Welcome to the Lab Notebook

getting-started
tutorial
setup
Introduction to using this Quarto-based lab notebook system
Author

Ariana Huffmyer

Published

January 15, 2024

Overview

This is a sample notebook entry to demonstrate the functionality of the lab notebook system. This entry explains how to create and manage your daily lab notebook entries.

How to Create New Entries

Step 1: Copy the Template

  1. Navigate to the posts/ directory
  2. Copy the _template.qmd file
  3. Rename it with a descriptive name (e.g., 2024-01-15-experiment-name.qmd)

Step 2: Edit the Metadata

Update the YAML frontmatter at the top of the file:

---
title: "Your Entry Title"
author: "Your Name"
date: "YYYY-MM-DD"
categories: [project-name, keyword1, keyword2]
description: "Brief description"
---

Important Metadata Fields

  • title: Clear, descriptive title for the entry
  • date: Date in YYYY-MM-DD format (used for sorting)
  • categories: List of projects, keywords, and topics (used for filtering)
  • description: Brief summary (appears in the listing)
  • draft: Set to true to hide the entry from the published site

Step 3: Write Your Content

Use standard Markdown and Quarto syntax to write your entry. You can include:

  • Text and formatting
  • Code blocks with syntax highlighting
  • Executable code (R, Python, Julia, etc.)
  • Figures and images
  • Tables
  • Mathematical equations
  • Interactive plots

Example: Code Block

```{r}
#| echo: true
#| eval: false

# This is an R code example
data <- read.csv("my_data.csv")
summary(data)
```

Example: Python Code

```{python}
#| echo: true
#| eval: false

# This is a Python code example
import pandas as pd
df = pd.read_csv("my_data.csv")
print(df.describe())
```

Example: Including Images

![Figure caption](../images/my_figure.png)

Organizing Your Notebook

Using Categories Effectively

Categories help you find related entries later. Good category practices:

  • Project names: Use consistent project identifiers (e.g., “coral-bleaching”, “RNA-seq”)
  • Keywords: Add relevant keywords (e.g., “fieldwork”, “analysis”, “methods”)
  • Topics: Include broader topics (e.g., “molecular-biology”, “statistics”)

Search and Filter

The lab notebook page has built-in search and filtering:

  • Search bar: Search for keywords in titles and content
  • Category filters: Click category tags to see all related entries
  • Sort options: Sort by date, title, or other fields

Best Practices

  1. Write entries promptly: Record observations while they’re fresh
  2. Be detailed: Include enough detail to reproduce your work
  3. Use consistent naming: Follow a naming convention for files
  4. Link related entries: Reference previous entries when relevant
  5. Include metadata: Always fill out categories and descriptions
  6. Version control: The notebook is version-controlled with Git

Next Steps

Resources


Happy note-taking! 📝🔬