mcp-research-toolkit

A comprehensive toolkit for building and managing Model Context Protocol (MCP) servers, with specific focus on PDF analysis and thesis writing assistance.

Component Ownership

This project includes several MCP components with different ownership:

PDF Analysis MCP (Custom Component): Copyright (c) 2024 Kanyuchi
Claude Memory MCP (Custom Component): Copyright (c) 2024 Kanyuchi
File Server MCP: Based on standard MCP implementations
Other MCPs: Third-party implementations (Perplexity, Octagon, etc.)

🌟 Features

PDF Analysis MCP Server: Advanced PDF processing and analysis capabilities
Claude Memory Integration: Persistent memory system for improved context awareness
Thesis Writing Tools: Specialized tools for academic research and writing
Multiple MCP Server Types: Support for various MCP servers including Perplexity, Octagon, and Sequential Thinking

🏗️ Architecture

graph TD
    A[Claude Desktop/Cursor IDE] --> B[MCP Host]
    B --> C{MCP Servers}
    
    C --> D[PDF Analysis MCP]
    C --> E[Claude Memory MCP]
    C --> F[File Server MCP]
    C --> G[Perplexity Ask MCP]
    C --> H[Octagon Research MCP]
    C --> I[Sequential Thinking MCP]
    C --> J[Task Master MCP]
    
    D --> D1["PDF Processing Tools<br/>- analyze_pdf<br/>- analyze_directory<br/>- find_relationships<br/>- search_claims<br/>- generate_summary<br/>- export_data"]
    
    E --> E1["Memory Tools<br/>- store_memory<br/>- retrieve_memory<br/>- list_memories<br/>- delete_memory<br/>- memory_stats"]
    
    F --> F1["File Tools<br/>- read_file<br/>- write_file<br/>- list_directory<br/>- get_file_info"]
    
    G --> G1["Research Tools<br/>- perplexity_ask"]
    
    H --> H1["Deep Research Tools<br/>- octagon_research"]
    
    I --> I1["Thinking Tools<br/>- sequential_analysis"]
    
    J --> J1["Task Tools<br/>- task_management<br/>- task_tracking"]

📋 Prerequisites

Python 3.8+
Node.js 14+
Virtual environment tool (venv)
Git

🚀 Getting Started

Clone the repository:

git clone [repository-url]
cd Mcp_Build_Protocol

Set up configuration:
- Copy example configuration files and add your API keys:
```
cp pdf_analysis_mcp/claude_desktop_config.example.json pdf_analysis_mcp/claude_desktop_config.json
```
- Update the configuration with your API keys

Set up Python environment:

cd pdf_analysis_mcp
python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate
pip install -r requirements.txt

Set up Node.js dependencies:
```
cd mcp-file-server
npm install
```

🔧 Configuration

The system requires several API keys for full functionality:

Perplexity API key
Octagon API key
Other provider-specific keys as needed

Add these to your configuration files as specified in the example configurations.

📚 Project Structure

pdf_analysis_mcp/: PDF analysis server implementation
claude-memory-mcp/: Claude memory system integration
mcp-file-server/: File serving capabilities
thesis_memory/: Thesis writing and research tools
thesis-memory-system/: Enhanced memory system for thesis work

🛠️ Usage

Start the PDF analysis server:

cd pdf_analysis_mcp
python test_fastmcp_server.py

Run the file server:
```
cd mcp-file-server
npm start
```
Configure Claude Desktop integration using the provided configuration files.

📖 Documentation

Detailed documentation is available in the following locations:

docs/: General documentation
pdf_analysis_mcp/README.md: PDF analysis server documentation
claude-memory-mcp/docs/: Claude memory system documentation

🤝 Contributing

Contributions are welcome! Please read our contributing guidelines before submitting pull requests.

📄 License

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

🔐 Security

Never commit API keys or sensitive credentials
Use example configuration files with placeholders
Follow security best practices when handling sensitive data

⚠️ Important Notes

Keep your API keys secure and never commit them to the repository
Regularly update dependencies to maintain security
Follow the provided setup instructions carefully

📞 Support

For support, please:

Check the documentation
Search existing issues
Create a new issue if needed

MCP Servers