MCP-Powered AI Research Engineer

Turn a single prompt into a full research report (web + your notes + code + charts).

An autonomous AI agent that researches, codes, and writes comprehensive reports using the Model Context Protocol (MCP).

⚡ One‑liner install

Option 1: Using uv (Recommended - Fast!)

git clone https://github.com/prabureddy/ai-research-agent-mcp.git \
  && cd ai-research-agent-mcp/server \
  && uv venv \
  && source .venv/bin/activate \
  && uv pip install -r requirements.txt

Option 2: Using pip (Traditional)

git clone https://github.com/prabureddy/ai-research-agent-mcp.git \
  && cd ai-research-agent-mcp/server \
  && python3 -m venv venv \
  && source venv/bin/activate \
  && pip3 install -r requirements.txt

⚡ Quick Start: Clone → Install → Configure Claude Desktop → Start researching in 5 minutes!

Who is this for?

• AI engineers doing research
• Indie hackers prototyping ideas
• Knowledge workers who live in Claude Desktop or Cursor

Overview

This system enables you to give a single command like:

"Compare electric scooters vs bikes for my commute and prototype a savings calculator"

And the agent autonomously:

• 🔍 Researches the web for relevant data
• 📚 Queries your personal knowledge base (notes, papers, docs)
• 💻 Writes and executes code (models, simulations, visualizations)
• 📊 Generates comprehensive reports with charts and analysis
• 🎯 Self-evaluates and logs quality metrics

---

Table of Contents

• Features
• Quick Start
• Architecture
• Configuration
• Usage
• Project Structure
• Troubleshooting
• Example Output
• Development
• Uninstallation
• Contributing
• License

---

Features

• ✅ Autonomous multi-step research
• ✅ Web search and content extraction
• ✅ RAG over personal knowledge base
• ✅ Safe code execution with output capture
• ✅ Structured report generation
• ✅ Self-evaluation and quality metrics
• ✅ Comprehensive logging and tracing
• ✅ Reproducible research runs

---

Quick Start

Get up and running in 5 minutes.

Prerequisites

• Python 3.10 or higher (Python 3.11+ recommended)
• Claude Desktop or Cursor IDE (MCP-compatible client)
• Git (for cloning the repository)
• uv (optional but recommended - install here) or pip
• (Optional) API keys for enhanced features

Installation Steps

1. Clone the Repository

git clone https://github.com/prabureddy/ai-research-agent-mcp.git
cd ai-research-agent-mcp

2. Install Dependencies

Option A: Using uv (Recommended - 10-100x faster!)

# Navigate to server directory
cd server

# Install uv if you haven't already
# macOS/Linux:
curl -LsSf https://astral.sh/uv/install.sh | sh
# Windows:
# powershell -c "irm https://astral.sh/uv/install.ps1 | iex"

# Create and activate virtual environment
uv venv
source .venv/bin/activate  # Windows: .venv\Scripts\activate

# Install required packages (much faster than pip!)
uv pip install -r requirements.txt

Option B: Using pip (Traditional)

# Navigate to server directory
cd server

# Create and activate virtual environment
python3.11 -m venv venv
source venv/bin/activate  # Windows: venv\Scripts\activate

# Install required packages
pip install -r requirements.txt

3. Configure Environment

# Return to project root
cd ..

# Copy example environment file
cp .env.example .env

# Edit .env with your preferred text editor (optional)
nano .env  # or vim, code, etc.

Environment Configuration (Optional):

# Optional: For Brave Search (better than DuckDuckGo)
BRAVE_API_KEY=your_brave_api_key_here

# Optional: For future Anthropic integrations
ANTHROPIC_API_KEY=your_anthropic_api_key_here

# Optional: Customize paths
RESEARCH_RUNS_DIR=./research_runs
KNOWLEDGE_BASE_DIR=./knowledge_base

# RAG uses local embeddings by default (no API key needed!)
USE_LOCAL_EMBEDDINGS=true
EMBEDDING_MODEL=all-MiniLM-L6-v2

⚠️ Important: Never commit your .env file to version control. It's already included in .gitignore.

Note: The system uses local sentence-transformers embeddings by default, so no API keys are required for RAG features!

