Introduction to Unix/Linux & Command Line Data Analysis

Heads up! This course may be archived and/or unavailable.

This two-part offering covers effective use of the Unix/Linux command-line environment:

Introduction to Unix/Linux

This part introduces the natural environment of bioinformatics: the Linux command line. Material will cover logging into remote machines, filesystem organization and file manipulation, and installing and using software (including examples such as HMMER, BLAST, and MUSCLE). Finally, we introduce the CGRB research infrastructure (including submitting batch jobs) and concepts for data analysis on the command line with tools such as grep and wc.

Command-Line Data Analysis

The Linux command-line environment has long been used for analyzing text-based and scientific data, and there are a large number of tools pre-installed for data analysis. These can be chained together to form powerful pipelines. Material in this part will cover these and related tools (including grep, sort, awk, sed, etc.) driven by examples of biological data in a problem-solving context that introduces programmatic thinking. This part also covers regular expressions, a useful syntax for matching and substituting string and sequence data. Individuals who complete both parts will receive a Certificate of Completion and a Digital Badge detailing the course information.