Getting Started with Obsidian

What is Obsidian?

Obsidian is a powerful note-taking and knowledge management app that stores all your files as plain markdown. You own your data—everything is stored locally on your computer, and you can sync it however you want (or not at all). This guide covers the basics and how to customize your workspace with plugins and themes.

Step 1: Install Obsidian

  1. Go to obsidian.md
  2. Click Download and choose your operating system (Windows, Mac, or Linux)
  3. Run the installer and follow the prompts
  4. Open Obsidian when installation is complete

Step 2: Open Your First Vault

A vault is a folder that Obsidian manages. Open Methods Hub provides a pre-configured vault.

2.1 Extract the Methods Vault

  1. Download Methods_Vault.zip from the Resources page
  2. Extract it to a location like:
    • Windows: C:\Users\YourName\Documents\Methods_Vault
    • Mac: ~/Documents/Methods_Vault
    • Linux: ~/Documents/Methods_Vault

2.2 Open the Vault in Obsidian

  1. Open Obsidian
  2. Click Open folder as vault
  3. Navigate to where you extracted Methods_Vault and select it
  4. Click Open

Obsidian will now show your vault with all the pre-configured folders and templates!

Step 3: Navigate Your Vault

The Sidebar

On the left side of Obsidian, you’ll see:

  • File Explorer: Shows all folders and files in your vault
  • Search: Find notes by keyword
  • Starred: Quick access to your favorite notes
  • Backlinks: See how notes are connected

The Ribbon (Left Edge)

The leftmost thin bar has icons for: - Create new note - Open vault settings - View help

The Main Editor

Click any note to open it and start writing. Notes are stored as .md (markdown) files.

Step 4: Community Plugins

Obsidian has a large community that creates plugins to extend functionality. Here’s how to install them.

4.1 Enable Community Plugins

By default, community plugins are disabled. To enable them:

  1. Click the Settings icon (gear icon) in the bottom left
  2. Go to Community plugins
  3. Click Turn on community plugins (if it’s greyed out, they’re already on)

4.2 Install a Plugin: QMD as Markdown

The textbook chapters are in .qmd format (Quarto markdown). Obsidian doesn’t recognize this format by default, but the qmd as md plugin fixes this.

To install it:

  1. In Settings, go to Community plugins
  2. Click Browse (or search icon)
  3. Search for “qmd as md” (by Daniel Borek)
  4. Click the result to open the plugin page
  5. Click Install
  6. Once installed, click Enable to turn it on

Now you can view and edit .qmd files just like regular markdown files!

4.3 Other Useful Plugins

Here are some community plugins that work great with the Open Methods Hub:

Plugin What It Does
Dataview Query and display your notes as databases/lists
Calendar Visual calendar for journal entries
Templater Advanced template features beyond Obsidian’s built-in system
Daily Notes Automatically create and link daily notes
Task Advanced task management with due dates and status
Excalidraw Draw diagrams and sketches within notes

To install any of these, repeat steps 2-5 above with the plugin name.

Step 5: Customize with Themes

Obsidian comes with a light and dark theme by default, but the community has created hundreds more. Here’s how to change themes.

5.1 Access Themes

  1. Open Settings (gear icon, bottom left)
  2. Go to Appearance
  3. Scroll to Themes section

5.2 Choose a Built-in Theme

Under “Manage”, you’ll see two built-in themes: - Default Light Theme - Default Dark Theme (recommended for long study sessions)

Click either to apply it immediately.

5.3 Install Community Themes

For custom themes from the community:

  1. Make sure community plugins are enabled (see Step 4.1)
  2. In Appearance, look for Manage button next to Themes
  3. Click Manage (or the folder icon)
  4. Click Browse in the top right
  5. Search for a theme name (e.g., “Minimal”, “Nord”, “Dracula”)
  6. Click the theme to see a preview
  7. Click Install and then Use

Step 6: Essential Settings

6.1 File Management

In Settings → Files & Links: - Default location for new notes: Choose where new notes appear (e.g., “Inbox” folder) - Show unsaved indicator: Helpful to know when to save

6.2 Editor Settings

In Settings → Editor: - Strict line breaks: Makes formatting more predictable - Line numbers: Toggle on/off based on preference - Indent size: Set to 2 or 4 spaces (2 is cleaner for markdown)

6.3 Hotkeys

In Settings → Hotkeys, you can set keyboard shortcuts for common actions: - Toggle sidebar (great for focus mode) - Create new note - Search in vault - Follow backlinks

6.4 Sync & Backup

In Settings → About, you’ll see sync options: - Obsidian Sync (paid): Cloud sync across devices - Git: Use Git to version control your vault (recommended for this course!) - Manual backups: Copy your vault folder regularly

For the Open Methods Hub, using Git is recommended so you can version control your work.

Step 7: Basic Markdown Syntax

Notes in Obsidian use markdown. Here are the essentials:

Syntax Result
# Heading 1 Large heading
## Heading 2 Medium heading
### Heading 3 Small heading
**Bold text** Bold text
*Italic text* Italic text
- List item Bullet list
1. Numbered item Numbered list
[Link text](https://example.com) Hyperlink
[[Note name]] Link to another note in your vault
> Quote Block quote
`code` Inline code

Step 8: Create Your First Note

Let’s practice:

  1. Click the “Create new note” icon (top left, looks like a page)
  2. Type a title like “My First Note”
  3. Start writing in markdown:
# My First Note

## What I'm Learning

- Obsidian basics
- Markdown syntax
- How to organize my research

## Goals

1. Complete the Open Methods Hub
2. Master data analysis
3. Tell stories with data
  1. Obsidian saves automatically—no need to click Save!
  2. Notice the file appears in your vault in the File Explorer (left sidebar)

Step 10: Tips for Success

Keep It Simple

Don’t over-customize at first. Start with the default theme and no plugins. Add what you need as you go.

Use the Vault Structure

The Methods_Vault comes pre-organized: - 00_Inbox: Capture ideas quickly here - 01_Journal: Weekly reflections - 02_Literature: Research notes and citations - 03_Project: Your active research work - 04_Resources: Attach images, PDFs, videos

Follow this structure to stay organized.

Back Up Your Work

If using Git:

git add .
git commit -m "Update research notes"
git push

Or regularly copy your Methods_Vault folder to an external drive.

Embrace Plain Text

One beauty of Obsidian is that everything is plain markdown. You can: - Open notes in any text editor - Version control with Git - Search with command-line tools - Never worry about proprietary formats

Troubleshooting

QMD Files Won’t Open

Make sure you’ve installed and enabled the qmd as md plugin (see Step 4.2).

Plugin Not Showing

Try restarting Obsidian. Sometimes plugins need to reload.

Can’t Find My Vault

Make sure you opened the correct folder as a vault. Look for a .obsidian folder inside your vault folder—that’s how Obsidian knows it’s a vault.

Performance Slow

If Obsidian feels sluggish: - Disable unused plugins - Check your note count (very large vaults may slow down) - Restart Obsidian

Next Steps

  1. ✅ Install Obsidian
  2. ✅ Extract and open the Methods_Vault
  3. ✅ Install the qmd as md plugin
  4. ✅ Choose a theme you like
  5. ✅ Create your first note
  6. ✅ Explore the vault structure
  7. Start the Open Methods Hub!

Resources

Questions?

If you get stuck: 1. Check the Obsidian Help documentation 2. Search the community forum 3. Check your vault’s .obsidian folder settings 4. Come to office hours!