diff --git a/README.md b/README.md
new file mode 100644
index 0000000..c01f2b4
--- /dev/null
+++ b/README.md
@@ -0,0 +1,231 @@
+# 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.
\ No newline at end of file
diff --git a/TEMPLATE-GUIDE.md b/TEMPLATE-GUIDE.md
new file mode 100644
index 0000000..09bc8a8
--- /dev/null
+++ b/TEMPLATE-GUIDE.md
@@ -0,0 +1,184 @@
+# Using OCEAN as a Template
+
+This directory contains the template system for creating new genomic data platforms based on the OCEAN architecture.
+
+## Quick Start for New Projects
+
+### 1. Copy and Configure
+
+```bash
+# Copy the template configuration
+cp template-config.yml my-species-config.yml
+
+# Edit the configuration for your species
+vim my-species-config.yml
+```
+
+### 2. Key Configuration Sections
+
+#### Project Information
+```yaml
+project:
+  name: "YourProject"  # Short name, used in code
+  full_name: "Your Species Genomics Platform"  # Display name
+  description: "Brief description of your platform"
+```
+
+#### Species Information
+```yaml
+species:
+  scientific_name: "Genus species"
+  common_name: "common name"
+  description: "the [adjective] [common name]"  # Used in sentences
+  emoji: "🧬"  # Optional branding emoji
+```
+
+#### Data Sources
+Update all URLs to point to your data:
+```yaml
+data_sources:
+  nr_blast: "https://your-server.com/blast-results.csv"
+  uniprot: "https://your-server.com/uniprot-annotations.txt" 
+  pathways: "https://your-server.com/pathway-data.csv"
+  gene_gff: "https://your-server.com/gene-annotations.gff3"
+```
+
+#### JBrowse Configuration
+```yaml
+jbrowse:
+  assemblies:
+    - name: "Your Assembly v1.0"
+      fasta_url: "https://your-server.com/genome.fasta"
+      fai_url: "https://your-server.com/genome.fasta.fai"
+```
+
+### 3. Generate Your Site
+
+```bash
+# Install Python dependencies
+pip install pyyaml jinja2
+
+# Generate your project files
+python setup-template.py my-species-config.yml
+
+# Copy your genome data files
+mkdir -p docs/jbrowse/data/v1/
+cp your-genome-files/* docs/jbrowse/data/v1/
+
+# Copy your images
+cp your-logo.png quarto/img/
+```
+
+### 4. Build and Test
+
+```bash
+cd quarto
+quarto preview  # Test locally
+quarto render   # Build for deployment
+```
+
+## Template Customization
+
+### Adding New Data Sections
+
+1. Add data sources to your config:
+```yaml
+data_sources:
+  new_data_type: "https://your-server.com/new-data.csv"
+```
+
+2. Modify `templates/explore.qmd.template` to add R code for your new data.
+
+3. Regenerate with `python setup-template.py your-config.yml`
+
+### Customizing Population/Study Information
+
+The template includes a flexible population information section:
+
+```yaml
+population_info:
+  enabled: true  # Set to false to hide completely
+  title: "Population Information"  # Customize section title
+  description: "Your study description"
+  
+  # Optional map
+  map_embed: "Google Maps embed URL"
+  
+  # Customizable location table
+  locations:
+    - name: "Site 1"
+      salinity: "High"
+      freshwater_input: "Low"
+      tidal_exchange: "High" 
+      human_influence: "Low"
+```
+
+You can:
+- Change column names by editing the template
+- Add/remove columns as needed
+- Disable the entire section with `enabled: false`
+
+### JBrowse Tracks
+
+The template creates basic gene, ncRNA, and repeat tracks. To add more:
+
+1. Add track data sources to your config
+2. Edit `templates/jbrowse-config.json.template` 
+3. Add new track definitions following JBrowse v3 syntax
+
+### Styling and Branding
+
+- Update `quarto/styles.css` for custom CSS
+- Replace `quarto/img/` files with your logos/images
+- Modify the celebration message and platform features in your config
+
+## Example Configurations
+
+See the `examples/` directory for:
+- `arabidopsis-config.yml` - Plant genomics example
+- Additional species examples (add your own!)
+
+## File Structure After Setup
+
+```
+your-project/
+├── template-config.yml          # Original template config
+├── my-species-config.yml        # Your customized config
+├── setup-template.py           # Template processor
+├── templates/                  # Template source files
+├── quarto/                     # Generated Quarto source
+│   ├── index.qmd               # Homepage
+│   ├── about.qmd               # About page with species info
+│   ├── explore.qmd             # Data exploration page
+│   ├── browse.qmd              # Genome browser page
+│   └── _quarto.yml             # Quarto configuration
+└── docs/                       # Generated website
+    ├── index.html
+    ├── jbrowse/
+    │   ├── config.json         # JBrowse configuration
+    │   └── data/               # Your genome data files
+    └── ...
+```
+
+## Tips for Success
+
+1. **Start Small**: Begin with basic gene and assembly data, add complexity later
+2. **Test Early**: Use `quarto preview` to test changes immediately  
+3. **Version Control**: Commit your config files and generated templates
+4. **Document Changes**: Keep notes on customizations for future reference
+5. **Community**: Share your configurations as examples for others
+
+## Troubleshooting
+
+### Common Issues
+
+1. **Missing Dependencies**: Install Quarto, R packages, and Python modules
+2. **Data URLs**: Ensure all data sources are publicly accessible
