News:Linux for Biologists e-book (free to read online)
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4 months ago
vimalkvn ▴ 290

Hi all, I wrote this book for students and researchers in biological sciences who are new to Linux. I believe some topics discussed might be useful for beginners in Bioinformatics as well.

Cover image of Linux for Biologists e-book

Outline of contents:

Getting started with Linux

  • What is Linux
  • Running a Linux virtual machine
  • The desktop
  • Available software
  • Files and directories

Getting software on Linux

  • The quick and easy method
  • Python packages
  • Perl modules
  • R packages
  • Conda packages
  • Debian Packages

Using the Linux command line

  • Shell and Terminal
  • Commands — an overview
  • Other useful commands
  • Editing text files using nano
  • Exercise — using the command-line
  • Notes

Getting started with Galaxy

  • Why use Galaxy?
  • Running Galaxy on your computer
  • Register a user account
  • Grant administrator privileges for user

Documentation

  • Managing references using Zotero
  • Creating a notebook using Zim
linux python galaxy conda virtual-machine • 722 views
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28 days ago
vimalkvn ▴ 290

Update: Sep 21, 2021

I have made the book available online:
https://linuxforbiologists.readthedocs.io/

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This will be quite helpful to beginners. Does Linux Mint translate well to usage in Ubuntu - all GNU binaries, perhaps? I recall Mint being a better UX version of Ubuntu way back when, have they diverged? I ask because most beginners use either Ubuntu or Red Hat flavors (if their institute is running a cluster), and learning on a GNU based system would help them.

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Thank you, Ram. Linux Mint is based on Ubuntu LTS, so from a user perspective, the transition wouldn't be that hard, I believe. Mint also uses Ubuntu package repositories so, the same packages (including GNU utilities and build tools) would be available for installation using apt or software manager or synaptic.

The major difference is the desktop environment used. Mint, by default, uses the Cinnamon desktop, which has a more traditional desktop feel — a start menu with applications, panel with list of open windows, a system tray etc., In contrast, Ubuntu uses the GNOME desktop, which has a modern look and feel but has a different layout and workflow, which might take a while for new users to get used to.

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Thank you, Vimal. I'll be sure to point your resource to beginners - there was sore need of this resource and I love your work.

Is your work funded by a grant or is all your time on this volunteered?

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That's great to hear. Thank you very much. This is done on my own time and I don't receive any funding at the moment.

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You could add a way to donate, both as a small compensation for your effort as well as for any upkeep operations. The Biostar Handbook works kind of like this (but on a larger scale with a commitment to regular updates), maybe something small along those lines might work for you too.

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Thank you very much for this suggestion.
I have now added some links for donation and sponsorship on the website and on the GitHub repository.

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