Warning

This README is under construction 🚧

How to start using this lab notebook

1. Download Obsidian
2. Open your terminal in MacOS Finder -> Applications -> Terminal
3. Navigate to the desired home directory for your Lab Notebook (e.g. cd /Users/elgin/Library/Documents/lab_notebooks)
4. git clone https://github.com/elginakin/obsidian_academic_lab_notebook_template.git
5. Open Obsidian
6. Open the git repository folder as a vault
   • 
7. Select the folder: obsidian_academic_lab_notebook_template
   • 
8. Proceed with the notebook introduction! in the _🎉 Welcome (Start Here) folder.

Introduction

👋 Welcome! This repository contains digital laboratory notebook (template) in (Obsidian)[https://obsidian.md/]. Its purpose is to provide academic users with a base-vault to alleviate part of the 'up time' typically experienced by new Obsidian users.

Motivation

This notebook is the result of my insatiable need to over-structure my life while navigating academia. I grew tired of using multiple applications to track experiments and constantly found myself running back and forth between my mountains of experimental notes and my literature notes only to deposit my thoughts in some third transient space ultimately splitting my notes across 3 'spaces'.

A more serious motivation for this lab notebook is the widespread challenge of reproducibility in the biological sciences.¹ While many contributing factors are conceptual, this notebook aims to address a practical one: reducing the time and effort required to document experimental design and results. In this new era of science, graduate students are generating more data than ever before. This is largely due to advancements in technology that allow us to extract more information from each experiment. While many Electronic Laboratory Notebook (ELN) solutions exist, I found that none fully met my specific needs.²

Important

This vault and the instructions herein were assembled in a MacOS environment thus paths within core and community Obsidian plugins may need manual curation to operate as expected.

This notebook relies on the following plugins for intended operation and use:

The plugins below have been chosen to significantly enhance the experience of the academic user. However, these plugins are typically maintained by the community and may have diminishing community support over time. While the Obsidian community is strong through Obsidian Forum

Core Plugins

Daily Notes

Templates

Community Plugins

Auto Link Title

Auto Note Mover

Automatic Table of Contents

Better Word Count

Calendar

Dataview

Excel to Markdown Table

Homepage

Iconize

Image Toolkit

Minimal Theme Settings

Omnisearch

Pandoc Plugin

Pandoc Reference List

Periodic Notes

Quiet Outline

Settings Search

Tag Wrangler

Tasks

Templater

Footnotes

1. Six factors affecting reproducibility in life science research and how to handle them ↩

2. Considerations for implementing electronic laboratory notebooks in an academic research environment | Nature Protocols ↩