+3. **File Paths**: Use absolute URLs for external data, relative paths for local files
+4. **JBrowse Data**: Ensure FASTA files have corresponding .fai index files
+
+### Getting Help
+
+- Check the main README.md for general setup instructions
+- Review example configurations in `examples/`
+- Submit issues with the `template` label for template-specific problems
\ No newline at end of file
diff --git a/docs/jbrowse/config.json b/docs/jbrowse/config.json
index 8590f7e..667a9d1 100644
--- a/docs/jbrowse/config.json
+++ b/docs/jbrowse/config.json
@@ -1,11 +1,12 @@
 {
   "baseUrl": "jbrowse/",
   "assemblies": [
+    
     {
       "name": "Assembly 1.0",
       "sequence": {
         "type": "ReferenceSequenceTrack",
-        "trackId": "custom_refseq",
+        "trackId": "assembly_1.0_refseq",
         "adapter": {
           "type": "IndexedFastaAdapter",
           "fastaLocation": {
@@ -17,11 +18,12 @@
         }
       }
     },
+    
     {
       "name": "Och_HapA",
       "sequence": {
         "type": "ReferenceSequenceTrack",
-        "trackId": "hapa_refseq",
+        "trackId": "och_hapa_refseq",
         "adapter": {
           "type": "IndexedFastaAdapter",
           "fastaLocation": {
@@ -32,29 +34,14 @@
           }
         }
       }
-    },
-    {
-      "name": "Och_HapB",
-      "sequence": {
-        "type": "ReferenceSequenceTrack",
-        "trackId": "hapb_refseq",
-        "adapter": {
-          "type": "IndexedFastaAdapter",
-          "fastaLocation": {
-            "uri": "https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/OCEAN/docs/jbrowse/data/HapB/Och_HapB_assembly.fa"
-          },
-          "faiLocation": {
-            "uri": "https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/OCEAN/docs/jbrowse/data/HapB/Och_HapB_assembly.fa.fai"
-          }
-        }
-      }
     }
+    
   ],
   "tracks": [
     {
       "type": "FeatureTrack",
       "trackId": "gene_annotations",
-      "name": "Gene Annotations",
+      "name": "Genes",
       "assemblyNames": ["Assembly 1.0"],
       "adapter": {
         "type": "Gff3Adapter",
@@ -82,159 +69,12 @@
           "uri": "https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/OCEAN/docs/jbrowse/data/v1/repeat.gff3"
         }
       }
-    },
-    {
-      "type": "QuantitativeTrack",
-      "trackId": "Pum_barcode02",
-      "name": "Pum_02",
-      "assemblyNames": ["Assembly 1.0"],
-      "adapter": {
-        "type": "BigWigAdapter",
-        "bigWigLocation": { "uri": "data/v1/exp_01/Pum_barcode02.bw" }
-      },
-      "color": "blue"
-    },
-    {
-      "type": "QuantitativeTrack",
-      "trackId": "Pum_barcode12_1",
-      "name": "Pum_12_1",
-      "assemblyNames": ["Assembly 1.0"],
-      "adapter": {
-        "type": "BigWigAdapter",
-        "bigWigLocation": { "uri": "data/v1/exp_01/Pum_barcode12_1.bw" }
-      },
-      "color": "blue"
-    },
-    {
-      "type": "QuantitativeTrack",
-      "trackId": "Pum_barcode13",
-      "name": "Pum_13",
-      "assemblyNames": ["Assembly 1.0"],
-      "adapter": {
-        "type": "BigWigAdapter",
-        "bigWigLocation": { "uri": "data/v1/exp_01/Pum_barcode13.bw" }
-      },
-      "color": "blue"
-    },
-    {
-      "type": "QuantitativeTrack",
-      "trackId": "Pum_barcode13_1",
-      "name": "Pum_13_1",
-      "assemblyNames": ["Assembly 1.0"],
-      "adapter": {
-        "type": "BigWigAdapter",
-        "bigWigLocation": { "uri": "data/v1/exp_01/Pum_barcode13_1.bw" }
-      },
-      "color": "blue"
-    },
-    {
-      "type": "QuantitativeTrack",
-      "trackId": "Qui_barcode01",
-      "name": "Qui_01",
-      "assemblyNames": ["Assembly 1.0"],
-      "adapter": {
-        "type": "BigWigAdapter",
-        "bigWigLocation": { "uri": "data/v1/exp_01/Qui_barcode01.bw" }
-      },
-      "color": "green"
-    },
-    {
-      "type": "QuantitativeTrack",
-      "trackId": "Qui_barcode01_1",
-      "name": "Qui_01_1",
-      "assemblyNames": ["Assembly 1.0"],
-      "adapter": {
-        "type": "BigWigAdapter",
-        "bigWigLocation": { "uri": "data/v1/exp_01/Qui_barcode01_1.bw" }
-      },
-      "color": "green"
-    },
-    {
-      "type": "QuantitativeTrack",
-      "trackId": "Qui_barcode02_1",
-      "name": "Qui_02_1",
-      "assemblyNames": ["Assembly 1.0"],
-      "adapter": {
-        "type": "BigWigAdapter",
-        "bigWigLocation": { "uri": "data/v1/exp_01/Qui_barcode02_1.bw" }
-      },
-      "color": "green"
-    },
-    {
-      "type": "QuantitativeTrack",
-      "trackId": "Qui_barcode12",
-      "name": "Qui_12",
-      "assemblyNames": ["Assembly 1.0"],
-      "adapter": {
-        "type": "BigWigAdapter",
-        "bigWigLocation": { "uri": "data/v1/exp_01/Qui_barcode12.bw" }
-      },
-      "color": "green"
-    },
-    {
-      "type": "QuantitativeTrack",
-      "trackId": "Rio_barcode03",
-      "name": "Rio_03",
-      "assemblyNames": ["Assembly 1.0"],
-      "adapter": {
-        "type": "BigWigAdapter",
-        "bigWigLocation": { "uri": "data/v1/exp_01/Rio_barcode03.bw" }
-      },
-      "color": "red"
-    },
-    {
-      "type": "QuantitativeTrack",
-      "trackId": "Rio_barcode03_1",
-      "name": "Rio_03_1",
-      "assemblyNames": ["Assembly 1.0"],
-      "adapter": {
-        "type": "BigWigAdapter",
-        "bigWigLocation": { "uri": "data/v1/exp_01/Rio_barcode03_1.bw" }
