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+# BRAIN Project - Modular Structure
+
+This document describes the modular structure implemented for the BRAIN Expression Template Decoder application.
+
+## Overview
+
+The application has been refactored to use Flask blueprints for better code organization and maintainability. The paper analysis functionality has been separated into its own module.
+
+## Project Structure
+
+```
+BRAINProject/
+├── app.py                          # Main Flask application
+├── blueprints/                     # Blueprint modules
+│   ├── __init__.py                # Package initialization
+│   └── paper_analysis.py          # Paper analysis blueprint
+├── templates/
+│   ├── index.html                 # Main page template
+│   └── paper_analysis.html        # Paper analysis page template
+├── static/
+│   ├── script.js                  # Main application JavaScript
+│   ├── paper_analysis.js          # Paper analysis JavaScript
+│   ├── brain.js                   # BRAIN API functions
+│   ├── decoder.js                 # Template decoder functions
+│   └── styles.css                 # Application styles
+└── requirements.txt               # Python dependencies
+```
+
+## Blueprint Structure
+
+### Paper Analysis Blueprint (`blueprints/paper_analysis.py`)
+
+The paper analysis functionality has been moved to a separate blueprint that includes:
+
+#### Routes:
+- `GET /paper-analysis/` - Paper analysis page
+- `POST /paper-analysis/api/test-deepseek` - Test Deepseek API connection
+- `POST /paper-analysis/api/analyze-paper` - Analyze uploaded papers
+
+#### Functions:
+- File processing functions for various formats (PDF, DOCX, RTF, LaTeX, Markdown, plain text)
+- Deepseek API integration functions
+- Text extraction and processing utilities
+
+### Main Application (`app.py`)
+
+The main application now focuses on:
+
+#### Routes:
+- BRAIN API authentication and session management
+- BRAIN operators and data fields API
+- Expression testing functionality
+- Main application routes
+
+#### Features:
+- Auto-dependency installation
+- BRAIN API integration
+- Session management for multiple users
+- Template decoding functionality
+
+## Benefits of This Structure
+
+1. **Modularity**: Related functionality is grouped together in blueprints
+2. **Maintainability**: Easier to maintain and update individual modules
+3. **Scalability**: Easy to add new blueprints for additional features
+4. **Separation of Concerns**: Each blueprint handles a specific domain
+5. **Testability**: Individual modules can be tested independently
+
+## URL Structure
+
+### Before Refactoring:
+- `/paper-analysis` - Paper analysis page
+- `/api/test-deepseek` - Test Deepseek API
+- `/api/analyze-paper` - Analyze paper
+
+### After Refactoring:
+- `/paper-analysis/` - Paper analysis page (blueprint)
+- `/paper-analysis/api/test-deepseek` - Test Deepseek API (blueprint)
+- `/paper-analysis/api/analyze-paper` - Analyze paper (blueprint)
+
+## Dependencies
+
+### Main Application Dependencies:
+- Flask
+- Flask-CORS
+- requests
+- pandas (for BRAIN API integration)
+
+### Paper Analysis Dependencies:
+- All main dependencies plus:
+- PyPDF2 or pdfplumber (for PDF processing)
+- python-docx (for Word documents)
+- docx2txt (for legacy DOC files)
+- striprtf (for RTF files)
+- PyMuPDF (alternative PDF library)
+
+## Adding New Blueprints
+
+To add a new blueprint:
+
+1. Create a new file in the `blueprints/` directory
+2. Define your blueprint:
+   ```python
+   from flask import Blueprint
+   
+   new_blueprint = Blueprint('new_feature', __name__, url_prefix='/new-feature')
+   
+   @new_blueprint.route('/')
+   def index():
+       return render_template('new_feature.html')
+   ```
+3. Import and register the blueprint in `app.py`:
+   ```python
+   from blueprints.new_feature import new_blueprint
+   app.register_blueprint(new_blueprint)
+   ```
+
+## Notes
+
+- The paper analysis JavaScript file (`static/paper_analysis.js`) has been updated to use the new blueprint URLs
+- The main index template has been updated to link to the correct blueprint route
+- Unused imports have been removed from the main application file
+- All paper analysis functionality remains intact but is now properly modularized