mcp-research-toolkit

# mcp-research-toolkit Copyright (c) 2024 Kanyuchi. All rights reserved. Licensed under the MIT License. See LICENSE file for details. 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 ```mermaid 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 1. Clone the repository: ```bash git clone [repository-url] cd Mcp_Build_Protocol ``` 2. Set up configuration: - Copy example configuration files and add your API keys: ```bash cp pdf_analysis_mcp/claude_desktop_config.example.json pdf_analysis_mcp/claude_desktop_config.json ``` - Update the configuration with your API keys 3. Set up Python environment: ```bash cd pdf_analysis_mcp python -m venv venv source venv/bin/activate # On Windows: venv\Scripts\activate pip install -r requirements.txt ``` 4. Set up Node.js dependencies: ```bash 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 1. Start the PDF analysis server: ```bash cd pdf_analysis_mcp python test_fastmcp_server.py ``` 2. Run the file server: ```bash cd mcp-file-server npm start ``` 3. 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: 1. Check the documentation 2. Search existing issues 3. Create a new issue if needed