-      },
-      "color": "red"
-    },
-    {
-      "type": "QuantitativeTrack",
-      "trackId": "Rio_barcode14",
-      "name": "Rio_14",
-      "assemblyNames": ["Assembly 1.0"],
-      "adapter": {
-        "type": "BigWigAdapter",
-        "bigWigLocation": { "uri": "data/v1/exp_01/Rio_barcode14.bw" }
-      },
-      "color": "red"
-    },
-    {
-      "type": "QuantitativeTrack",
-      "trackId": "Rio_barcode14_1",
-      "name": "Rio_14_1",
-      "assemblyNames": ["Assembly 1.0"],
-      "adapter": {
-        "type": "BigWigAdapter",
-        "bigWigLocation": { "uri": "data/v1/exp_01/Rio_barcode14_1.bw" }
-      },
-      "color": "red"
-    },
-    {
-      "type": "QuantitativeTrack",
-      "trackId": "SRR30335149",
-      "name": "SRR30335149",
-      "assemblyNames": ["Assembly 1.0"],
-      "adapter": {
-        "type": "BigWigAdapter",
-        "bigWigLocation": { "uri": "https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/OCEAN/docs/jbrowse/data/v1/SRR30335149.sorted.sp.bedGraph.bw" }
-      },
-      "color": "purple"
-    },
+    }
+  ],
+  "plugins": [
     {
-      "type": "FeatureTrack",
-      "trackId": "deg_annotations",
-      "name": "DEG",
-      "assemblyNames": ["Assembly 1.0"],
-      "adapter": {
-        "type": "Gff3Adapter",
-        "gffLocation": { "uri": "data/v1/exp_01/DEG.gtf" }
-      }
+      "name": "UMDUrlPlugin",
+      "url": "umd_plugin.js"
     }
   ]
 }
\ No newline at end of file
diff --git a/examples/arabidopsis-config.yml b/examples/arabidopsis-config.yml
new file mode 100644
index 0000000..b49483f
--- /dev/null
+++ b/examples/arabidopsis-config.yml
@@ -0,0 +1,91 @@
+# Example Template Configuration for Arabidopsis thaliana
+# This demonstrates how to adapt the platform for a different species
+
+# Project Information
+project:
+  name: "ArabGenome"
+  full_name: "Arabidopsis thaliana Genomic Analysis Platform"
+  description: "An integrated web platform for plant genomics research"
+  
+# Species Information  
+species:
+  scientific_name: "Arabidopsis thaliana"
+  common_name: "thale cress"
+  description: "the model plant organism"
+  emoji: "🌱"
+
+# Website Configuration
+website:
+  title: "ArabGenome"
+  theme: "flatly"
+  github_repo: "https://github.com/yourlab/arabgenome"
+  contact_message: "For questions or feedback, please submit an issue"
+  
+# Genome Browser Configuration
+jbrowse:
+  version: "v3.6.4"
+  assemblies:
+    - name: "TAIR10"
+      fasta_url: "https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas"
+      fai_url: "https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas.fai"
+
+# Data Sources - Update these URLs to your actual data
+data_sources:
+  nr_blast: "https://example.com/data/arabidopsis_nr_blast.csv"
+  uniprot: "https://example.com/data/arabidopsis_uniprot.txt"  
+  pathways: "https://example.com/data/arabidopsis_pathways.csv"
+  gene_gff: "https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_gff3/TAIR10_GFF3_genes.gff"
+  
+  # Genome browser specific
+  gene_annotations: "data/TAIR10_genes.gff3"
+  ncrna_annotations: "data/TAIR10_ncrna.gff3"
+  repeat_annotations: "data/TAIR10_repeats.gff3"
+
+# Population/Study Information - Customize for your research
+population_info:
+  enabled: true
+  title: "Ecotype Information"
+  description: "Analysis includes multiple Arabidopsis ecotypes from different geographic regions"
+  
+  # No map needed for this example
+  map_embed: ""
+  
+  locations:
+    - name: "Columbia (Col-0)"
+      salinity: "N/A"
+      freshwater_input: "Temperate climate"
+      tidal_exchange: "N/A"
+      human_influence: "Laboratory strain"
+    - name: "Landsberg erecta (Ler)"
+      salinity: "N/A"
+      freshwater_input: "European origin"
+      tidal_exchange: "N/A"
+      human_influence: "Wild collected"
+    - name: "Wassilewskija (Ws)"
+      salinity: "N/A"
+      freshwater_input: "European origin"
+      tidal_exchange: "N/A"
+      human_influence: "Wild collected"
+      
+  # Genetic relatedness
+  genetic_relatedness:
+    enabled: true
+    image_url: "https://example.com/arabidopsis_phylogeny.png"
+
+# Featured Views
+featured_views:
+  - title: "Flowering Time Genes"
+    url: "jbrowse/?loc=Chr5:25000000-26000000"
+  - title: "Disease Resistance Cluster"  
+    url: "jbrowse/?loc=Chr1:21000000-22000000"
+
+# Custom branding
+branding:
+  logo_image: "img/arabidopsis.png"
+  celebration_message: "Explore the plant genome!"
+  platform_features:
+    - "🧬 Genome browser for *Arabidopsis thaliana*"
+    - "🔍 Transcriptomic data"  
+    - "📊 Interactive tools for gene expression and pathway analysis"
+    - "🧠 Curated annotations including GO terms and metabolic pathways"
+    - "🌐 Data sharing & collaboration hub for the plant research community"
\ No newline at end of file
diff --git a/quarto/_quarto.yml b/quarto/_quarto.yml
index ae2b256..f86da4e 100644
--- a/quarto/_quarto.yml
+++ b/quarto/_quarto.yml
@@ -21,5 +21,4 @@ format:
   html:
     theme: simplex
     css: styles.css
-
     toc: true
\ No newline at end of file
diff --git a/quarto/about.qmd b/quarto/about.qmd
index a4baa36..e3e03b7 100644
--- a/quarto/about.qmd
+++ b/quarto/about.qmd
@@ -10,12 +10,17 @@ OCEAN is an integrated web platform dedicated to advancing research on
 *Ostrea chilensis*, the Chilean flat oyster.
 
