RobertsLab · Copilot · Aug 27, 2025 · Aug 27, 2025
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+# Genomic Data Platform Template
+
+This repository serves as a template for creating integrated genomic data platforms with built-in genome browsers. It was originally developed for *Ostrea chilensis* (Chilean flat oyster) research but has been generalized for use with any species.
+
+## Features
+
+- 🧬 **Integrated Genome Browser**: Built-in JBrowse genome browser for interactive genomic data exploration
+- 📊 **Interactive Data Tables**: R-powered tables for annotations, BLAST results, and pathway data  
+- 🎨 **Responsive Web Interface**: Clean, modern website built with Quarto
+- 🔧 **Easy Customization**: Template-driven configuration system
+- 📱 **Mobile Friendly**: Works on desktop and mobile devices
+- 🌐 **GitHub Pages Ready**: Easy deployment to GitHub Pages
+
+## Technology Stack
+
+- **[Quarto](https://quarto.org/)**: Website generation and R integration
+- **[JBrowse](https://jbrowse.org/)**: Genome browser component
+- **R**: Data analysis and interactive tables
+- **YAML**: Configuration management
+
+## Quick Start
+
+### 1. Prerequisites
+
+- [Quarto](https://quarto.org/docs/get-started/) (>= 1.0)
+- [R](https://www.r-project.org/) (>= 4.0) with packages:
+  - `tidyverse`
+  - `DT` 
+  - `readxl`
+  - `plotly`
+- Python (>= 3.6) with `pyyaml` and `jinja2`
+
+### 2. Setup Your Project
+
+1. **Fork or clone this repository**
+   ```bash
+   git clone https://github.com/RobertsLab/OCEAN.git
+   cd OCEAN
+   ```
+
+2. **Install Python dependencies**
+   ```bash
+   pip install pyyaml jinja2
+   ```
+
+3. **Configure your project**
+
+   Copy and edit the configuration file:
+   ```bash
+   cp template-config.yml my-project-config.yml
+   ```
+
+   Edit `my-project-config.yml` with your species and project information:
+   ```yaml
+   # Project Information
+   project:
+     name: "MyGenome"
+     full_name: "My Species Genome Project"
+     description: "An integrated platform for my species research"
+
+   # Species Information  
+   species:
+     scientific_name: "Species scientificus"
+     common_name: "common species name"
+     description: "the common species"
+     emoji: "🧬"
+
+   # Update data sources with your URLs
+   data_sources:
+     nr_blast: "https://example.com/path/to/nr.csv"
+     uniprot: "https://example.com/path/to/uniprot.txt"
+     # ... etc
+   ```
+
+4. **Generate your project files**
+   ```bash
+   python setup-template.py my-project-config.yml
+   ```
+
+5. **Add your genomic data**
+
+   Place your genome files in the appropriate directories:
+   ```
+   docs/jbrowse/data/
+   ├── v1/
+   │   ├── your-genome.fasta
+   │   ├── your-genome.fasta.fai
+   │   ├── genes.gff3
+   │   └── annotations/
+   └── tracks/
+   ```
+
+6. **Build and preview**
+   ```bash
+   cd quarto
+   quarto preview
+   ```
+
+### 3. Customize Further
+
+#### Website Styling
+- Edit `quarto/styles.css` for custom styling
+- Modify `quarto/_quarto.yml` for navigation and theme changes
+
+#### Genome Browser
+- Update JBrowse configuration in `docs/jbrowse/config.json`
+- Add track data to `docs/jbrowse/data/`
+- Configure assemblies, annotations, and quantitative tracks
+
+#### Data Sources
+- Update URLs in your config file to point to your data
+- Modify R code in `explore.qmd` template for custom analysis
+
+## Configuration Reference
+
+### Project Settings
+```yaml
+project:
+  name: "ProjectName"           # Short identifier
+  full_name: "Full Project Name" # Display name
+  description: "Project description"
+```
+
+### Species Information
+```yaml
+species:
+  scientific_name: "Genus species"
+  common_name: "common name"
+  description: "descriptive text"
+  emoji: "🧬"  # Optional branding emoji
+```
+
+### Data Sources
+All data source URLs can be customized:
+```yaml
+data_sources:
+  nr_blast: "URL to BLAST results CSV"
+  uniprot: "URL to UniProt annotations"
+  pathways: "URL to pathway data"
+  gene_gff: "URL to gene annotations GFF"
+```
+
+### Population/Study Data
+The template includes optional population study components:
+```yaml
+population_info:
+  enabled: true  # Set to false to hide this section
+  title: "Population Information"
+  description: "Study description"
+  map_embed: "Google Maps embed URL"
+  locations:
+    - name: "Site 1"
+      salinity: "High"
+      # ... other characteristics
+```
+
+### JBrowse Configuration
+Define genome assemblies and basic tracks:
+```yaml
+jbrowse:
+  version: "v3.6.4"
+  assemblies:
+    - name: "Assembly Name"
+      fasta_url: "URL to FASTA file"
+      fai_url: "URL to FASTA index"
+```
+
+## Directory Structure
+
+```
+your-project/
+├── template-config.yml          # Main configuration
+├── setup-template.py           # Template processor
+├── templates/                  # Template files
+│   ├── index.qmd.template
+│   ├── about.qmd.template
+│   ├── explore.qmd.template
+│   ├── _quarto.yml.template
+│   └── jbrowse-config.json.template
+├── quarto/                     # Generated Quarto source
+│   ├── index.qmd
+│   ├── about.qmd
+│   ├── explore.qmd
+│   ├── _quarto.yml
+│   ├── img/
+│   └── styles.css
+└── docs/                       # Generated website
+    ├── index.html
+    ├── about.html
+    ├── jbrowse/
+    │   ├── config.json
+    │   ├── data/
+    │   └── index.html
+    └── ...
+```
+
+## Deployment
+
+### GitHub Pages
+1. Push your repository to GitHub
+2. Enable GitHub Pages in repository settings
+3. Set source to `/docs` folder
+4. Your site will be available at `https://username.github.io/repository-name`
+
+### Manual Deployment
+Build the site and deploy the `docs/` folder to any web server:
+```bash
+cd quarto
+quarto render
+# Upload docs/ folder to your web server
+```
+
+## Examples
+
+See the original OCEAN project configuration for a complete example of a working genomic data platform.
+
+## Contributing
+
+Feel free to submit issues and enhancement requests! This template is designed to be flexible and extensible.
+
+## License
+
+This template is provided under the same license as the original OCEAN project.
+
+## Citation
+
+If you use this template for your research, please cite the original OCEAN project and any relevant publications.
+
+---
+
+**Need help?** Check the [Issues](https://github.com/RobertsLab/OCEAN/issues) page or submit a new issue with the `template` label.