MEDS Computing Requirements & Software Installation Guide

Author

UCSB MEDS

Modified

July 1, 2024

Incoming MEDS students should follow the steps detailed in this software installation guide before summer orientation – there will be a dedicated troubleshooting session during orientation, should you need help completing any of the installations.

Please carefully read through the computing requirements & recommendations section before deciding on what computer to purchase / use ahead of MEDS.

Installation Guide

1. Install or update R

Visit cloud.r-project.org to download the most recent version of R for your operating system. You should have at least version 4.4.0 (released 2024-04-24) running when you start MEDS.

2. Install or update RStudio

While R is a programming language, RStudio is a software (often referred to as an IDE, Integrated Development Environment) that provides R programmers with a neat, easy-to-use interface for coding in R. There are a number of IDEs out there, but RStudio is arguably the best and definitely most popular among R programmers.

NOTE: You need both R and RStudio installed

RStudio will not work without R installed, and you won’t particularly enjoy using R without having RStudio installed. Be sure to install both!

Image Credit: Exploratory Data Analysis in R, by Manny Gimond

  • New install: To install RStudio, visit rstudio.com/products/rstudio/. Download the free (“Open Source Edition”) Desktop version for your operating system. You should install the most up-to-date version available that is supported by your operating system.

  • Update: If you already have RStudio and need to update, open RStudio, and under Help (in the top menu), choose Check for updates. If you have the most recent release, it will return No update available. You are running the most recent version of RStudio. Otherwise, you should follow the instructions to install an updated version.

  • Open RStudio (click on the logo shown below):

Note for Mac users: you may need to install command line tools and XQuartz.

If upon opening RStudio you are prompted to install Command Line Tools, do it.

  • To install command line tools (if you’re not automatically prompted), run xcode-select --install in the RStudio Terminal
  • To install XQuartz, visit xquartz.org

(Note for Windows users: Windows machines should already have command line tools installed, and XQuartz is only required for Macs).

3. Install Quarto if necessary (automatically installed with RStudio)

Quarto is a scientific publishing tool built on Pandoc that allows R, Python, Julia, and ObservableJS users to create dynamic documents, websites, books and more.

Quarto is included with RStudio v2022.07.1+ so there no need for a separate download/install if you have the latest version of RStudio! You can find all releases (current, pre, and older releases) on the Quarto website download page, should you want/need to reference them.

4. Check for git

You should already have git on your device, but let’s check for it anyway.

  • Open RStudio

  • In the Terminal, run the following command (choose the option for your operating system):

RStudio Terminal
which git
RStudio Terminal
where git
  • If you get something that looks like a file path to git on your computer (e.g. /usr/local/bin/git on a Mac, C:\Program Files\Git\mingw64\bin\git.exe on Windows, though it could differ slightly on your computer), then you have git installed. If you instead get no response at all, you should download & install git here: git-scm.com/downloads
An aside: We’ll be using git a lot throughout MEDS.

GitHub’s Git Guides are a really wonderful resource to refer to!

5. Create a GitHub account

  • If you don’t already have a GitHub account, go to https://github.com and create one. Check out Jenny Bryan’s Happy Git with R, Ch. 4 for some helpful considerations when choosing a username. We suggest that you use a personal email or your @bren.ucsb.edu email when setting up your account (rather than your @ucsb.edu email, which will be deactivated after you graduate).

6. Configure git

  • In RStudio, open the Terminal. Run the following commands (by pressing return after each line). Be sure to replace the username (keep the quotation marks!) with your GitHub username and the email with the email you used for your GitHub account.
RStudio Terminal
git config --global user.name "Jane Doe"
git config --global user.email janedoe@example.com
  • Then, in the Terminal run the following, and carefully check that the name and email returned match your GitHub information:
RStudio Terminal
git config --list --global
IMPORTANT: If you’re configuring git on a Bren server (e.g. Taylor or Tsosie), you must also run the following in the Terminal 
RStudio Terminal
git config --global credential.helper 'cache --timeout=10000000'

This prevents important credentials (e.g. a GitHub Personal Access Token, PAT, which you’ll set in step #7) from being removed from the server’s memory. You do not need to complete this step when configuring git on your local computer.

7. Store your GitHub personal access token (PAT)

First: What even is a personal access token? From GitHub’s documentation:

Personal access tokens (PATs) are an alternative to using passwords for authentication to GitHub when using the GitHub API or the command line.

This means that in order to push your work (files, scripts, etc.) from your laptop (or any other computer) to GitHub, you’ll need to first to generate a PAT. Importantly, you’ll need to generate a PAT for each computer you wish to work from. For example, we will complete the following steps to create a PAT for your personal laptop, but you’ll also need to create a PAT if/when you choose to work on a second computer at home or any of the Bren servers. Good news is that you can follow these same steps when you’re ready to set up additional PATs on other machines. For now, let’s get a PAT for our personal laptop squared away:

  • Once you have git configured successfully, install the {usethis} package in R by running the following in the RStudio Console:
RStudio Console
install.packages(“usethis”)

A lot of scary looking red text will show up while this is installing - don’t panic. If you get to the end and see something like below (with no error) it’s installed successfully.

  • Run the following in the RStudio Console:
RStudio Console
usethis::create_github_token()
  • Enter your GitHub password if/when prompted. You’ll be taken to a screen that looks like this:

  • In the Note field, you should see some autopopulated text: R:GITHUB_PAT. We suggest changing this to something that signifies what machine it’s being used for. For example, if you are generating a PAT for your laptop, you might choose to rename it, My Personal Laptop.