4. Create Required Directories

# Create directories for data storage
mkdir -p research_runs knowledge_base data/vector_db logs

5. Configure Claude Desktop

macOS: Edit ~/Library/Application Support/Claude/claude_desktop_config.json

Windows: Edit %APPDATA%\Claude\claude_desktop_config.json

Linux: Edit ~/.config/Claude/claude_desktop_config.json

Find your absolute paths first:

# In your project directory, run:
pwd
# Example output: /Users/yourname/Projects/ai-research-agent-mcp

# Find your Python path (if using venv):
which python  # or: which python3.11
# Example output: /Users/yourname/Projects/ai-research-agent-mcp/server/venv/bin/python3.11

Configuration Template:

Add the following configuration, replacing the paths and environment variables with your actual values:

{
  "mcpServers": {
    "research-engineer": {
      "command": "/absolute/path/to/python",
      "args": [
        "/absolute/path/to/ai-research-agent-mcp/server/src/server.py"
      ],
      "env": {
        "BRAVE_API_KEY": "your_brave_api_key_here_or_remove_this_line",
        "ANTHROPIC_API_KEY": "your_anthropic_api_key_here_or_remove_this_line",
        "SEARCH_PROVIDER": "duckduckgo",
        "MAX_SEARCH_RESULTS": "10",
        "EMBEDDING_MODEL": "all-MiniLM-L6-v2",
        "USE_LOCAL_EMBEDDINGS": "true",
        "VECTOR_DB_PATH": "/absolute/path/to/ai-research-agent-mcp/data/vector_db",
        "CHUNK_SIZE": "1000",
        "CHUNK_OVERLAP": "200",
        "SANDBOX_TIMEOUT": "30",
        "SANDBOX_MAX_MEMORY_MB": "512",
        "ALLOWED_PACKAGES": "numpy,pandas,matplotlib,seaborn,scipy,scikit-learn",
        "RESEARCH_RUNS_DIR": "/absolute/path/to/ai-research-agent-mcp/research_runs",
        "KNOWLEDGE_BASE_DIR": "/absolute/path/to/ai-research-agent-mcp/knowledge_base",
        "LOG_LEVEL": "INFO",
        "LOG_FILE": "/absolute/path/to/ai-research-agent-mcp/logs/research_engineer.log"
      }
    }
  }
}

⚠️ Important Notes:

• Use absolute paths for all file paths (no ~ or relative paths)
• If using a virtual environment, use the Python path from inside the venv
• Remove or leave empty any API keys you don't have (DuckDuckGo works without keys)
• All paths in env must be absolute paths

Example for macOS/Linux (with venv):

{
  "mcpServers": {
    "research-engineer": {
      "command": "/Users/yourname/Projects/ai-research-agent-mcp/server/venv/bin/python3.11",
      "args": [
        "/Users/yourname/Projects/ai-research-agent-mcp/server/src/server.py"
      ],
      "env": {
        "SEARCH_PROVIDER": "duckduckgo",
        "MAX_SEARCH_RESULTS": "10",
        "USE_LOCAL_EMBEDDINGS": "true",
        "EMBEDDING_MODEL": "all-MiniLM-L6-v2",
        "VECTOR_DB_PATH": "/Users/yourname/Projects/ai-research-agent-mcp/data/vector_db",
        "RESEARCH_RUNS_DIR": "/Users/yourname/Projects/ai-research-agent-mcp/research_runs",
        "KNOWLEDGE_BASE_DIR": "/Users/yourname/Projects/ai-research-agent-mcp/knowledge_base",
        "LOG_FILE": "/Users/yourname/Projects/ai-research-agent-mcp/logs/research_engineer.log"
      }
    }
  }
}

Example for macOS/Linux (with uv):

