A Model Context Protocol (MCP) server that provides intelligent research data management using vector embeddings and semantic search. This server enables you to save, organize, and retrieve research content using ChromaDB and OpenAI embeddings, deployed on AWS EC2.

Screenshots

Features

• Vector-Based Storage: Store research content with semantic embeddings using ChromaDB
• Semantic Search: Query your research data using natural language with similarity-based retrieval
• Topic Organization: Organize research into separate topic-based databases
• Duplicate Detection: Automatic deduplication using content hashing
• RESTful API: HTTP-based MCP server using FastMCP's streamable-http transport
• OpenAI Embeddings: Uses OpenAI's text-embedding-3-small model for high-quality semantic search

Tools Available

The server exposes five powerful tools through the MCP protocol:

1. save_research_data - Save research content to vector database
2. search_research_data - Semantic search through saved research
3. list_research_topics - View all available research topics
4. delete_research_topic - Remove a topic and its data
5. get_topic_info - Get detailed information about a specific topic

Architecture

Research Assistant MCP Server
├── FastMCP Server (streamable-http transport)
├── ChromaDB (Vector Database)
├── OpenAI Embeddings (text-embedding-3-small)
└── LangChain (Document Processing)

Prerequisites

• Python 3.13+
• OpenAI API key (Get one here)
• AWS EC2 instance (for deployment)

Installation

Local Setup

1. Clone the repository

   git https://github.com/CyprianFusi/mcp-research-server-on-EC2.git
   cd mcp-research-server-on-EC2
   

2. Install dependencies using uv

   pip install uv
   uv sync
   

   Or using pip:

   pip install -r requirements.txt
   

3. Configure environment variables

   Create a .env file in the project root:

   OPENAI_API_KEY=your_openai_api_key_here
   

   Replace your_openai_api_key_here with your actual OpenAI API key from OpenAI Platform.

4. Run the server

   python server.py
   

AWS EC2 Deployment

Step 1: Launch EC2 Instance

1. Launch an Amazon Linux 2 or Amazon Linux 2023 EC2 instance
2. Configure security group to allow:
   • SSH (port 22)
   • Custom TCP (port for your MCP server if exposing externally)
3. Download your key pair (.pem file)

Step 2: Connect to EC2

From Windows:

ssh -i "your-key.pem" ec2-user@your-ec2-public-dns

From macOS/Linux:

chmod 400 your-key.pem
ssh -i "your-key.pem" ec2-user@your-ec2-public-dns

Step 3: Install Anaconda

Follow the setup guide in anaconda_setup.md:

# Update system
sudo yum update -y

# Download Anaconda
curl -O https://repo.anaconda.com/archive/Anaconda3-2025.06-0-Linux-x86_64.sh

# Install Anaconda
bash Anaconda3-2025.06-0-Linux-x86_64.sh

# Add to PATH
export PATH="/home/ec2-user/anaconda3/bin:$PATH"
echo 'export PATH="/home/ec2-user/anaconda3/bin:$PATH"' >> ~/.bashrc
source ~/.bashrc

# Initialize conda
conda init bash
source ~/.bashrc

Step 4: Setup MCP Server

# Clone your repository
git clone https://github.com/CyprianFusi/mcp-research-server-on-EC2.git
cd mcp-research-server-on-EC2

# Install dependencies
pip install uv
uv sync

# Configure environment variables
echo "OPENAI_API_KEY=your_openai_api_key_here" > .env

# Important: Replace 'your_openai_api_key_here' with your actual OpenAI API key
nano .env  # Edit the file to add your real API key

# Run the server
python server.py

Step 5: Run as Background Service (Optional)

Create a systemd service file:

sudo nano /etc/systemd/system/mcp-research.service

Add the following:

[Unit]
Description=Research Assistant MCP Server
After=network.target

[Service]
Type=simple
User=ec2-user
WorkingDirectory=/home/ec2-user/mcp-research-server-on-EC2
Environment="OPENAI_API_KEY=your_openai_api_key_here"
ExecStart=/home/ec2-user/anaconda3/bin/python server.py
Restart=always
RestartSec=10

[Install]
WantedBy=multi-user.target

Important: Replace your_openai_api_key_here with your actual OpenAI API key in the service file.

Enable and start the service:

sudo systemctl daemon-reload
sudo systemctl enable mcp-research
sudo systemctl start mcp-research
sudo systemctl status mcp-research

Configuration

The server uses the following default configuration (defined in server.py):

EMBED_MODEL = "text-embedding-3-small"
API_URL = "https://api.openai.com/v1/embeddings"
CHROMA_DB_ROOT = "./research_chroma_dbs"

Environment Variables

The following environment variable is required:

• OPENAI_API_KEY: Your OpenAI API key for accessing the embeddings API

Create a .env file in the project root:

OPENAI_API_KEY=sk-...your-key-here

The server uses python-dotenv to automatically load environment variables from the .env file.

Usage

Tool: save_research_data

Save research content to the vector database.

Parameters:

• content (List[str]): List of text content to save
• topic (str, optional): Topic name for organizing data (default: "default")

Example:

{
  "content": [
    "Machine learning is a subset of artificial intelligence...",
    "Neural networks are inspired by biological neurons..."
  ],
  "topic": "machine_learning"
}

Returns:

Successfully saved 2 new documents to topic: machine_learning (skipped 0 duplicates)

Tool: search_research_data

Search through saved research using semantic similarity.

