Workshop Description (Advanced Course)
Biological data (e.g., from sequencing) continues to grow rapidly, and day-to-day work of a bioinformatician increasingly requires efficient facility with command line management, preparation, computation over, and summarization of large files. As the most ubiquitous and stable interface to command line computing, advanced use of the universal “glue” that is command line shells (e.g., GNU BASH) is an important skill. Large computations also often require sophisticated use of the Hoffman2 job queueing system. This Workshop will go over (with examples) advanced shell features (complex pipelines, functions, control flow, arrays, string manipulation, arithmetic, robustness) and parallelization (both on any single machine, as well as with the Hoffman2 job array system).
Workshop Materials
Day 1
Review UNIX I; shell features
Day 2
More shell features
Day 3
Hoffman2 queue system
Technical Requirements
- Hoffman2 Cluster Access is required.
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
Workshop Details
Prerequisites: UNIX Command Line I (W1a) and Unix Command Line (W1b)
Length: 3 days, 3 hrs per day
Level: Advanced
Location: Boyer 529
Seats Available: 28
Spring 2025 Dates
May 13, 14, and 15
1:30 PM – 4:30 PM
REGISTRATION IS OPEN!