{
  "mcpServers": {
    "research-engineer": {
      "command": "uv",
      "args": [
        "run",
        "--directory",
        "/Users/yourname/Projects/ai-research-agent-mcp/server",
        "python",
        "src/server.py"
      ],
      "env": {
        "SEARCH_PROVIDER": "duckduckgo",
        "MAX_SEARCH_RESULTS": "10",
        "USE_LOCAL_EMBEDDINGS": "true",
        "EMBEDDING_MODEL": "all-MiniLM-L6-v2",
        "VECTOR_DB_PATH": "/Users/yourname/Projects/ai-research-agent-mcp/data/vector_db",
        "RESEARCH_RUNS_DIR": "/Users/yourname/Projects/ai-research-agent-mcp/research_runs",
        "KNOWLEDGE_BASE_DIR": "/Users/yourname/Projects/ai-research-agent-mcp/knowledge_base",
        "LOG_FILE": "/Users/yourname/Projects/ai-research-agent-mcp/logs/research_engineer.log"
      }
    }
  }
}

Example for Windows:

{
  "mcpServers": {
    "research-engineer": {
      "command": "C:/Users/yourname/Projects/ai-research-agent-mcp/server/venv/Scripts/python.exe",
      "args": [
        "C:/Users/yourname/Projects/ai-research-agent-mcp/server/src/server.py"
      ],
      "env": {
        "SEARCH_PROVIDER": "duckduckgo",
        "MAX_SEARCH_RESULTS": "10",
        "USE_LOCAL_EMBEDDINGS": "true",
        "EMBEDDING_MODEL": "all-MiniLM-L6-v2",
        "VECTOR_DB_PATH": "C:/Users/yourname/Projects/ai-research-agent-mcp/data/vector_db",
        "RESEARCH_RUNS_DIR": "C:/Users/yourname/Projects/ai-research-agent-mcp/research_runs",
        "KNOWLEDGE_BASE_DIR": "C:/Users/yourname/Projects/ai-research-agent-mcp/knowledge_base",
        "LOG_FILE": "C:/Users/yourname/Projects/ai-research-agent-mcp/logs/research_engineer.log"
      }
    }
  }
}

6. Restart Claude Desktop

Completely quit and restart Claude Desktop for changes to take effect.

Verify Installation

In Claude Desktop, type:

List available tools

You should see: web_search, web_research, execute_code, create_research_run, etc.

Your First Research Task

Try this simple task:

Research the current state of electric vehicles in 2026. 
Include market size, major players, and growth trends. 
Create a simple visualization showing EV adoption over time.

The agent will:

1. Search the web for EV data
2. Write Python code to create a chart
3. Present findings with sources

---

Architecture

System Overview

┌─────────────────────────────────────────────────────────────┐
│                    Claude Desktop / Cursor                   │
│                     (MCP Client/Host)                        │
└────────────────────────┬────────────────────────────────────┘
                         │ MCP Protocol (stdio)
                         │
┌────────────────────────▼────────────────────────────────────┐
│                    MCP Server (Python)                       │
│  ┌──────────────────────────────────────────────────────┐  │
│  │              Tool Registry & Router                   │  │
│  └──────────────────────────────────────────────────────┘  │
│                                                              │
│  ┌──────────────┐  ┌──────────────┐  ┌──────────────┐     │
│  │ Web Research │  │   RAG Tool   │  │Code Sandbox  │     │
│  │              │  │              │  │              │     │
│  │ • Search     │  │ • Embeddings │  │ • Restricted │     │
│  │ • Scrape     │  │ • ChromaDB   │  │   Python     │     │
│  │ • Extract    │  │ • Query      │  │ • Safe Exec  │     │
│  └──────────────┘  └──────────────┘  └──────────────┘     │
│                                                              │
│  ┌──────────────┐  ┌──────────────┐                        │
│  │  Workspace   │  │  Evaluator   │                        │
│  │              │  │              │                        │
│  │ • File I/O   │  │ • Metrics    │                        │
│  │ • Organize   │  │ • Critique   │                        │
│  │ • Manage     │  │ • Quality    │                        │
│  └──────────────┘  └──────────────┘                        │
└─────────────────────────────────────────────────────────────┘
                         │
                         ▼
        ┌────────────────────────────────────┐
        │      External Services              │
        │                                     │
        │  • DuckDuckGo / Brave Search       │
        │  • OpenAI Embeddings API           │
        │  • Web Scraping (HTTP)             │
        └────────────────────────────────────┘
                         │
                         ▼
        ┌────────────────────────────────────┐
        │      Local Storage                  │
        │                                     │
        │  • research_runs/                  │
        │  • knowledge_base/                 │
        │  • data/vector_db/                 │
        │  • logs/                           │
        └────────────────────────────────────┘

