Workshop Description

This workshop will cover the basic concepts of UNIX operating system and shell scripting. Workshop provides hands on skills to confidently use the command line interface on either a local (laptop) or remote (hoffman2 cluster) computers running Unix system. The workshop teaches 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://www.dropbox.com/s/ggv7ijwateim7zt/day1_Unix.pdf?dl=0 

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://www.dropbox.com/s/xorsuvk1cugiyw8/day2_Unix.pdf?dl=0 
Video: https://www.youtube.com/watch?v=ArbOG6YpakU 

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://www.dropbox.com/s/88wu7svvfur8upw/day3_Unix.pdf?dl=0
Video: https://www.youtube.com/watch?v=PHmfgIuOMFQ

Workshop Materials

  • Attendees are required to have a Hoffman2 account. To apply for an account, click here.
  • Attendees are strongly encouraged to bring a laptop computer capable of accessing UCLA’s WiFi.
  • Please download class materials w1-files.zip

Instructor

Serghei Mangul, Ph.D is a postdoctoral fellow at computational genetics group led by Eleazar Eskin which is affiliated with both the Computer Science Department and the Human Genetics Department. His research interests include development of integrated methods for high-throughput genomic data analysis. Before joining UCLA, Dr. Mangul received his B.S. in Applied Mathematics at Moldova State University in 2007 and M.S. and Ph.D. in Bioinformatics at Georgia State University in 2012. His general interests include computational biology, bioinformatics, next-generation sequencing, high-throughput genomics, discrete algorithms and combinatorial optimization.

Email: serghei@cs.ucla.edu
Website: https://sergheimangul.wordpress.com/

Workshop Details

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

Spring Dates

4/4/17 – 4/6/17, 9:30 AM