  • Next, you’ll see a section called Select scopes with reasonable options already selected for you. Do not change anything. Just scroll down to the bottom of that page and click the green Generate token button:

  • Copy the generated PAT to your clipboard

  • Back in RStudio, run the following in the Console:

RStudio Console
gitcreds::gitcreds_set()

This will prompt you to paste the PAT you just copied from GitHub. Paste the PAT, press Enter to run. You should see something like this show up if all is well so far (you’ll have pasted your PAT where the example below says “REDACTED”):

  • In the RStudio Console, run:
RStudio Console
usethis::git_sitrep()

Does it return information about your connected GitHub account that looks something like below? Great! You’ve configured git and successfully stored your PAT.

A note on expiring tokens:

Setting an expiration date on personal access tokens is highly recommended in order to keep your information secure. GitHub will send you an email when it’s time to regenerate a token that’s about to expire. Follow the email prompts, then use gitcreds::gitcreds_set() to reset your token.

8. Install Anaconda

Anaconda is a distribution of the Python and R programming languages that aims to simplify package management and deployment. You’ll need to download the Graphical Installer, which provides a graphical user interface (GUI) to facilitate writing code. Choose the option for your operating system:

Click here to download 64-bit Graphical Installer for MacOS. This might pop open a new tab with a “redirecting you to…” phrase, but Anaconda should be downloading at the same time. It might take a couple minutes. After it’s downloaded, click it and hit Allow if you see the following:

Follow the installation steps to complete Anaconda installation.

Click here to download the 64-bit Graphical Installer Anaconda for Windows. Run the executable to install, which will look something like this:

9. Install VS Code

Visual Studio Code (aka VS Code) is a language-agnostic source-code editor – it’s works similarly to RStudio, but allows users to install extensions which add support for lots of different languages, debuggers, tools, etc. Download VS Code for your operating system here.

10. Install Cyberduck

Cyberduck is a program that allows you to browse files on a remote server. Download here.

11. Install UCSB’s Pulse Secure Campus VPN (Virtual Private Network)

For secure remote access to the UCSB’s campus network when you’re not physically present on campus, you’ll need to download and install the Pulse Secure VPN client. This will allow you to access UCSB’s technology resources (including servers, journal subscriptions, etc.) anytime and from anywhere.

See this Bren Zendesk article for directions on how to get started.

12. Create your Slack account and join MEDS

  • Click here to join our UCSB-MEDS Slack Workspace

  • Customize your profile with your name and photo (adding a photo helps instructors and TAs learn your names more quickly!).

  • Join the summer course channels (#eds-212, #eds-221, #eds-214, #eds-217)

13. Access Google apps through your @ucsb.edu account

Once enrolled and your UCSBnetID is activated, you will have access to your UCSB Connect Account which provides email, calendaring, and collaboration services. You must use this account (UCSBnetID@ucsb.edu) to log in and access all of your Google Apps (including Google Calendar, Google Drive, etc.).

The MEDS Google Calendar contains all classes and events relevant for our MEDS students. Feel free to add this to your calendar if you find it helpful. To do so, log in to Google Calendar using your @ucsb.edu credentials > Click on the + next to “Other calendars” on the left-hand side of your screen and choose “Browse resources” > Click the drop down arrow next to “bren” and check the box next to “bren-calendar-meds”

14. Request key card access to Bren / NCEAS

New students must request an Access ID Card (aka your UCSB photo identification), which are available for pickup at the UCEN 24 hours after your request is made. We recommend submitting your request before summer orientation, so that it’s ready for pickup during your first day on campus.

Once you receive your Access ID Card, you must complete this form to gain key card access to Bren (after hours) and NCEAS (all hours).


~ END Installation Guide ~


Computing requirements & recommendations

The MEDS program requires all students to have a personal laptop to use during the program. Our curriculum is designed to work across different operating systems and computers, as long as they meet some minimum requirements.

Specifically, your computer should:

  • be no more than 4 years old, and in any case be fully supported by the manufacturer. For example, Apple won’t repair anything that’s more than 7 years old
  • be running Windows, macOS, or Linux (Please note that we offer limited support for Linux)
  • have at least 50 GB storage space available for MEDS applications and coursework
  • have at least 8 GB of RAM (the more the better!)
  • have a 64-bit CPU
Be sure to install the latest operating system

If you already have a laptop that you plan to use in MEDS, be sure to install the latest operating system before the program begins:

  • Mac users: be sure to update macOS to the newest supported version, as indicated by System Preferences→Software Update.
  • Windows users: you should have Windows 10 installed

If you are purchasing a new computer:

We recommend:

  • at least 16 GB of RAM
  • at least 512 GB of SSD (not “disk”!) storage
  • the manucafturer’s extended warranty or service plan (e.g., AppleCare+).

You can purchase a Macbook Air using the higher education discount for $899 before tax and AppleCare. A PC can cost anywhere from $500 to more than $3,000; you generally get what you pay for.

Loaner equipment

If your computer breaks or dies, we can typically loan you a Windows laptop for up to a month (which should be long enough to have your computer repaired or to purchase a new one).

Home setup

You may consider having a dedicated computer setup that includes an external monitor, keyboard, and / or mouse at home. A stable at-home WiFi connection is necessary for completing work remotely (i.e. off-campus).


~ END Computing Requirements & Recommendations ~