Core Components

1. MCP Server (server/src/server.py)

Responsibilities:

• Expose tools via MCP protocol
• Route tool calls to appropriate handlers
• Handle errors and logging
• Manage server lifecycle

Technology:

• Python 3.10+
• MCP SDK (mcp package)
• Async/await for I/O operations

2. Web Research Tool (server/src/tools/web_research.py)

Responsibilities:

• Search the web for information
• Scrape and extract clean content
• Handle rate limiting and retries

Components:

• Search Providers: DuckDuckGo (default, no API key), Brave Search (optional)
• Content Extraction: Trafilatura for main content, BeautifulSoup for metadata

3. RAG Tool (server/src/tools/rag_tool.py)

Responsibilities:

• Index documents into vector database
• Semantic search over knowledge base
• Support multiple file formats (Markdown, PDF, DOCX)

Components:

• Vector Database: ChromaDB (persistent, local)
• Embeddings: OpenAI text-embedding-3-small
• Chunking strategy: 1000 chars with 200 char overlap

4. Code Sandbox (server/src/tools/code_sandbox.py)

Responsibilities:

• Execute Python code safely
• Capture output and plots
• Enforce resource limits

Security Layers:

1. RestrictedPython: AST-level code restrictions
2. Resource Limits: Memory and CPU constraints
3. Timeout: Execution time limits
4. Allowed Packages: Whitelist of safe libraries (numpy, pandas, matplotlib, etc.)

5. Workspace Tool (server/src/tools/workspace.py)

Responsibilities:

• Organize research outputs
• Manage file I/O
• Track research runs

Directory Structure:

research_runs/
└── YYYY-MM-DD_HHMMSS_task-name/
    ├── metadata.json
    ├── report.md
    ├── evaluation.json
    ├── sources.json
    ├── code/
    │   └── *.py
    ├── charts/
    │   └── *.png
    └── data/
        └── *.json

6. Evaluator Tool (server/src/tools/evaluator.py)

Responsibilities:

• Quality assessment
• Self-critique generation
• Metrics tracking

Quality Metrics (0-10 scale):

• Clarity, Data Grounding, Completeness, Code Quality, Actionability, Confidence

---

Configuration

Environment Variables

See .env.example for all available configuration options:

# Search Configuration
BRAVE_API_KEY=...           # Optional: Better search than DuckDuckGo
SEARCH_PROVIDER=duckduckgo  # duckduckgo or brave
MAX_SEARCH_RESULTS=10

# RAG Configuration (uses local embeddings by default)
USE_LOCAL_EMBEDDINGS=true
EMBEDDING_MODEL=all-MiniLM-L6-v2
VECTOR_DB_PATH=./data/vector_db
CHUNK_SIZE=1000
CHUNK_OVERLAP=200

# Code Sandbox Configuration
SANDBOX_TIMEOUT=30
SANDBOX_MAX_MEMORY_MB=512

# Directory Configuration
RESEARCH_RUNS_DIR=./research_runs
KNOWLEDGE_BASE_DIR=./knowledge_base

# Logging
LOG_LEVEL=INFO

Cursor IDE Configuration (Alternative)

1. Open Cursor Settings

Press Cmd+, (Mac) or Ctrl+, (Windows/Linux)

2. Search for "MCP"

Find the MCP Servers configuration section.

3. Add Server Configuration

Add the same configuration as Claude Desktop (see section 5 above for detailed examples).

Basic Example:

{
  "research-engineer": {
    "command": "/absolute/path/to/python",
    "args": [
      "/absolute/path/to/ai-research-agent-mcp/server/src/server.py"
    ],
    "env": {
      "SEARCH_PROVIDER": "duckduckgo",
      "USE_LOCAL_EMBEDDINGS": "true",
      "VECTOR_DB_PATH": "/absolute/path/to/data/vector_db",
      "RESEARCH_RUNS_DIR": "/absolute/path/to/research_runs",
      "KNOWLEDGE_BASE_DIR": "/absolute/path/to/knowledge_base"
    }
  }
}

Using uv:

{
  "research-engineer": {
    "command": "uv",
    "args": [
      "run",
      "--directory",
      "/absolute/path/to/ai-research-agent-mcp/server",
      "python",
      "src/server.py"
    ],
    "env": {
      "SEARCH_PROVIDER": "duckduckgo",
      "USE_LOCAL_EMBEDDINGS": "true"
    }
  }
}

---

Usage

Basic Research Task

Simple Query

Research the pros and cons of electric scooters vs bikes for urban commuting.

