05.11.2025 Update: Theme & Style Settings

It was pointed out to me that when the vault is downloaded, the theme and style settings that are in the example images are not displayed. I will work on fixing it so this is automaticly included when someone uses the vault for the first time, but in the meantime you can use the following settings to achieve the same look:

Theme: Minimal
Plugin: Minimal Theme Settings

Go to the "Minimal Theme Settings" plug and set the following

Light mode color scheme: Rose Pine
Light mode background contrast: Low contrast
Dark mode color scheme: Rose Pine
Dark mode background contrast: Default
Colorful window frame: on
Colorful active states: on
Colorful headings: on
Trim file names in sidebars: on
Workspace borders: on
Underline external links: on
Image grids: on

23.02.2025 Update: Issues with CSS, JS, templates, and functioning of the vault have been fixed.

Thank you to those on git who pointed out the issues! If any other problems arise with basic functioning of the vault, let me know.

29.01.2025 Update: Plugin Folder Successfully Uploaded 🎉

The .obsidian/plugins/ folder has now been successfully uploaded. Please make sure to enable all CSS snippets by going to Settings > Appearance > Scroll to the bottom and enable all the snippets.

If you clone this repository, all necessary plugins should be available. Let me know if there are any other issues to fix.

Sciencia Vault

Welcome to the Sciencia Vault! This vault is designed to support anyone navigating the challenges the life sciences, whether you're pursuing a graduate degree, a junior scientist, or managing multiple academic projects. With its structured layout and focus on efficient note-taking and project organization, this vault will help you stay on top of your coursework, research, and professional goals.

What's Inside?

This is my first coding project, and it’s taken me about a year to create and test this system (a heartfelt thanks to my colleagues who tested early versions!). Along the way, I refined it into a model that saves time, boosts productivity in the lab, and reduces the headache of organization in the long run.

The core idea of this vault is that a little effort goes a long way. Every day, there are tasks to add, update, and plan—activities that are unavoidable in research. I wanted to create something that makes those day-to-day functions easier and more intuitive: a central hub where all the information is connected and accessible. The beauty of this system is that the more you build into it, the greater the payback.

Using the Zettelkasten method, I’ve transformed how I research papers, remember references, and maintain a repository of sentences I can use—already in my own voice and fully cited. Over time, this has become a web of interconnected ideas, papers, and notes, allowing me to retrieve critical information quickly without hours of searching. By integrating this system with a GPT API key, or even the free Smart Connections plugin, you can harness AI to uncover patterns and relationships within your work. This means:

Finding connections between research paper notes (written in your own words and already cited).
Avoiding lost meeting notes.
Keeping track of contributions in collaborative projects.
Creating hubs of information that naturally draw related insights together.
Developing a personal assistant that grows alongside your research.

In short, this vault doesn’t just store information—it actively helps you think, plan, and organize better.

How This Vault Has Helped Me

So far, my own vault has helped me:

Write abstracts for conference deadlines in record time.
Keep track of tasks and key takeaways from meetings.
Manage complex projects with many moving parts and collaborators.
Apply insights from classes, seminars, and conferences directly to my lab work.
Stay on top of small and large tasks that used to pile up and get forgotten.

For me, this system is an invaluable tool that I’m excited to continue developing throughout my Ph.D. It grows and evolves as my research does, becoming even more useful over time.

How It Can Help You

Whether you’re a graduate student, an junior project leader, or someone managing multiple projects, this vault can:

Make research feel less overwhelming and more streamlined.
Help you focus on the science instead of drowning in administrative details.
Turn the small, day-to-day tasks into manageable and meaningful progress.
Provide a stress-free way to stay organized and save time.

In short, this vault can take the pressure off, make research a little more fun, and help you unlock more of your creative and intellectual potential.

