Virtual Machines — Setup Guide for Ubuntu, R, RStudio, and Biostrings

Author: phD Caterina Giachino Contact: caterina.giachino@unina.it

A step-by-step guide to help beginners learn how to work with Virtual Machines, install Ubuntu Linux, and set up a bioinformatics environment with R, RStudio, and the Biostrings package.

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📘 Table of Contents

1. What is a Virtual Machine?
2. Creating the Ubuntu Virtual Machine
3. Installing R and RStudio
4. Installing Biostrings
5. Your Learning Environment

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1. What is a Virtual Machine?

A Virtual Machine (VM) is a software-based computer that runs inside your actual computer.

A VM allows you to:

• Create a safe, isolated environment for experiments
• Install operating systems (e.g., Ubuntu Linux) without modifying your real machine
• Practice programming and bioinformatics
• Reset or delete the environment at any time

In this guide, we will use VMware Workstation 17 Player to create a VM running Ubuntu 22.04. Then we will install R, RStudio, and the Biostrings package for sequence analysis.

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2. Creating the Ubuntu Virtual Machine

Step 1 — Download Ubuntu

Download the ISO image from: 🔗 https://ubuntu.com/download/desktop

Use: ubuntu-22.04.1-desktop-amd64.iso

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Step 2 — Create the VM in VMware Player

1. Open VMware Workstation 17 Player
2. Click Create a New Virtual Machine
3. Select the Ubuntu ISO
4. Continue with the default settings until resource allocation

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Step 3 — Allocate System Resources

Suggested configuration:

• RAM: 4–8 GB
• Processors: 4 cores
• Keyboard layout: Italian

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Step 4 — Ubuntu Installation Settings

Inside the installer, select:

• Normal installation
• Install third-party software (graphics, Wi-Fi, etc.)
• Disk option → Erase disk and install Ubuntu
• Virtual disk size → ≥ 35 GB

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Step 5 — First Boot Settings

After installation:

• Skip the online account
• Skip feedback
• Skip "Ubuntu Pro"
• Install all system updates
• Switch to Full Screen in VMware Player

Your Ubuntu system is now ready! 🎉

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3. Installing R and RStudio

Open the Terminal: CTRL + ALT + T

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Step 1 — Add the CRAN Repository Key

wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | \
sudo tee /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc

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Step 2 — Install version tools

sudo apt install lsb-core
sudo apt-get install lsb-release
lsb_release -v

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Step 3 — Add R repository (Ubuntu 22.04 – Jammy)

sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/"

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Step 4 — Install R

sudo apt update
sudo apt install --no-install-recommends r-base

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Optional — Add additional precompiled R packages

sudo add-apt-repository ppa:c2d4u.team/c2d4u4.0+
sudo apt update

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Step 5 — Install RStudio Desktop

Download the .deb file: 🔗 https://posit.co/download/rstudio-desktop/

Install it:

sudo apt install ./rstudio-*.deb

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4. Installing Biostrings

We install only Biostrings.

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Option A — Install via Ubuntu repositories

sudo apt-get update
sudo apt-get install r-bioc-biostrings

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Option B — Install directly inside R (recommended)

Start R:

if (!require("BiocManager")) install.packages("BiocManager")
BiocManager::install("Biostrings")

Only the required dependencies will be installed. ✔

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5. Your Learning Environment

You now have a fully functional virtual environment for:

• Working safely with Linux
• Practicing R and RStudio
• Learning sequence manipulation
• Using Biostrings for DNA/RNA/protein analysis

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When I first entered the world of Bioinformatics, I was not yet confident with coding. I was afraid that a wrong command could break my computer — a computer I had bought with my own savings. Using a Virtual Machine completely changed my experience: it allowed me to experiment freely, make mistakes, learn, and explore without fear of damaging anything. I am deeply grateful to my engineering friends, who encouraged me and pushed me to overcome this first difficulty. I hope this setup can help people who, like me, felt overwhelmed at the beginning.

Keep learning, be curious, and don’t be afraid to try things out. This VM is your protected, dedicated workspace for learning bioinformatics.

Have fun, everyone! 🚀