 The platform offers:\
-• 🧬 Genome browser for *O. chilensis*\
+
+• 🧬 Genome browser for {species.scientific_name}\
+
 • 🔍 Epigenetic data\
-• 📊 Interactive tools for gene expression and regulatory region
-analysis\
+
+• 📊 Interactive tools for gene expression and regulatory region analysis\
+
 • 🧠 Curated annotations including GO terms and pathway associations\
-• 🌐 Data sharing & collaboration hub for the oyster research community
+
+• 🌐 Data sharing & collaboration hub for the research community\
+
 
 ::: badges
 <p><a href="https://github.com/RobertsLab/OCEAN/releases">
@@ -29,26 +34,32 @@ analysis\
 
 # Featured Genome Browser Views 👀
 
+
 -   ### [Gene Expression following Heat Exposure](https://robertslab.github.io/OCEAN/jbrowse/?session=share-bS-rRTROpE&password=r9vWX)
- 
--    ### [DEG MSTRG.1743.1 zoom](https://oystergen.es/jbrowse/?session=share-fpBeSAviSo&password=scJyF)
+
+-   ### [DEG MSTRG.1743.1 zoom](https://oystergen.es/jbrowse/?session=share-fpBeSAviSo&password=scJyF)
+
 
 ------------------------------------------------------------------------
 
+
 # Population Information
 
 ## Site Location Information
 
 Our focus to date is from oysters from three locales
 
-<iframe src="https://www.google.com/maps/d/u/0/embed?mid=19nWyrDGOjq34Fy3nmXB-walLF1yjNdY&amp;ehbc=2E312F&amp;noprof=1" width="90%" height="480">
+<iframe src="https://www.google.com/maps/d/u/0/embed?mid=19nWyrDGOjq34Fy3nmXB-walLF1yjNdY&ehbc=2E312F&noprof=1" width="90%" height="480">
 
 </iframe>
 
 | Location | Salinity | Freshwater Input | Tidal Exchange | Human Influence |
 |--------------|--------------|----------------|--------------|--------------|
+
 | Río Pudeto | Moderate (brackish) | Moderate river inflow | Moderate | Moderate |
+
 | Pumalín | Low (oligohaline) | High (glacial & river) | Low | Low (pristine) |
+
 | Isla Quihua | High (marine) | Low to moderate | High | Moderate to high |
 
 
@@ -56,3 +67,5 @@ Our focus to date is from oysters from three locales
 ## Genetic Relatedness
 
 ![](http://gannet.fish.washington.edu/seashell/snaps/Monosnap_Monosnap_2025-08-03_15-06-38.png)
+
+
diff --git a/quarto/explore.qmd b/quarto/explore.qmd
index 103ff43..fe0ce76 100644
--- a/quarto/explore.qmd
+++ b/quarto/explore.qmd
@@ -15,14 +15,11 @@ library(readxl)
 library(plotly)
 library(readr)
 library(dplyr)
-
 ```
 
-
 ## NCBI NR BLAST
 