Main Directories

000 Zettelkasten: A collection of interconnected notes using the Zettelkasten method. These atomic notes will help you link ideas, organize your thoughts, and foster creative insights.
100 Lab Notes: Perfect for recording experiments, observations, and research insights. This section is your go-to for managing your scientific workflows.
200 Courses: Organize all your course materials, lecture notes, and study resources in one place for easy access and review.
300 MOCs (Maps of Content): These serve as thematic hubs, helping you navigate your notes and find relevant information quickly.
Reference Notes: Store and manage citations, references, or external resources that you frequently use in your work.
Files: A repository for images, PDFs, and other attachments linked within your notes.
Templates: Ready-to-use templates to keep your notes consistent and save time when creating new entries.

Key File

Dashboard.md: Your command center for managing research tasks, tracking milestones, and staying organized throughout your graduate journey.

Map of Content Previews

Basic Structure of the Vault

Zettelkasten Methodology: Build a web of interconnected ideas to deepen your understanding and spark creativity.
Buttons & Integrated Templates: Save time and maintain consistency across all your notes.
Maps of Content: Navigate your vault effortlessly with thematic entry points.
Tailored for Learning: Stay on top of research, coursework, and professional development with purpose-built tools.

Getting Started

Method 1:

Install Obsidian: If you don’t have it yet, download and install Obsidian.

Clone the Repository:

git clone https://github.com/clairechabot/Sciencia_Vault.git

Open the "Sciencia_Vault" folder within Github as a vault.

Method 2:

Install Obsidian: If you don’t have it yet, download and install Obsidian.
Go to the < > Code Button on the "Sciencia_Vault" mainpage.
Download the ZIP file.
Open the "Sciencia_Vault" folder within the ZIP file in Github as a vault.

For either method, make sure to enable and trust plugins in order for the vault to funciton.

Open the Vault

Launch Obsidian.
Select "Open folder as vault."
Choose the cloned repository.
Select "Trust Author and enable plugins." If not, the vault will not function.
Enable all CSS snippets by going to Settings > Appearance > Scroll to the bottom and enable all the snippets.
Close and re-load the vault to ensure all CSS snippets are working.

Plugins

This is a list of plugins that I've integrated into the vault's structure. Some are more for aesthetics, and others are essential. Feel free to customize for your own personal use!

Admonition
Banners What I use to make the MOC's and homepage more aesthetically pleasing. If you don't like the banners, take out this plugin and delete them.
Callout Manager
Completed Task Display: Essential for the vault to function. Also very satisfying.
Copilot: An AI Copilot in Obsidian. This is not essential, but if you build upon your vault with the zettelkasten method and your project notes, this can help with parsing information together that you've gathered over time. You do have to pay for an API key.
Dataview: Essential for the vault to function.
Emoji Toolbar: Quickly search for and insert emojis into your notes.
Highlightr
Homepage: Open a specified note, canvas, or workspace on startup, or set it for quick access later. This is used for the "Ph.D. Dashboard".
Iconize
Janitor: Performs cleanup tasks on the Obsidian vault. Really helpful to know what orphan notes you might have or junk that's floating about.
Linter: Formats and styles your notes, including YAML tags, aliases, arrays, and metadata. I have some set-up in this vault already, but feel free to customize it.
Meta Bind: Essential if you like the buttons. I like the buttons.
Minimal Theme Settings
Multi Properties
Natural Language Dates: Create date-links based on natural language. (i.e. write "today" or "next Friday" after you create a task and it will insert the correct date).
Obsidian Columns
Omnisearch : I believe this is essential to navigating your vault. At the moment, its better than the integrated obsidian vault search. I use it to look through my zettles and see what notes I have already and want to reference, or search through other documents in obsidian.
Pandoc: This plugin helps you convert your pages in Obsidian to DOCX, ePub, and PDF. I find the PDF useful for the protocols I put in my vault when I want to print them out for the lab or share with others.
PodNotes: This is useful if you like learning through podcasts and want to organise your notes from said podcasts into zettles later for referencing!
Pomodoro: The pomodoro method helped me when I was writing my MSc. thesis, and having it integrated in the vault when I need to lock-in and work is really nice! Not necessary, but I find it useful. You can find an explanation of the technique on the plugin page.
Quick Add: Seemlessly add templates around your vault.
Smart Connections: AI plugin to chat with your notes.
Style Settings
Supercharged Links
Tasks: This one is necessary for how the vault is set-up, and also quite satisfying I might add.
Templater: Another necessary plugin, this helps you integrate and call-up the custom templates within the vault.
Time Stamper: If you use this vault as a lab notebook, and need to stamp your experiment entries, then this plugin is very useful.
Tracker: I used this to add small summaries of information around the vault (i.e. work hours called up from the daily notes).
Widgets: This was added for the clock on the homepage, as well as the quotes around the vault, but you can also add widgets for countdowns to deadlines on your homepage as well.
Wordy: Really helpful for when you're trying to write your original zettles or other notes within the vault.
Zotero Integration: Necessary if you want to easily integrate the zettlekasten system within your vault. See Artem Kirsanov's videos linked in the "Resources & Reference" section below to learn more.

