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




Technical Requirements

  • TBD


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:



Workshop Details

Prerequisites: Intro to UNIX (W1)
Length: 3 days, 3 hrs per day
Level: Advanced
Location: Boyer 529
Seats Available: 28

Spring 2023 Dates

May 2, 3, and 4
1:30 PM – 4:30 PM