The Ultimate Obsidian Setup for PhD Students & Academics (Second Brain for Researchers)

Research is hard and difficult. I always acknowledge that. But there is a way to make it frictionless and easy to maintain — using Obsidian as your note-taking system and managing your research project inside Obsidian.

In this guide, I’ll show you five Obsidian plugins and settings that transform your research workflow and build your research second brain.

Why Obsidian for Research?

As a PhD student or academic researcher, you juggle:

• Reading papers and taking notes
• Managing literature reviews
• Tracking meetings with supervisors
• Organizing experiments and data
• Maintaining research logs
• Managing deadlines and tasks

Instead of jumping between multiple tools, you can manage your entire research project inside Obsidian.

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Step 1: Setting Up Your Research Hub

Download and Install Obsidian

Visit obsidian.md and download Obsidian for your platform.

Understanding “Vaults”

When you first open Obsidian, you’ll see three options:

1. Create a new vault
2. Open folder as vault
3. Open vault from Obsidian Sync

Important: A “vault” is just Obsidian’s terminology for a folder. That’s it — simple as that.

Creating Your Research Hub

1. Click Create new vault
2. Name it something like “Research Hub”
3. Crucially, select a location that’s backed up automatically (like OneDrive, Google Drive, or Dropbox)

💡 Pro Tip: Since you’re building a knowledge base for your entire research career, store it in a cloud-synced folder from day one.

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5 Essential Plugins for Research Workflow

1️⃣ PDF++ (Literature Review Plugin)

PDF++ is a game-changer for researchers. It allows you to:

• Highlight PDFs directly inside Obsidian
• Convert paper highlights into notes with bidirectional linking
• Jump from note → exact PDF location instantly
• Track where every quote came from (essential for citations)

How it works:

1. Install PDF++ from Community Plugins
2. Open a PDF in Obsidian
3. Select text and use “Copy with callout” to create a linked note
4. When your supervisor asks “Where did you get this line?”, click and the PDF opens at that exact location

🔗 Deep dive: PDF++ Plugin Video

2️⃣ Templates Plugin

Templates allow you to replicate consistent formatting across your research notes.

What you can create:

• Research logs
• Meeting notes with supervisors
• Literature review templates
• Daily research journals
• Experiment tracking notes

Setup:

1. Enable the Templates core plugin
2. Create a “Templates” folder
3. Create templates with YAML front matter:

   ---
   title: 
   date: 
   tags: [log]
   ---
   

Usage: Insert templates with one click to populate headers, dates, tags, and structure automatically.

3️⃣ Natural Language Dates

This plugin makes timestamping effortless and consistent.

Features:

• Type @today to insert today’s date
• Type @tomorrow for tomorrow’s date
• Type @2026-01-02 for any date
• Automatically creates linked notes for dates

Use cases:

• Research journal entries
• Meeting notes with supervisors
• Experiment logs
• Project milestones

📅 Perfect for keeping track of when things happened — essential for research documentation.

4️⃣ Tasks Plugin (Research Task Management)

Transform your meeting notes into actionable tasks.

How it works:

1. In any note, create a task: ```markdown
   • Submit project report #task due:today
   • Complete experiment #task due:tomorrow ```
2. Tasks automatically appear in your task manager
3. Set due dates directly in notes

Integration with Daily Notes: Create a task code block to collect all tasks from your vault:

```tasks
not done
due today
```

🎯 Pro tip: Use daily notes as your research control center to see all tasks in one place.

5️⃣ Daily Notes (Your Research Control Center)

Daily Notes is a core plugin that automatically creates a new note each day.

Why it’s essential:

• Creates a daily research journal automatically
• Collects all tasks from your vault
• Plans your research day in one place
• Tracks experiments, meetings, and ideas over time

Setup:

1. Enable Daily Notes core plugin
2. Configure date format
3. Open “Today’s daily note” anytime

Workflow:

• Each morning: Review your daily note
• During the day: Log tasks and notes
• Each evening: Plan tomorrow’s research goals

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Putting It All Together: Your Research Second Brain

Here’s how these plugins work together to create a frictionless research system:

Daily Workflow:

1. Morning: Open Obsidian → Daily note shows tasks + schedule
2. Literature Review: Use PDF++ to read papers and create linked notes
3. Meetings: Use Templates + Natural Language Dates for meeting notes
4. Task Tracking: Create tasks in notes, see them all in Daily Notes
5. Evening: Log research progress, plan tomorrow’s tasks

Long-term Benefits:

• ✅ Never lose a reference — everything is linked and searchable
• ✅ Instant citation tracking — jump from note to paper location
• ✅ Reduced mental load — one system, not five tools
• ✅ Research documentation — dates and context preserved
• ✅ Long-term knowledge base — build your research second brain

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Who Is This For?

• PhD students managing literature reviews and experiments
• Academic researchers juggling multiple projects
• Graduate students learning research workflows
• Research engineers building knowledge systems
• Knowledge workers managing complex projects

If you do research, writing, or long-term thinking, this workflow will help.

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Resources Mentioned

• Obsidian Download: obsidian.md
• Obsidian Starter Playlist: Watch here
• PDF++ Deep Dive: Video tutorial

• Tasks Plugin Tutorial: Part 1

  Part 2

• Free Obsidian Starter Kit: shuvangkardas.com/obsidian-starter-kit

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Final Thoughts

Research doesn’t have to be overwhelming. With the right setup in Obsidian, you can:

• Stop losing references
• Answer “where did this come from?” instantly
• Track experiments, meetings, and ideas over time
• Reduce mental load
• Focus on thinking and writing, not tool-hopping

This is how I build my Research Second Brain using Obsidian.

If you found this helpful, share it with fellow researchers! 👩‍🔬👨‍🔬

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