NIH Grant Typst Templates

A modern, reproducible workflow for creating NIH grant applications using Typst, with integrated support for R and Python data analysis via Quarto.

🚀 Quick Start

# Clone the repository
git clone https://github.com/brainworkup/nih-grant-typst.git
cd nih-grant-typst

# Set up the environment (choose one)
conda env create -f environment.yml  # Recommended: includes everything
# OR
pip install -r requirements.txt      # Python only
# OR
Rscript -e "install.packages(c('tidyverse', 'ggplot2', 'patchwork', 'viridis'))"  # R only

# Compile example templates
./scripts/compile_templates.sh

📋 Features

• ✅ NIH-compliant formatting - Automated margins, fonts, and page limits
• ✅ Multiple grant types - R01, R03, with more coming soon
• ✅ Integrated data analysis - Seamless R and Python integration
• ✅ Reproducible research - Quarto-based progress reports
• ✅ Smart reference management - BibTeX with NIH-style formatting
• ✅ Version control friendly - Clean text-based format
• ✅ Automated compilation - GitHub Actions for PDF generation
• ✅ Modular components - Reusable sections across grants

🏗️ Repository Structure

nih-grant-typst/
├── templates/             # Typst templates for grant applications
│   ├── R01/               # R01 grant template
│   ├── R03/               # R03 grant template
│   └── shared/            # Shared components (aims, budget)
├── scripts/               # Helper scripts and analysis code
│   ├── analysis/          # Data analysis scripts
│   │   ├── figures/       # R/Python scripts for figures
│   │   └── tables/        # R scripts for tables
│   └── helpers/           # Utility scripts
├── quarto/                # Progress report templates
├── data/                  # Data organization structure
│   ├── raw/               # Original, unmodified data
│   ├── cleaned/           # Processed, analysis-ready data
│   └── scripts/           # Data processing scripts
├── examples/              # Example outputs and figures
└── outputs/               # Compiled PDFs (generated)

📖 Complete Usage Guide

Creating Your First Grant

1. Choose Your Template

# For an R01 grant
cp -r templates/R01 my_r01_grant

# For an R03 grant
cp -r templates/R03 my_r03_grant

2. Customize Your Grant

Edit the main file (e.g., my_r01_grant/R01.typ):

#import "config.typ": *
#import "../shared/specific_aims.typ": specific_aims_example
#import "../shared/budget.typ": budget_example

// Update with your information
#show: nih-grant.with(
  title: "Your Grant Title Here",
  pi: "Dr. Your Name",
  institution: "Your Institution"
)

// Add your content
#specific_aims[
  Your specific aims content here...
]

3. Compile Your Grant

# Using the helper script
./scripts/compile_templates.sh

# Or compile directly with correct root setting
typst compile --root . my_r01_grant/R01.typ outputs/my_r01_grant.pdf

🔬 Integrating Data Analysis

Option 1: R Analysis with Quarto

Create a Quarto document for your analysis:

---
title: "Data Analysis for NIH Grant"
format: 
  html: default
  typst: default
---

```{r}
#| label: fig-results
#| fig-cap: "Primary outcome analysis"

library(ggplot2)
data <- read.csv("data/cleaned/results.csv")

ggplot(data, aes(x = time, y = outcome, color = group)) +
  geom_line() +
  theme_minimal() +
  labs(title = "Treatment Effect Over Time")

ggsave("outputs/figures/primary_outcome.png", dpi = 300)

Reference in your Typst document:

```typst
#figure(
  image("outputs/figures/primary_outcome.png"),
  caption: [Treatment effect over time showing significant improvement in the intervention group.]
)

Option 2: Python Analysis

# scripts/analysis/figures/generate_figures.py
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns

# Load and analyze data
data = pd.read_csv('data/cleaned/results.csv')
sns.set_style("whitegrid")

# Create publication-quality figure
fig, ax = plt.subplots(figsize=(8, 6))
sns.lineplot(data=data, x='time', y='outcome', hue='group', ax=ax)
ax.set_title('Treatment Effect Over Time')
plt.savefig('outputs/figures/python_analysis.png', dpi=300, bbox_inches='tight')

📊 Data Organization

Follow our structured approach for reproducible research:

data/
├── raw/                    # Never modify these files
│   ├── behavioral/         # Original behavioral data
│   ├── neuroimaging/       # MRI/fMRI data
│   └── clinical/           # Clinical assessments
├── cleaned/                # Processed data with documentation
│   ├── behavioral/         # Analysis-ready datasets
│   └── processing_logs/    # Document all transformations
└── scripts/                # Processing scripts
    └── preprocessing/      # Data cleaning code

📚 Working with References

Managing Citations

Add references to references.bib:

@article{smith2023example,
  title = {Example Study Title},
  author = {Smith, Jane and Doe, John},
  journal = {Journal of Example Studies},
  volume = {42},
  pages = {123--456},
  year = {2023},
  doi = {10.1234/example}
}

Cite in Typst:

Previous research has shown significant effects @smith2023example.

Format References for NIH

# Convert to NIH style
python scripts/helpers/reference_formatter.py references.bib --format nih

# Check for duplicates
python scripts/helpers/reference_formatter.py references.bib --check-duplicates

📝 Creating Progress Reports

Generate professional progress reports using Quarto:

cd quarto
quarto render progress-report.qmd --to pdf
quarto render progress-report.qmd --to html

🎨 Available Templates

R01 - Research Project Grant

• Purpose: Major research projects
• Research Strategy: 12 pages
• Budget: Modular or detailed
• Duration: Up to 5 years
• View template

R03 - Small Grant Program

• Purpose: Limited research projects
• Research Strategy: 6 pages
• Budget: $50,000/year maximum
• Duration: Up to 2 years
• View template

Coming Soon

• R21 - Exploratory/Developmental Research
• K99/R00 - Pathway to Independence
• F31 - Predoctoral Fellowship

🛠️ Advanced Features

VSCode Integration

We include configurations for optimal development:

• Typst syntax highlighting and preview
• Integrated compilation tasks (Ctrl+Shift+B)
• Recommended extensions for R, Python, and Quarto

Automated Validation

Ensure your grant meets NIH requirements:

# Check page limits (coming soon)
python scripts/helpers/validate_grant.py outputs/my_grant.pdf --type R01

# Validate formatting
python scripts/helpers/check_formatting.py outputs/my_grant.pdf

Custom Components

Create reusable components for your grants:

// templates/shared/my_custom_section.typ
#let my_section(content) = {
  heading(level: 1, [MY CUSTOM SECTION])
  set par(first-line-indent: 0.5in)
  content
}

🤝 Contributing

We welcome contributions! See our Contributing Guidelines.

Ways to Contribute

• Add new grant templates
• Improve existing templates
• Share helper scripts
• Enhance documentation
• Report issues

📄 License

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

🙏 Acknowledgments

• Typst community for the excellent typesetting system
• NIH for grant formatting guidelines
• Contributors who have improved these templates

📧 Support

• Issues: GitHub Issues
• Discussions: GitHub Discussions

---

Remember: Always check the latest NIH guidelines as requirements may change.