Class Overview

This class will introduce novices to essential Unix commands for getting started in bioinformatics. Unix is an operating system like Windows and MacOS. However, in Unix, users interact with the computer by issuing commands rather than through a point-and-click interface. The ability to use Unix is important as many bioinformatics software are written to work on Unix and Unix-like operating systems. For instance, see the list of software available on the Bioconda repository. Further, bioinformatics often deals with large and complex datasets such as those derived from Next Generation Sequencing (NGS), which are too cumbersome to analyze on a personal computer with limited computation power. Thus, bioinformatics is commonly performed on high performance computing systmes such as the one at NIH known as Biowulf. Biowulf runs on Linux (a Unix-like operating system) and has around 1000 scientific applications installed, including those for Next Generation Sequencing (NGS) analysis. Biowulf staff maintain and update the system as well as the installed software.

Learning Objectives

After this class, participants should be familiar with Unix commands needed to get started with bioinformatics including:

• Signing onto Biowulf
• Navigating through Biowulf's directories
• Working with files
• Launching and working with software installed on Biowulf
• Starting graphical packages on Biowulf HPC OnDemand