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Linux for Biologists
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  • 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
        • Requirements
        • Importing the virtual machine image
        • Starting the virtual machine
        • Stopping the 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
    • 4.2. 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
  • 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
    • 6.3. Integrating Zotero in LibreOffice
  • 7. Note-taking
    • 7.1. Features of Zim
    • 7.2. Installing Zim
    • 7.3. Creating a notebook
    • 7.4. Taking notes
    • 7.5. Exporting notes and notebooks
    • 7.6. Activating more features using plugins
    • 7.7. Getting help
  • 8. Glossary
  • 9. Credits
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6. Reference management#

Zotero is a free and open-source software for collecting and organizing scientific research articles and other publications.

Articles can be organized using collections and tags, and can be included as citations in the documents you create.

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  • 6.1. Installing Zotero
  • 6.2. Collecting references from the web
  • 6.3. Integrating Zotero in LibreOffice
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6.1. Installing Zotero
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5.4.4. Verifying admin access
Copyright © 2023, Vimalkumar Velayudhan
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