 ```{r, echo=FALSE}
-
 # Read the CSV file
 nr_data <- read_csv("http://gannet.fish.washington.edu/seashell/snaps/nr.csv")
 
@@ -42,6 +39,7 @@ datatable(
   rownames = FALSE
 )
 ```
+
 ## UniProt
 
 ```{r, echo=FALSE}
@@ -62,11 +60,9 @@ datatable(
 )
 ```
 
-
 ## Pathways 
 
 ```{r, echo=FALSE}
-
 # Read your Pathway CSV
 # Read the CSV
 df <- read_csv("http://gannet.fish.washington.edu/seashell/snaps/pathway_table.csv")
@@ -94,7 +90,6 @@ datatable(
 )
 ```
 
-
 ## Gene GFF 
 
 ```{r, echo=FALSE}
@@ -105,8 +100,6 @@ gff <- read_tsv(
   col_names = c("seqid", "source", "type", "start", "end", "score", "strand", "phase", "attributes")
 )
 
-
-
 datatable(
   gff,
   extensions = 'Buttons',
@@ -117,8 +110,4 @@ datatable(
   ),
   filter = "top"
 )
-
-
-
-```
-
+```
\ No newline at end of file
diff --git a/quarto/index.qmd b/quarto/index.qmd
index 73ab195..991c539 100644
--- a/quarto/index.qmd
+++ b/quarto/index.qmd
@@ -6,9 +6,8 @@ editor:
     wrap: 72
 ---
 
-OCEAN (***O**stra **c**hilensis*: **E**pigénoma **A**nálisis en **N**et)
-is an integrated web platform dedicated to advancing research on *Ostrea
-chilensis*, the Chilean flat oyster. By combining high-resolution
+Ostrea chilensis: Epigénoma Análisis en Net
+is an integrated web platform dedicated to advancing research on *Ostrea chilensis*, the Chilean flat oyster. By combining high-resolution
 genomic data with cutting-edge epigenomic insights, OCEAN supports
 researchers exploring gene regulation, environmental plasticity, and
 resilience in this ecologically important marine species.
@@ -29,5 +28,5 @@ Browser</a>]{style="font-size: 1.1em;"}
 </a>
 :::
 
