Introduction to Unix and Biowulf

Joe Wu, PhD
NCI CCR Bioinformatics Training and Education Program
August 14, 2025
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

• This class is meant for the novices.
• Will not make participants experts but materials learn form the basis for learning advanced Unix skills.
• 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