Hotkeys

Useful shortcuts that are already integrated with the vaults structure and plugins. Customize them as you'd like! I've included a list here of the ones I find most useful (and have on a sticky note on my desk).

Add file property: Command (⌘) / Ctrl + ;
Close window: Command (⌘) / Ctrl + Shift + W
Open command palette: Command (⌘) / Ctrl + P
Toggle Completed Task View: Command (⌘) / Ctrl + C
Create new note: Command (⌘) / Ctrl + N
Create note to the right: Command (⌘) / Ctrl + Shift + N
Open today's daily note: Command (⌘) / Ctrl + D
Open emoji picker: Command (⌘) / Ctrl + J
Open graph view: Command (⌘) / Ctrl + G
Open Highlightr: Command (⌘) / Ctrl + H
Open homepage: Command (⌘) / Ctrl + Q
Insert Markdown link: Command (⌘) / Ctrl + K
Lint the current file: Command (⌘) / Ctrl + Option (⌥) / Alt + L
Open current tab in new window: Command (⌘) / Ctrl + W
PodNotes: Capture Timestamp: Command (⌘) / Ctrl + L
Search current file: Command (⌘) / Ctrl + Option (⌥) / Alt + F
Create or edit task: Control (⌃) / Ctrl + T
Templater → Replace templates in the active file: Command (⌘) / Ctrl + Option (⌥) / Alt + R
Insert template: Command (⌘) / Ctrl + T
TimeStamper: Insert preconfigured date stamp: Command (⌘) / Ctrl + Shift + O
TimeStamper: Insert preconfigured time stamp: Command (⌘) / Ctrl + Shift + P
Toggle bold: Command (⌘) / Ctrl + B
Toggle italic: Command (⌘) / Ctrl + I
Unique note creator: Create new unique note: Command (⌘) / Ctrl + U (Important for creating Reference Notes.)

Recommended Apps

Zotero
Zotero is a powerful reference management tool that can be integrated with Zettelkasten notes to streamline your workflow. Artem’s videos (referenced below) provide excellent guidance on how to use Zotero effectively alongside Obsidian and the Zettelkasten method. Download Zotero here.

Resources & References

To better understand and incorporate the Zettelkasten method into your workflow, check out these helpful videos by Artem Kirsanov:

My simple note-taking setup | Zettelkasten in Obsidian | Step-by-step guide
This video provides a clear introduction to the Zettelkasten method and its implementation in Obsidian.
Zettelkasten workflow for research papers | Zotero & Obsidian link
A deep dive into effective linking strategies that enhance the Zettelkasten method.

Artem's other videos for insights on Obsidian are also very helpful!

The Daily Note/Work Note, "People", "Meetings" templates in this vault were adapted directly from Dan Berg's blog, which has been an invaluable resource:

The Electronic Lab Notebook (ELN) aspect of this vault was inspired by a post on the Obsidian forum by "drosophila":

Laboratory Notebook + Integrated Task Management System for Bench Scientists

License

This project is licensed under the MIT License. See the LICENSE file for details.

Contributing

Your feedback and contributions are welcome! Feel free to fork the repository and submit pull requests for improvements or new features. Let’s make this an even better tool for scientists.

If you have any questions or run into issues, please open an issue or reach out.

Good luck out there y'all!