-For questions or feedback, [please submit an
-issue](https://github.com/RobertsLab/OCEAN/issues/new/choose) 🧬
+For questions or feedback, please submit an issue, [please submit an
+issue](https://github.com/RobertsLab/OCEAN/issues/new/choose) 🧬
\ No newline at end of file
diff --git a/setup-template.py b/setup-template.py
new file mode 100755
index 0000000..be0bdfc
--- /dev/null
+++ b/setup-template.py
@@ -0,0 +1,84 @@
+#!/usr/bin/env python3
+"""
+Template processor for genomic data platform
+Generates project files from templates and configuration
+"""
+
+import yaml
+import json
+import os
+import sys
+from pathlib import Path
+from jinja2 import Environment, FileSystemLoader, Template
+
+def load_config(config_path):
+    """Load YAML configuration file"""
+    with open(config_path, 'r') as f:
+        return yaml.safe_load(f)
+
+def process_template(template_path, output_path, config):
+    """Process a single template file"""
+    env = Environment(loader=FileSystemLoader(Path(template_path).parent))
+    template = env.get_template(Path(template_path).name)
+    
+    # Render the template
+    rendered = template.render(**config)
+    
+    # Write to output file
+    with open(output_path, 'w') as f:
+        f.write(rendered)
+    
+    print(f"Generated: {output_path}")
+
+def setup_project(config_path):
+    """Set up a new project from templates"""
+    # Load configuration
+    config = load_config(config_path)
+    
+    # Create directories
+    quarto_dir = Path("quarto")
+    docs_dir = Path("docs") 
+    jbrowse_dir = docs_dir / "jbrowse"
+    
+    quarto_dir.mkdir(exist_ok=True)
+    jbrowse_dir.mkdir(parents=True, exist_ok=True)
+    
+    # Template mappings: (template_file, output_file)
+    templates = [
+        ("templates/index.qmd.template", "quarto/index.qmd"),
+        ("templates/about.qmd.template", "quarto/about.qmd"), 
+        ("templates/explore.qmd.template", "quarto/explore.qmd"),
+        ("templates/browse.qmd.template", "quarto/browse.qmd"),
+        ("templates/_quarto.yml.template", "quarto/_quarto.yml"),
+        ("templates/jbrowse-config.json.template", "docs/jbrowse/config.json")
+    ]
+    
+    # Process each template
+    for template_file, output_file in templates:
+        if Path(template_file).exists():
+            process_template(template_file, output_file, config)
+        else:
+            print(f"Warning: Template {template_file} not found")
+    
+    print(f"\nProject setup complete! Website title: {config['website']['title']}")
+    print(f"Species: {config['species']['scientific_name']}")
+    print("\nNext steps:")
+    print("1. Update your data sources in template-config.yml")
+    print("2. Add your genome data files to docs/jbrowse/data/")
+    print("3. Build the website with: quarto render quarto/")
+
+def main():
+    if len(sys.argv) != 2:
+        print("Usage: python setup-template.py <config-file>")
+        print("Example: python setup-template.py template-config.yml")
+        sys.exit(1)
+    
+    config_file = sys.argv[1]
+    if not Path(config_file).exists():
+        print(f"Error: Config file {config_file} not found")
+        sys.exit(1)
+    
+    setup_project(config_file)
+
+if __name__ == "__main__":
+    main()
\ No newline at end of file
diff --git a/template-config.yml b/template-config.yml
new file mode 100644
index 0000000..f54efbe
--- /dev/null
+++ b/template-config.yml
@@ -0,0 +1,95 @@
+# Template Configuration for Genomic Data Platform
+# Copy this file and customize for your species/project
+
+# Project Information
+project:
+  name: "OCEAN"  # Short name for the project
+  full_name: "Ostrea chilensis: Epigénoma Análisis en Net"  # Full project name
+  description: "An integrated web platform dedicated to advancing research"
+  
+# Species Information  
+species:
+  scientific_name: "Ostrea chilensis"
+  common_name: "Chilean flat oyster"
+  description: "the Chilean flat oyster"
+  emoji: "🦪"  # Optional emoji for branding
+
+# Website Configuration
+website:
+  title: "OCEAN"
+  theme: "simplex"
+  github_repo: "https://github.com/RobertsLab/OCEAN"
+  contact_message: "For questions or feedback, please submit an issue"
+  
+# Genome Browser Configuration
+jbrowse:
+  version: "v3.6.4"
+  assemblies:
+    - name: "Assembly 1.0"
+      fasta_url: "https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/OCEAN/docs/jbrowse/data/v1/merged_out.fasta.TBtools.fa"
+      fai_url: "https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/OCEAN/docs/jbrowse/data/v1/merged_out.fasta.TBtools.fa.fai"
+    - name: "Och_HapA"  
+      fasta_url: "https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/OCEAN/docs/jbrowse/data/HapA/Och_HapA_assembly.fa"
+      fai_url: "https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/OCEAN/docs/jbrowse/data/HapA/Och_HapA_assembly.fa.fai"
+
+# Data Sources (URLs to annotation and other data files)
+data_sources:
+  # Annotation data
+  nr_blast: "http://gannet.fish.washington.edu/seashell/snaps/nr.csv"
+  uniprot: "http://gannet.fish.washington.edu/seashell/snaps/uniprot.txt"  
+  pathways: "http://gannet.fish.washington.edu/seashell/snaps/pathway_table.csv"
+  gene_gff: "http://gannet.fish.washington.edu/seashell/snaps/gene.gff3"
+  
+  # Genome browser specific
+  gene_annotations: "data/v1/GN.gene.gff3"
+  ncrna_annotations: "data/v1/ncRNA.gff3"