Parameters:

• query (str): Search query
• topic (str, optional): Topic to search in (default: "default")
• max_results (int, optional): Maximum results to return (default: 5)

Example:

{
  "query": "What is deep learning?",
  "topic": "machine_learning",
  "max_results": 3
}

Returns:

==================================================
Result 1 (Similarity: 0.892):
Deep learning is a subset of machine learning...
==================================================
Result 2 (Similarity: 0.845):
Neural networks with multiple layers...
==================================================

Tool: list_research_topics

List all available research topics.

Returns:

Topic: machine_learning (15 documents)
Topic: python_programming (8 documents)
Topic: cloud_computing (12 documents)

Tool: get_topic_info

Get detailed information about a research topic.

Parameters:

• topic (str): Topic name

Example:

{
  "topic": "machine_learning"
}

Returns:

Topic Information: machine_learning
- ChromaDB Collection: research_machine_learning
- Document Count: 15
- Hash Records: 15
- Database Path: /path/to/research_chroma_dbs/machine_learning
- Embedding Model: text-embedding-3-small
- OPENAI URL: https://api.openai.com/v1/embeddings

Tool: delete_research_topic

Delete a research topic and all its data.

Parameters:

• topic (str): Topic name to delete

Example:

{
  "topic": "old_research"
}

Returns:

Successfully deleted topic: Old Research

Project Structure

8_Deploy_MCP_Server_on_EC2/
├── server.py                    # Main MCP server implementation
├── pyproject.toml              # Project dependencies
├── uv.lock                     # Locked dependencies
├── anaconda_setup.md           # EC2 Anaconda installation guide
├── .env                        # Environment configuration
├── .python-version             # Python version specification
├── research_chroma_dbs/        # ChromaDB storage (created at runtime)
│   ├── topic1/
│   ├── topic2/
│   └── ...
└── asserts/                    # UI screenshots
    ├── ui_1.png
    ├── ui_2.png
    └── ...

Dependencies

Key dependencies from pyproject.toml:

• fastmcp>=2.13.2 - MCP server framework
• chromadb>=1.3.5 - Vector database
• langchain>=1.1.3 - Document processing framework
• langchain-chroma>=1.0.0 - ChromaDB integration
• langchain-openai>=1.1.1 - OpenAI embeddings integration
• langchain-core>=1.1.2 - Core LangChain functionality
• mcp[cli]>=1.23.2 - MCP CLI tools
• python-dotenv - Environment variable management

Troubleshooting

OpenAI API Key Issues

Problem: Error: OpenAI API key not found or AuthenticationError

Solution:

# Verify .env file exists and contains your API key
cat .env

# Should output:
# OPENAI_API_KEY=sk-...

# If not, create the .env file:
echo "OPENAI_API_KEY=your_actual_key_here" > .env

For EC2 deployment:

• Ensure the .env file is in the working directory
• Alternatively, set the environment variable in the systemd service file
• Verify the API key is valid at OpenAI Platform

OpenAI API Rate Limits

Problem: RateLimitError: Rate limit exceeded

Solution:

• Reduce the number of documents being embedded at once
• Upgrade your OpenAI API plan for higher rate limits
• Implement retry logic with exponential backoff (built into langchain-openai)

ChromaDB Permission Errors

Problem: Permission denied when accessing research_chroma_dbs/

Solution:

# Fix permissions
chmod -R 755 research_chroma_dbs/

# On EC2, ensure ec2-user owns the directory
sudo chown -R ec2-user:ec2-user research_chroma_dbs/

Network Connection Issues

Problem: Error: Cannot connect to OpenAI API

Solution:

1. Verify internet connectivity: curl https://api.openai.com
2. Check firewall settings allow outbound HTTPS connections
3. On EC2, ensure security group allows outbound traffic to OpenAI API
4. Verify no proxy settings are interfering with the connection

EC2 Connection Timeout

Problem: Cannot connect to EC2 instance

Solution:

1. Check security group allows SSH (port 22) from your IP
2. Verify instance is running
3. Ensure .pem file has correct permissions: chmod 400 your-key.pem
4. Use correct username: ec2-user for Amazon Linux

Performance Considerations

• Embedding Generation: OpenAI API calls typically complete in 100-500ms per document
• Search Speed: Semantic search is typically sub-second for databases with <10,000 documents
• Storage: ChromaDB stores embeddings on disk; plan for ~1KB per document
• API Costs: OpenAI's text-embedding-3-small costs $0.02 per 1M tokens (very cost-effective)
• Rate Limits: Free tier: 3 RPM, Tier 1: 500 RPM, Tier 2: 5000 RPM
• Batch Processing: For large datasets, consider batching documents to optimize API usage

Security Notes

• The server runs on localhost by default
• For production deployment, implement proper authentication
• Secure your EC2 instance with appropriate security groups
• CRITICAL: Never commit .env files with sensitive credentials to version control
• Add .env to your .gitignore file
• Rotate your OpenAI API keys regularly
• Use environment-specific API keys (separate keys for development and production)
• Monitor your OpenAI API usage dashboard for unexpected activity
• On EC2, use IAM roles and AWS Secrets Manager for production deployments (recommended over .env files)

Contributing

Contributions are welcome! Please:

1. Fork the repository
2. Create a feature branch
3. Make your changes
4. Submit a pull request

License

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

Support

For issues and questions:

• Open an issue on GitHub
• Check existing issues for solutions
• Review the MCP Documentation

Acknowledgments

• FastMCP - MCP server framework
• ChromaDB - Vector database
• OpenAI - Embeddings API
• LangChain - LLM application framework

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Built with the Model Context Protocol for intelligent research management.