grant-name/
├── .claude/                    # Claude Code config (optional)
├── .gitignore
├── CLAUDE.md                   # Claude instructions
├── README.md                   # Overview, timeline, collaborators
├── coapplicant_details/        # Co-applicant information
│   ├── coapplicant1.md
│   └── coapplicant2.md
├── correspondence/             # Email correspondence, queries
├── data/                       # Planning data
│   ├── milestones.csv          # Milestone tracking
│   └── plan.csv                # Work package timeline
├── docs/                       # Call documentation, guidance
│   └── call-specification.pdf
├── submission/                 # Main submission documents
│   ├── application.qmd         # Full application
│   ├── research_vision.qmd     # Research vision/summary
│   ├── approach.qmd            # Technical approach
│   ├── team_capability.qmd     # Team and capability
│   ├── references.bib          # Bibliography
│   ├── schematics/             # Figures and diagrams
│   └── cell-numeric.csl        # Citation style
└── slides/                     # Presentation materials (optional)

# [Grant Title]

[Brief description of the grant application]

## Timeline

| Date | Milestone |
|------|-----------|
| [Date] | Collaborator list agreed |
| [Date] | Case for support drafted |
| [Date] | All sections complete |
| [Date] | Final submission deadline |

## Collaborators

| Name | Institution | Role |
|------|-------------|------|
| PI Name | Institution | Lead applicant |
| Co-I Name | Institution | [Work package/expertise] |

## Structure

- `/submission/`: Main application documents
- `/docs/`: Call documentation and guidance
- `/coapplicant_details/`: Co-applicant information
- `/data/`: Planning data (milestones, timeline)

# CLAUDE.md

This file provides guidance to Claude Code when working with this repository.

## Repository Overview

This repository contains a [FUNDER] grant application focused on [TOPIC].
The project aims to [BRIEF OBJECTIVE].

## Document Structure

- `/submission/`: Main application documents
- `/docs/`: Call documentation and guidance
- `/coapplicant_details/`: Co-applicant information
- `/data/`: Planning data (milestones, timeline)

## Language Requirements

Always respond in British English (UK).

## Word Count Utilities

```bash
# Count words in a QMD file (excluding YAML header and references)
cat submission/document.qmd | sed '1,4d' | sed '/# References/,$d' | sed 's/\[@[^]]*\]//g' > temp.txt && wc -w temp.txt && rm temp.txt

### .gitignore

## Quarto Document Setup

### Application Document Header

```yaml
---
title: "Application Title"
format:
  pdf:
    documentclass: article
    geometry:
      - margin=2.5cm
    fontsize: 11pt
    include-in-header:
      - text: |
          \usepackage{fancyhdr}
          \pagestyle{fancy}
bibliography: references.bib
csl: cell-numeric.csl
---

---
title: "Research Vision"
format:
  pdf:
    documentclass: article
    geometry:
      - margin=2.5cm
    fontsize: 11pt
bibliography: references.bib
csl: cell-numeric.csl
---

milestone_id,work_package,description,month,type,deliverable
M1,WP1,Initial framework design complete,6,S,Software prototype
M2,WP1,Core module implementation,12,S,Release v1.0
M3,WP2,First training workshop,12,T,Workshop materials
M4,WP3,Methods paper submitted,18,P,Publication

activity_id,work_package,activity,lead,start_month,end_month,dependencies
A1.1,WP1,Literature review,PI,1,3,
A1.2,WP1,Framework design,PI,3,6,A1.1
A2.1,WP2,Training materials,Co-I,6,12,A1.2

# Basic word count
wc -w submission/document.qmd

# Accurate count (excludes YAML header, references section, citations)
cat submission/document.qmd | \
  sed '1,/^---$/d' | \
  sed '/^---$/,$d' | \
  sed '/# References/,$d' | \
  sed 's/\[@[^]]*\]//g' | \
  wc -w

Recent outbreaks of Ebola, COVID-19 and mpox have demonstrated the value of
modelling for synthesising data for rapid evidence to inform decision making.
Methods used to synthesise available data in real time broadly fall into two
classes: either combining results from multiple, smaller models calibrated in
isolation (the _pipeline approach_, e.g., [@huisman2022]), or representing a
single model tuned to the specific scenario (the _joint model_ approach,
e.g., [@birrell2024;@Watson2024-vj]).

# [Name]

## Affiliation
[Institution, Department]

## Role in Project
[Specific responsibilities, work packages]

## Track Record
[Key achievements relevant to the grant]

## Contribution
[What they bring to the project]