+  repeat_annotations: "https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/OCEAN/docs/jbrowse/data/v1/repeat.gff3"
+
+# Population/Study Information (customize or remove sections as needed)
+population_info:
+  enabled: true
+  title: "Population Information"
+  description: "Our focus to date is from oysters from three locales"
+  
+  # Location data
+  map_embed: "https://www.google.com/maps/d/u/0/embed?mid=19nWyrDGOjq34Fy3nmXB-walLF1yjNdY&ehbc=2E312F&noprof=1"
+  
+  locations:
+    - name: "Río Pudeto"
+      salinity: "Moderate (brackish)"
+      freshwater_input: "Moderate river inflow"
+      tidal_exchange: "Moderate"
+      human_influence: "Moderate"
+    - name: "Pumalín"
+      salinity: "Low (oligohaline)"
+      freshwater_input: "High (glacial & river)"
+      tidal_exchange: "Low"
+      human_influence: "Low (pristine)"
+    - name: "Isla Quihua"
+      salinity: "High (marine)"
+      freshwater_input: "Low to moderate"
+      tidal_exchange: "High"
+      human_influence: "Moderate to high"
+      
+  # Genetic relatedness
+  genetic_relatedness:
+    enabled: true
+    image_url: "http://gannet.fish.washington.edu/seashell/snaps/Monosnap_Monosnap_2025-08-03_15-06-38.png"
+
+# Featured Views (for genome browser)
+featured_views:
+  - title: "Gene Expression following Heat Exposure"
+    url: "https://robertslab.github.io/OCEAN/jbrowse/?session=share-bS-rRTROpE&password=r9vWX"
+  - title: "DEG MSTRG.1743.1 zoom"  
+    url: "https://oystergen.es/jbrowse/?session=share-fpBeSAviSo&password=scJyF"
+
+# Custom branding
+branding:
+  logo_image: "img/ocean.png"
+  celebration_message: "¡Diviértete explorando el océano!"  # Optional custom message
+  platform_features:
+    - "🧬 Genome browser for {species.scientific_name}"
+    - "🔍 Epigenetic data"  
+    - "📊 Interactive tools for gene expression and regulatory region analysis"
+    - "🧠 Curated annotations including GO terms and pathway associations"
+    - "🌐 Data sharing & collaboration hub for the research community"
\ No newline at end of file
diff --git a/templates/_quarto.yml.template b/templates/_quarto.yml.template
new file mode 100644
index 0000000..07b46cb
--- /dev/null
+++ b/templates/_quarto.yml.template
@@ -0,0 +1,24 @@
+project:
+  type: website
+  output-dir: ../docs  # Goes to root-level docs/ folder
+
+website:
+  title: "{{ website.title }}"
+  navbar:
+    left:
+      - text: About
+        file: about.qmd
+      - text: Annotations
+        href: explore.qmd
+      - text: Genome Browser
+        href: jbrowse/index.html
+    right:
+      - icon: github
+        href: {{ website.github_repo }}
+        aria-label: GitHub
+
+format:
+  html:
+    theme: {{ website.theme }}
+    css: styles.css
+    toc: true
\ No newline at end of file
diff --git a/templates/about.qmd.template b/templates/about.qmd.template
new file mode 100644
index 0000000..97ba150
--- /dev/null
+++ b/templates/about.qmd.template
@@ -0,0 +1,58 @@
+---
+title: "About"
+format: html 
+editor: 
+  markdown: 
+    wrap: 72
+---
+
+{{project.name}} is an integrated web platform dedicated to advancing research on
+*{{species.scientific_name}}*, {{species.description}}.
+
+The platform offers:\
+{% for feature in branding.platform_features %}
+• {{feature}}\
+{% endfor %}
+
+::: badges
+<p><a href="{{ website.github_repo }}/releases">
+<img src="https://img.shields.io/github/v/release/{{ website.github_repo.replace('https://github.com/', '') }}"/>
+</a>
+<img src="https://img.shields.io/github/last-commit/{{ website.github_repo.replace('https://github.com/', '') }}"/>
+<img src="https://img.shields.io/badge/jbrowse-{{ jbrowse.version }}-darkblue"/></p>
+:::
+
+------------------------------------------------------------------------
+
+# Featured Genome Browser Views 👀
+
+{% for view in featured_views %}
+-   ### [{{ view.title }}]({{ view.url }})
+{% endfor %}
+
+------------------------------------------------------------------------
+
+{% if population_info.enabled %}
+# {{ population_info.title }}
+
+## Site Location Information
+
+{{ population_info.description }}
+
+<iframe src="{{ population_info.map_embed }}" width="90%" height="480">
+
+</iframe>
+
+| Location | Salinity | Freshwater Input | Tidal Exchange | Human Influence |
+|--------------|--------------|----------------|--------------|--------------|
+{% for location in population_info.locations %}
+| {{ location.name }} | {{ location.salinity }} | {{ location.freshwater_input }} | {{ location.tidal_exchange }} | {{ location.human_influence }} |
+{% endfor %}
+
+{% if population_info.genetic_relatedness.enabled %}
+## Genetic Relatedness
+
+![]({{ population_info.genetic_relatedness.image_url }})
+{% endif %}
+
+{% endif %}
\ No newline at end of file
diff --git a/templates/browse.qmd.template b/templates/browse.qmd.template
new file mode 100644
index 0000000..77c6e23
--- /dev/null
+++ b/templates/browse.qmd.template
@@ -0,0 +1,7 @@
+## Explore the Genome
+
+::: {.iframe-container}
+
+<iframe src="jbrowse/index.html" width="100%" height="800px" style="border: none;"></iframe>
+
+:::
\ No newline at end of file
diff --git a/templates/explore.qmd.template b/templates/explore.qmd.template
new file mode 100644
index 0000000..b1a94b2
--- /dev/null
+++ b/templates/explore.qmd.template
@@ -0,0 +1,113 @@
+---
+title: "Genome Annotation"
+format: html
+editor: visual
+execute:
+  echo: true
+  warning: false
