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Course overview

Biowulf is the high-performance compute cluster (HPC) at NIH and runs Linux, a Unix-like operating system. It offers more compute power than a personal computer and has over 900 software applications installed, including those for bioinformatics. Using Biowulf requires working knowledge of a command line interface. This course series will teach the basic Unix commands needed to get started working with your NGS data on Biowulf.

Course Expectations / Learning Objectives

After this course, participants will be able to

  • Log onto the NIH High Performance Compute Cluster Biowulf
  • Navigate the folder and file (directory) structure on a Unix system
  • View directory content
  • Copy, move, rename, and delete files and folders
  • Find and work with bioinformatics applications that are installed on Biowulf
  • Run interactive, swarm and batch jobs on Biowulf
  • Work with and perform basic wrangling tasks on text files and tabular data

Course schedule and topical outline

  • Lesson 1 (Monday, January 22, 2024):
  • Lesson 2 (Wednesday, January 24, 2024):
  • Lesson 3 (Monday, January 29, 2024):
    • Copy, move,rename, and deleting files and folders using Unix commands
    • Lesson 3 recording
  • Lesson 4 (Wednesday, January 31, 2024):
    • Working on interactive sessions
    • File transfer on Helix
    • Working with software installed on Biowulf
    • Lesson 4 recording
  • Lesson 5 (Monday, February 5, 2024):
  • Lesson 6 (Wednesday, February 7, 2024):
    • Using Unix commands to work with and performing basic wrangling tasks for text files and tabular data.
    • Lesson 6 recording

Participants will use student accounts provided by Biowulf for this course series. See student assignments.