The agent will:

1. Search the web for relevant information
2. Organize findings
3. Present a summary

Comprehensive Research with Code

Deep dive: Compare electric scooters vs bikes for my 5-mile daily commute. 
Build a cost calculator in Python that shows total cost of ownership over 3 years.
Include purchase price, maintenance, electricity/none, and create visualizations.

The agent will:

1. Research costs, maintenance, and usage data
2. Build a Python cost calculator
3. Create comparison charts
4. Write a comprehensive report
5. Save everything to a research run directory
6. Self-evaluate the work

Tool Usage Examples

Web Research

Search only:

Use web_search to find the latest news about AI regulation in 2026

Comprehensive research with scraping:

Use web_research to gather detailed information about multifamily real estate cap rates, 
and scrape the top 5 results for full content

Scrape specific URL:

Scrape this article and summarize the key points: https://example.com/article

Knowledge Base (RAG)

Index your notes:

Index all files in my knowledge_base directory so I can query them later

Query knowledge base:

Query my knowledge base for information about real estate investment strategies

Combine web + knowledge base:

Research current EV market trends using both web search and my personal notes 
in the knowledge base

Code Execution

Simple calculation:

Write Python code to calculate the compound annual growth rate (CAGR) 
for an investment that grew from $10,000 to $25,000 over 5 years

Data analysis:

Create a Python script that:
1. Generates sample sales data for 12 months
2. Calculates moving averages
3. Creates a line chart with trend line
4. Prints summary statistics

Financial modeling:

Build a mortgage calculator in Python that:
- Takes loan amount, interest rate, and term
- Calculates monthly payment
- Shows amortization schedule
- Creates a chart showing principal vs interest over time

Best Practices

1. Be Specific

❌ Vague:

Research AI

✅ Specific:

Research the current state of large language models in 2026, focusing on:
- Model sizes and capabilities
- Training costs
- Commercial applications
- Regulatory challenges

2. Request Structure

❌ Unstructured:

Tell me about real estate

✅ Structured:

Research multifamily real estate investment in 2026:
1. Current market conditions
2. Financial modeling
3. Risk analysis
4. Recommendations

3. Combine Tools

✅ Effective:

Research electric vehicle adoption rates using:
1. Web search for latest statistics
2. My knowledge base for past analysis
3. Python code to project future adoption
4. Visualizations of trends

4. Request Evaluation

✅ Quality-focused:

After completing the analysis, evaluate your work and tell me:
- What data sources were most valuable?
- What are the limitations of this analysis?
- What would make this analysis more robust?

---

Project Structure

Complete file and directory structure:

ai-research-agent-mcp/
│
├── README.md                          # This file - complete documentation
├── LICENSE                            # MIT License
├── .gitignore                         # Git ignore rules
├── .env.example                       # Example environment variables
│
├── server/                            # MCP Server implementation
│   ├── requirements.txt               # Python dependencies
│   ├── pyproject.toml                 # Project metadata and build config
│   │
│   └── src/                           # Source code
│       ├── __init__.py                # Package initialization
│       ├── server.py                  # Main MCP server entry point
│       ├── config.py                  # Configuration management
│       │
│       └── tools/                     # Tool implementations
│           ├── __init__.py            # Tools package initialization
│           ├── web_research.py        # Web search and scraping
│           ├── rag_tool.py            # Vector RAG for knowledge base
│           ├── code_sandbox.py        # Safe Python code execution
│           ├── workspace.py           # File and workspace management
│           └── evaluator.py           # Quality evaluation and critique
│
├── agent/                             # Agent orchestration
│   └── prompts/                       # System prompts and templates
│       └── research_agent.md          # Main research agent prompt
│
├── config/                            # Configuration files
│   └── claude_desktop_config.json     # Example Claude Desktop config
│
├── examples/                          # Example tasks and outputs
│   └── example_research_task.md       # Detailed example with expected output
│
├── knowledge_base/                    # Personal knowledge base (user content)
│   └── example_notes.md               # Example notes for RAG
│
├── research_runs/                     # Research output directory (created at runtime)
│   └── YYYY-MM-DD_HHMMSS_task-name/   # Individual research run
│       ├── metadata.json              # Run metadata
│       ├── report.md                  # Final report
│       ├── evaluation.json            # Self-evaluation
│       ├── sources.json               # Data sources
│       ├── code/                      # Generated code
│       │   └── *.py
│       ├── charts/                    # Visualizations
│       │   └── *.png
│       └── data/                      # Data files
│           └── *.json
│
├── data/                              # Data storage (created at runtime)
│   └── vector_db/                     # ChromaDB vector database
│
└── logs/                              # Log files (created at runtime)
    └── research_engineer.log          # Application logs