+  message: false
+---
+
+```{r setup, include=FALSE}
+library(tidyverse)
+library(DT)
+library(readxl)
+library(plotly)
+library(readr)
+library(dplyr)
+```
+
+## NCBI NR BLAST
+
+```{r, echo=FALSE}
+# Read the CSV file
+nr_data <- read_csv("{{ data_sources.nr_blast }}")
+
+# Subset the relevant columns
+nr_subset <- nr_data[, c("query_name", "nr.hit_name", "description", "E value")]
+
+# Create interactive datatable
+datatable(
+  nr_subset,
+  extensions = 'Buttons',
+  options = list(
+    dom = 'Bfrtip',
+    buttons = c('copy', 'csv', 'excel', 'pdf', 'print'),
+    pageLength = 4
+  ),
+  filter = "top",
+  rownames = FALSE
+)
+```
+
+## UniProt
+
+```{r, echo=FALSE}
+# Read the tab-delimited file from the URL
+uniprot_data <- read_tsv("{{ data_sources.uniprot }}")
+
+# Display as an interactive datatable
+datatable(
+  uniprot_data,
+  extensions = 'Buttons',
+  options = list(
+    dom = 'Bfrtip',
+    buttons = c('copy', 'csv', 'excel', 'pdf', 'print'),
+    pageLength = 4
+  ),
+  filter = "top",
+  rownames = FALSE
+)
+```
+
+## Pathways 
+
+```{r, echo=FALSE}
+# Read your Pathway CSV
+# Read the CSV
+df <- read_csv("{{ data_sources.pathways }}")
+
+# Create clickable link column
+df <- df %>%
+  mutate(Link = paste0(
+    "<a href='jbrowse/function/pathway/", PathwayId, ".png' target='_blank'>", PathwayId, "</a>"
+  ))
+
+# Move Link column to position 3
+df <- df %>%
+  select(1:2, Link, everything())
+
+# Display interactive table
+datatable(
+  df,
+  escape = FALSE,
+  extensions = 'Buttons',
+  options = list(
+    dom = 'Bfrtip',
+    buttons = c('copy', 'csv', 'excel', 'pdf', 'print'),
+    pageLength = 6
+  )
+)
+```
+
+## Gene GFF 
+
+```{r, echo=FALSE}
+# Read the GFF3 file (skip comment lines starting with "#")
+gff <- read_tsv(
+  "{{ data_sources.gene_gff }}",
+  comment = "#",
+  col_names = c("seqid", "source", "type", "start", "end", "score", "strand", "phase", "attributes")
+)
+
+datatable(
+  gff,
+  extensions = 'Buttons',
+  options = list(
+    dom = 'Bfrtip',
+    buttons = c('copy', 'csv', 'excel', 'pdf', 'print'),
+    pageLength = 6
+  ),
+  filter = "top"
+)
+```
\ No newline at end of file
diff --git a/templates/index.qmd.template b/templates/index.qmd.template
new file mode 100644
index 0000000..620894a
--- /dev/null
+++ b/templates/index.qmd.template
@@ -0,0 +1,32 @@
+---
+title: "Explore the Ocean"
+format: html 
+editor: 
+  markdown: 
+    wrap: 72
+---
+
+{{ project.full_name }}
+is an integrated web platform dedicated to advancing research on *{{ species.scientific_name }}*, {{ species.description }}. By combining high-resolution
+genomic data with cutting-edge epigenomic insights, {{ project.name }} supports
+researchers exploring gene regulation, environmental plasticity, and
+resilience in this ecologically important marine species.
+
+::: {style="text-align: center; font-size: 1.5em; margin-top: 2em;"}
+{{ branding.celebration_message }}
+:::
+
+![]({{ branding.logo_image }}){fig-align="center"
+width="450px"}
+
+::: {style="display: flex; align-items: center; gap: 1em;"}
+[👉 <a href="jbrowse/index.html">Explore JBrowse Genome
+Browser</a>]{style="font-size: 1.1em;"}
+
+<a href="{{ website.github_repo }}/releases">
+<img src="https://img.shields.io/github/v/release/{{ website.github_repo.replace('https://github.com/', '') }}" style="height: 1.4em;"/>
+</a>
+:::
+
+{{ website.contact_message }}, [please submit an
+issue]({{ website.github_repo }}/issues/new/choose) 🧬
\ No newline at end of file
diff --git a/templates/jbrowse-config.json.template b/templates/jbrowse-config.json.template
new file mode 100644
index 0000000..b42ec96
--- /dev/null
+++ b/templates/jbrowse-config.json.template
@@ -0,0 +1,63 @@
+{
+  "baseUrl": "jbrowse/",
+  "assemblies": [
+    {% for assembly in jbrowse.assemblies %}
+    {
+      "name": "{{ assembly.name }}",
+      "sequence": {
+        "type": "ReferenceSequenceTrack",
+        "trackId": "{{ assembly.name | lower | replace(' ', '_') }}_refseq",
+        "adapter": {
+          "type": "IndexedFastaAdapter",
+          "fastaLocation": {
+            "uri": "{{ assembly.fasta_url }}"
+          },
+          "faiLocation": {
+            "uri": "{{ assembly.fai_url }}"
+          }
+        }
+      }
+    }{% if not loop.last %},{% endif %}
+    {% endfor %}
+  ],
+  "tracks": [
+    {
+      "type": "FeatureTrack",
+      "trackId": "gene_annotations",
+      "name": "Genes",
+      "assemblyNames": ["{{ jbrowse.assemblies[0].name }}"],
+      "adapter": {
+        "type": "Gff3Adapter",
+        "gffLocation": { "uri": "{{ data_sources.gene_annotations }}" }
+      }
+    },
+    {
+      "type": "FeatureTrack",
+      "trackId": "ncrna_annotations",
+      "name": "ncRNA",
+      "assemblyNames": ["{{ jbrowse.assemblies[0].name }}"],
+      "adapter": {
+        "type": "Gff3Adapter",
+        "gffLocation": { "uri": "{{ data_sources.ncrna_annotations }}" }
+      }
+    },
+    {
+      "type": "FeatureTrack",
+      "trackId": "repeat_annotations",
+      "name": "Repeats",
+      "assemblyNames": ["{{ jbrowse.assemblies[0].name }}"],
+      "adapter": {
+        "type": "Gff3Adapter",
+        "gffLocation": {
+          "uri": "{{ data_sources.repeat_annotations }}"
+        }
+      }
+    }
+  ],
+  "plugins": [
+    {
+      "name": "UMDUrlPlugin",
+      "url": "umd_plugin.js"
+    }
+  ]
+}
\ No newline at end of file