Linux for Biologists

A beginner’s guide for students or researchers in biological sciences.

Learn how to use the Linux desktop and included software, run 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
    • 2.1.1. Linux distribution
    • 2.1.2. Desktop environment
    • 2.1.3. This book uses Linux Mint
  • 2.2. Running a Linux desktop
    • 2.2.1. Running Linux as a virtual machine
    • 2.2.2. The Desktop
    • 2.2.3. Changing system settings
  • 2.3. Available software
    • 2.3.1. Files — manage files and directories
    • 2.3.2. Firefox — browse the web
    • 2.3.3. Text Editor — create and edit text files
    • 2.3.4. LibreOffice — edit documents and spreadsheets
    • 2.3.5. Terminal — access the command-line
    • 2.3.6. Screenshot — take screenshots of desktop or windows
    • 2.3.7. Software Manager — install software from repositories
    • 2.3.8. GNU Image Manipulation Program — edit images
    • 2.3.9. Inkscape — create vector graphics
    • 2.3.10. Notes
  • 2.4. Files and directories
    • 2.4.1. Your home directory
    • 2.4.2. Hidden files and directories
    • 2.4.3. Important files in home directory
    • 2.4.4. File and directory names are case-sensitive
    • 2.4.5. Accessing the root filesystem
    • 2.4.6. Transferring files between systems
• 3. Getting software
  • 3.1. The quick and easy method
    • 3.1.1. Requirements
    • 3.1.2. Finding and installing software
    • 3.1.3. Removing installed software
    • 3.1.4. Updating installed software
    • 3.1.5. Notes
  • 3.2. Python packages
    • 3.2.1. Requirements
    • 3.2.2. Searching for a package on PyPI
    • 3.2.3. Installing a Python package
    • 3.2.4. Updating an installed package
    • 3.2.5. Removing an installed package
    • 3.2.6. Using installed packages
    • 3.2.7. Python virtual environments
    • 3.2.8. Notes
  • 3.3. Perl modules
    • 3.3.1. Requirements
    • 3.3.2. Configuring local-lib module
    • 3.3.3. Searching for a module on CPAN
    • 3.3.4. Installing a Perl module
    • 3.3.5. Using installed modules
  • 3.4. R packages
    • 3.4.1. Requirements
    • 3.4.2. Starting an R session
    • 3.4.3. Installing a package from CRAN
    • 3.4.4. Installing a package from Bioconductor
    • 3.4.5. Updating an R package
    • 3.4.6. Removing an R package
    • 3.4.7. Notes
  • 3.5. Conda packages
    • 3.5.1. Requirements
    • 3.5.2. Installing Conda
    • 3.5.3. Using Conda
    • 3.5.4. Notes
  • 3.6. Debian packages
    • 3.6.1. Requirements
    • 3.6.2. Installing a Debian package
    • 3.6.3. Upgrading installed software
    • 3.6.4. Removing installed software
    • 3.6.5. Notes
• 4. Using the command line
  • 4.1. Shell and Terminal
    • 4.1.1. The shell prompt
  • 4.2. An overview of commands
    • 4.2.1. Command options
    • 4.2.2. Getting help on using commands
    • 4.2.3. date — display current date and time
    • 4.2.4. cd — change directory
    • 4.2.5. mkdir — create new directory
    • 4.2.6. rmdir — remove empty directory
    • 4.2.7. ls — list files
    • 4.2.8. cp — copy files
    • 4.2.9. cat — display contents of files or combine them
    • 4.2.10. less — view and navigate file contents
    • 4.2.11. head — print first few lines of a file
    • 4.2.12. tail — print last few lines of a file
    • 4.2.13. mv — move a file or directory
    • 4.2.14. rm — remove files or directories
    • 4.2.15. echo — display text or values of variables
  • 4.3. Other useful commands
    • 4.3.1. df — report disk usage
    • 4.3.2. du — estimate disk usage of files or directories
    • 4.3.3. find — search for files
    • 4.3.4. free — view free and used memory
    • 4.3.5. locate — find files using their names
    • 4.3.6. which — locate a command
  • 4.4. Editing text files using nano
    • 4.4.1. Create new file
    • 4.4.2. Pasting text from clipboard
    • 4.4.3. Saving changes
    • 4.4.4. Exit nano
  • 4.5. Exercise — using the command-line
    • 4.5.1. Summary of steps
    • 4.5.2. Get sample data
    • 4.5.3. Install NCBI BLAST+ package
    • 4.5.4. Download query sequence
    • 4.5.5. Download protein sequence database
    • 4.5.6. Search database using query sequence
  • 4.6. Notes
    • 4.6.1. Adding directories to PATH
    • 4.6.2. Dealing with spaces in file names
• 5. Galaxy
  • 5.1. Why use Galaxy?
    • 5.1.1. What can you use Galaxy for?
    • 5.1.2. Why run Galaxy on your computer?
  • 5.2. Running Galaxy on your computer
    • 5.2.1. Check system requirements
    • 5.2.2. Getting the latest release of Galaxy
    • 5.2.3. Creating a Python virtual environment
    • 5.2.4. Starting Galaxy
    • 5.2.5. Stopping Galaxy
  • 5.3. Registering a user account
    • 5.3.1. Managing your account
  • 5.4. Granting admin privileges for user
    • 5.4.1. Creating a configuration file
    • 5.4.2. Adding user to list of admin users
    • 5.4.3. Restarting Galaxy
    • 5.4.4. Verifying admin access
• 6. Reference management
  • 6.1. Installing Zotero
  • 6.2. Collecting references from the web
    • 6.2.1. Installing Zotero Connector
  • 6.3. Integrating Zotero in LibreOffice
    • 6.3.1. Installing Word Processor add-in
• 7. Note-taking
  • 7.1. Features of Zim
  • 7.2. Installing Zim
  • 7.3. Creating a notebook
  • 7.4. Taking notes
    • 7.4.1. Basic text formatting
    • 7.4.2. Inserting images
    • 7.4.3. Adding more pages
    • 7.4.4. Deleting or renaming pages
  • 7.5. Exporting notes and notebooks
  • 7.6. Activating more features using plugins
    • 7.6.1. Enabling a plugin
  • 7.7. Getting help
• 8. Glossary
• 9. Credits

Index

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Last updated: Apr 19, 2022