Course Overview

Biowulf is the Unix-based high-performance compute cluster at NIH and houses over 900 softwares including those used for bioinformatics analysis. While most are used to working with point-and-click operating systems such as Windows or Mac, working in a command-line driven environment such as Biowulf can be intimidating. This course series will help participant overcome fear of working on high-performance computing clusters so that they can start taking advantage of the resources available for their bioinformatics and data science needs.

Course Expectations / Learning Objectives

After this course, participants will be able to

1. Log onto the NIH High Performance Compute Cluster known as Biowulf
2. Navigate the folder and file (directory) structure on a Unix system
3. Work with very large Next Generation Sequencing (NGS) files on a Unix system
4. Find and load bioinformatics applications that are installed on Biowulf
5. Run interactive, swarm and batch jobs on Biowulf

Course schedule and topical outline

• Lesson 1 (September 7th, 2023):
  • Overview of Unix and Biowulf
  • Logging into Biowulf
  • Lesson 1 recording
• Lesson 2 (September 14th, 2023):
  • Navigating around the Biowulf directory structure
  • Lesson 2 recording
• Lesson 3 (September 21st, 2023):
  • Working with files and directories
  • Interactive sessions
  • Exploring Next Generation Sequencing data
  • Lesson 3 recording
• Lesson 4 (September 28th, 2023):
  • Bioinformatics applications on Biowulf
  • Submitting batch jobs
    • Swarm
    • Shell script
  • Lesson 4 recording

student account assignment