Key Files Explained

| File | Purpose | |------|---------| | server/src/server.py | Main MCP server with tool registry | | server/src/config.py | Configuration loading and validation | | server/src/tools/web_research.py | Web search and scraping | | server/src/tools/rag_tool.py | Vector database and semantic search | | server/src/tools/code_sandbox.py | Safe Python code execution | | server/src/tools/workspace.py | File I/O and research run management | | server/src/tools/evaluator.py | Quality metrics and self-critique |

---

Troubleshooting

Common Issues and Solutions

ImportError: attempted relative import with no known parent package

Problem:

ImportError: attempted relative import with no known parent package

Solution: The server has been updated to handle both direct execution and module execution. Run:

cd server
python3.11 src/server.py

Filelock Version Incompatibility

Problem:

TypeError: BaseFileLock.__init__() got an unexpected keyword argument 'mode'

Solution:

pip3 install --upgrade filelock

Server Not Starting in Claude Desktop

Problem: Claude Desktop shows "Server not found" or the server doesn't appear in the tools list.

Checklist:

1. ✅ Verify the path in claude_desktop_config.json is absolute
2. ✅ Check that Python 3.11 is installed: which python3.11
3. ✅ Ensure all dependencies are installed: pip3 install -r requirements.txt
4. ✅ Restart Claude Desktop completely (quit and reopen)
5. ✅ Check logs for errors

Sentence Transformers Model Download

Problem: First run takes a long time or shows download progress.

Solution: This is normal behavior. The sentence-transformers model (~90MB) is being downloaded on first use. The model is cached locally and subsequent runs will be much faster.

Module Not Found Errors

Problem:

ModuleNotFoundError: No module named 'mcp'

Solution:

cd server
pip3 install -r requirements.txt

# Or if using a virtual environment:
python3.11 -m venv venv
source venv/bin/activate  # Windows: venv\Scripts\activate
pip install -r requirements.txt

Debugging Tips

Check Server Logs

tail -f logs/research_engineer.log

Test Server Import

cd server
python3.11 -c "from src.server import app; print('✓ Server imports successfully')"

Verify Python Version

python3.11 --version
# Should be 3.11 or higher

Check Environment Variables

cat .env

---

Example Output

Each research task creates a structured output:

research_runs/
└── 2026-02-06_multifamily-real-estate/
    ├── report.md              # Final comprehensive report
    ├── model.py               # Cash-flow model code
    ├── analysis.ipynb         # Jupyter notebook
    ├── charts/                # Generated visualizations
    │   ├── sensitivity.png
    │   └── cashflow.png
    ├── sources.json           # Data sources and citations
    └── evaluation.json        # Quality metrics and self-critique

---

Development

# Run tests
pytest tests/

# Format code
black server/ agent/

# Type checking
mypy server/ agent/

---

Uninstallation

To completely remove the MCP Research Engineer from your system:

1. Remove from Claude Desktop

Edit your Claude Desktop configuration file:

macOS: ~/Library/Application Support/Claude/claude_desktop_config.json Windows: %APPDATA%\Claude\claude_desktop_config.json Linux: ~/.config/Claude/claude_desktop_config.json

Remove the research-engineer entry from mcpServers:

{
  "mcpServers": {
    // Remove this entire block:
    // "research-engineer": { ... }
  }
}

Restart Claude Desktop.

