Linux for Biologists

A beginner’s guide to Linux for students and researchers in biological sciences.

In this book, you will learn how to use a Linux desktop, included software, basic commands, and work with files and directories.

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Table of Contents

• 1. About this book
  • 1.1. Who is it for?
  • 1.2. What you will learn
  • 1.3. The author
• 2. Getting started
  • 2.1. An overview of Linux
  • 2.2. Running a Linux desktop
  • 2.3. Using included software
  • 2.4. Files and directories
• 3. Getting software
  • 3.1. The quick and easy method
  • 3.2. Python packages
  • 3.3. Perl modules
  • 3.4. R packages
  • 3.5. Conda packages
  • 3.6. Debian packages
• 4. Using the command line
  • 4.1. Shell and Terminal
  • 4.2. Basic commands
  • 4.3. Editing text files using nano
  • 4.4. Exercise: Run a local BLAST+ database search
  • 4.5. Points to note
• 5. Reference management
  • 5.1. Installing Zotero
  • 5.2. Collecting references from the web
  • 5.3. Integrating Zotero in LibreOffice
• 6. Note-taking
  • 6.1. Features of Zim
  • 6.2. Installing Zim
  • 6.3. Creating a notebook
  • 6.4. Taking notes
  • 6.5. Exporting notes and notebooks
  • 6.6. Activating more features using plugins
  • 6.7. Getting help
• 7. Glossary
• 8. Credits

Index

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Last updated: Mar 18, 2024