Introduction to Unix and Biowulf

Joe Wu, PhD
NCI CCR Bioinformatics Training and Education Program
February 12, 2026
ncibtep@nih.gov

Background on Unix

• A computer operating system like Windows and MacOS.
• Interact with computer through a terminal and by issuing commands in the terminal (so no graphical user interface or GUI).
• There are many Unix like operating system such as Linux. Even MacOS is based on Unix.

Why learn Unix

• Efficiently process large datasets.
• Bioinformatics/NGS analysis software are written to work on Unix and Unix-like systems.
• Bioinformatics analyses often require researchers to work on high performance computing systems such as Biowulf at NIH, which requires command line knowledge.
• Write scripts to ensure reproducibility and reusability.

Background on Biowulf

• Biowulf is the Unix-based high performance computing system at NIH.
• Has around 1000 scientific applications (including those for NGS analysis) installed.
• Biowulf staff maintain the system and updates software.
• Biowulf HPC OnDemand is a feature that enables users to access Biowulf and graphical applications such as R Studio and Jupyter Lab from a web browser.

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