Digital note taking with Obsidian for scientists: Basics

Scientific workflows: Tools and Tips 🛠️

2026-10-15

What is this lecture series?

Scientific workflows: Tools and Tips 🛠️

📅 Every 3rd Thursday 🕓 4-5 p.m. 📍 Webex

  • One topic from the world of scientific workflows
  • Material provided online
  • If you don’t want to miss a lecture
  • For credit points: Send me a short message (Email or Webex)

Workshop goals

  • Overview of Obsidian and its possibilities
  • Get started with your own notebook
  • Know if Obsidian is the tool for you

Overview

  1. Introduction to Obsidian
    • Basic functionality
    • Set up your own notebook
    • Organize your notes in folders
  1. Practical workflows for PhD students
    • Plan your days with daily notes
    • Manage your tasks
    • What else you can do

Organization

  • Live demo + Hands-on
  • Questions anytime

Important links

Find all workshop material and links here: workshop page

If you didn’t install Obsidian yet, you can do so now from https://obsidian.md/

What makes notes useful?

  • 🔎 Searchable → digital
  • 📆 Sustainable
    • Can you understand them in years?
    • Does the software still exist?
  • 🧱 Open and simple formats
  • 🔗 Connected
  • 😃 Easy and enjoyable to write

Obsidian

  • Free for personal use
  • All major OS and mobile devices
  • Notes are simple Markdown files
  • Local first: Keeps your notes private
  • Very simple at its core
  • Extend and customize with plugins

Obsidian basics

How to get started with your first notebook

The two most important shortcuts

  • Ctrl/Cmd + O: Find or create a note
    • Good to avoid duplicate notes
  • Ctrl/Cmd + P: Command palette
    • Everything you can do in your vault, e.g. insert a table, export as PDF

Your turn

✏️ Exercise 1 (15 min):

Obsidian basics

  • Stay in this meeting
  • Questions: In the chat or just unmute yourself and share your screen if needed

Organize your notes

Organize your notes in folders

  • Goal: Easily store and find your notes again

  • The crucial questions: Which folders/categories?

    • One option: the PARA system

Sketch of a storage box divided into four differently colored drawers, each containing a few notes.

The PARA system

By Tiago Forte: 4 core categories (= main folders) to sort your notes

Sketch of a storage box with four drawers labelled Projects, Areas, Resources and Archive.

Projects

  • Things you work on right now

  • Things with a deadline

  • Examples

    • Paper XYZ
    • Prepare workshop XYZ
    • Renovate my living room

  • Subfolders for each project

PARA sketch with the Projects drawer highlighted.

Areas

  • Ongoing responsibilities without a concrete deadline

  • Examples

    • PhD: bureaucratic things, overarching topics
    • Lab: notes on your research group
    • Finances

PARA sketch with the Areas drawer highlighted.

Resources

  • Reference and learning materials

  • Topics you are interested in

  • Useful for the future

  • Examples

    • Literature notes
    • Tutorials
    • Documentation

PARA sketch with the Resources drawer highlighted.

Archive

  • Old, finished work and projects

PARA sketch with the Archive drawer highlighted.

Daily notes

Plan your day and capture what comes up

Your turn

✏️ Exercise 2 (15 min):

Daily notes

Tasks

Collect tasks from your whole vault

Your turn

✏️ Exercise 3 (10 min):

The Tasks plugin

What else you can do

  • Zettelkasten: Connect your ideas in small, linked notes
  • Literature notes from Zotero
  • Project hubs for tasks, meetings and notes
  • …

The demo vault

Examples, templates, and workflow guides from today and more:

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

Download and instructions on the workshop page

Wrap-up

  • Obsidian is not one system
    • Implement only what you find useful
  • The most important: actually writing notes
  • Start simple, add workflows later
  • For more checkout the exercises, demo vault and resources on the workshop page

Next lecture/workshop

Topic: tba


📅 26.11.2026 🕓 4-5 p.m. 📍 Webex

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📧 For topic suggestions and/or feedback send me an email

The end :)

Questions?