Serghei Mangul.

Introduction to Unix, Part 2 of 3. Taught by Dr. Serghei Mangul.

Introduction to Unix, Part 3 of 3. Taught by Dr. Serghei Mangul.

Reviews

I learned much more than when I tried to learn this on my own!
Fall 2018 Student

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.

Fall 2018 Student
I appreciate greatly that this course is offered for free. It is incredibly helpful for graduate students who may not have studied coding in past work, but want to leverage computation to advance our research. Thanks!
Fall 2018 Student
It’s a great workshop. Highly recommend for whoever wants to learn -omics analysis without any programming background!
Fall 2018 Student

It was great! I have learned a lot!

Fall 2017 Student

Workshop Details

Prerequisites: None
Length: 3 days, 3 hrs per day
Level: Introductory
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 28

Fall 2019 Dates

October 8, 9, and 10, 2019
9:30 AM to 12:30 PM