Digital note taking with Obsidian for scientists: Basics

Published

October 15, 2026

Description

Notes, paper summaries, ideas and to-do lists tend to pile up across scattered files, hard to search and harder to connect. Obsidian is a free note-taking app that keeps them in one linked, searchable place, stored as plain text files on your own computer.

In this hands-on workshop for researchers (no prior experience needed), you learn to set up and structure your own notebook and link related notes, ideas and papers so they’re easy to find again. You also build a daily-note workflow to plan your days and track tasks, and use templates for notes you write often. You leave with a starter setup and materials to build on.

Slides in full screen     Download PDF slides

TipExercises

Step-by-step guides for the hands-on parts of the workshop:

For reference: Markdown cheatsheet

Demo vault

The demo vault contains the examples, templates, and workflow guides from the workshop and more:

  • Daily notes and tasks
  • Project hubs with tasks and meetings
  • Zettelkasten
  • Literature notes from Zotero
  • Web clippings

Download demo vault

Open the demo vault in Obsidian

  1. Download the ZIP file and unzip it (Right-click → Extract / Unzip). You should now see a normal folder called notebook_demo.
  2. Open Obsidian.
  3. In the bottom left corner, click on the vault name and then Manage vaults.

Obsidian vault switcher in the bottom left corner. A list of vaults is open, with the option Manage vaults at the bottom.

  1. Click Open folder as vault.
  2. Select the unzipped demo vault folder and click Open.
  3. Obsidian may ask whether you trust the vault. Confirm to enable the plugins (Calendar, Tasks, Zotero Integration), they are needed for the workflows.

How to use the demo vault

  • Start with the README note. It links to all workflow guides in the folder Workflow guides.
  • Use the vault as a reference and a toolbox meant for inspiration:
    • Open it next to your own vault
    • Copy templates or small parts you like
    • Ignore everything that doesn’t fit your workflow

Resources

Obsidian

Synchronization and import

  • Official Obsidian sync: Paid service to sync your notes across devices. As a student or scientist, you get a 40% discount (find out here how)
  • If you just connect two computers and not mobile devices, you can also put your vault into a cloud storage like Google Drive
  • Importer plugin: Import notes from other apps like Notion, Microsoft OneNote, Google Keep, Apple Notes, …

Organize your notes

Zettelkasten and literature notes