2. Deactivate Virtual Environment

If you have an active virtual environment:

deactivate

3. Remove Project Directory

# Navigate to parent directory
cd ..

# Remove the entire project
rm -rf ai-research-agent-mcp

⚠️ Warning: This will permanently delete all your research runs, knowledge base, and configuration. Make sure to backup any important data first!

4. Optional: Backup Important Data

Before uninstalling, you may want to backup:

# Backup your research outputs
cp -r ai-research-agent-mcp/research_runs ~/backup/research_runs

# Backup your knowledge base
cp -r ai-research-agent-mcp/knowledge_base ~/backup/knowledge_base

# Backup your configuration
cp ai-research-agent-mcp/.env ~/backup/.env

5. Clean Up Python Packages (Optional)

If you want to remove the Python packages that were installed:

# If you used a virtual environment, just delete it
rm -rf ai-research-agent-mcp/server/venv

# If you installed globally (not recommended), uninstall packages:
pip uninstall -y mcp chromadb sentence-transformers duckduckgo-search trafilatura httpx beautifulsoup4 lxml pypdf python-docx RestrictedPython

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Contributing

Contributions are welcome! Here's how you can help:

Reporting Issues

If you find a bug or have a feature request:

1. Check if the issue already exists in GitHub Issues
2. If not, create a new issue with:
   • Clear description of the problem or feature
   • Steps to reproduce (for bugs)
   • Expected vs actual behavior
   • Your environment (OS, Python version, etc.)

Pull Requests

1. Fork the repository
2. Create a feature branch: git checkout -b feature/your-feature-name
3. Make your changes
4. Test thoroughly
5. Commit with clear messages: git commit -m "Add feature: description"
6. Push to your fork: git push origin feature/your-feature-name
7. Open a Pull Request with a clear description

Development Setup

# Clone your fork
git clone https://github.com/prabureddy/ai-research-agent-mcp.git
cd ai-research-agent-mcp

# Create virtual environment
cd server
python3.11 -m venv venv
source venv/bin/activate

# Install dependencies including dev tools
pip install -r requirements.txt
pip install pytest black mypy

# Run tests
pytest tests/

# Format code
black server/ agent/

# Type checking
mypy server/ agent/

Code Style

• Follow PEP 8 guidelines
• Use type hints where appropriate
• Add docstrings to functions and classes
• Write tests for new features
• Keep commits atomic and well-described

Areas for Contribution

• 🐛 Bug fixes
• ✨ New tool implementations
• 📚 Documentation improvements
• 🧪 Test coverage
• 🎨 UI/UX improvements
• 🌐 Additional search providers
• 📊 New visualization types
• 🔒 Security enhancements

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What's Next?

Try progressively more complex tasks:

Level 1: Simple Research

Research the benefits of meditation

Level 2: Research + Code

Research average home prices in major US cities and create a bar chart

Level 3: Comprehensive Analysis

Analyze whether solar panels are worth it for a home in California.
Include cost analysis, payback period calculation, and recommendations.

Level 4: Full Research Project

Deep dive: Should I invest in multifamily real estate in 2026?
- Research market conditions
- Build cash-flow model
- Run sensitivity analysis
- Create visualizations
- Write comprehensive report
- Self-evaluate the analysis

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Getting Help

If you encounter issues:

1. Check the logs: tail -f logs/research_engineer.log
2. Verify environment variables: cat .env
3. Test Python imports:

   python -c "import mcp; print('MCP OK')"
   python -c "import chromadb; print('ChromaDB OK')"
   

4. Check Claude Desktop logs (Help → View Logs)
5. Review the Troubleshooting section above
6. Open an issue on GitHub if you need further assistance

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Support

• 📖 Documentation
• 🐛 Issue Tracker
• 💬 Discussions

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Acknowledgments

• Built with Model Context Protocol (MCP)
• Powered by Claude by Anthropic
• Uses ChromaDB for vector storage
• Web scraping with Trafilatura

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License

MIT

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Enjoy your AI Research Engineer! 🚀