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

Serghei Mangul, Ph.D., is currently a Postdoctoral Fellow with Eleazar Eskin (Department of Computer Science) at  UCLA. He holds a Collaboratory Fellowship from Institute for Quantitative and Computational Biosciences (QCB).

Dr. Mangul’s research focuses on developing bioinformatics methods to leverage large-scale high-throughput genomics datasets to better understand the biology of disease. His flagship product is Read Origin Protocol (ROP),  a tool for discovering the source of all RNA-Seq reads originated from complex RNA molecules recombined T and B cell receptors and microbial communities. ROP was applied across 1 trillion reads across 10641 samples. Dr. Mangul is also interested in bioinformatics education and pedagogy. He is leading an undergraduate research group, focused on genomic research. His philosophy on how to engage undergraduates in genomic research is presented here.

Email: smangul@ucla.edu
Website: http://www.sergheimangul.com/

Videos

Introduction to Unix, Part 1 of 3. Taught by Dr. Serghei Mangul (http://www.sergheimangul.com/).

Introduction to Unix, Part 2 of 3. Taught by Dr. Serghei Mangul (http://www.sergheimangul.com/).

Introduction to Unix, Part 3 of 3. Taught by Dr. Serghei Mangul (http://www.sergheimangul.com/).

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

Winter 2019 Dates

January 15, 16, and 17, 2019
2:00 PM – 5:00 PM