Qwen Code

Building AI Scientists with Qwen Code and ToolUniverse

Qwen Code integrates with ToolUniverse via MCP

Overview

Qwen Code is a coding agent CLI that can query and edit large codebases and automate workflows. Integrated with the Model Context Protocol (MCP), it can connect to ToolUniverse to power evidence-based scientific research from your terminal.

┌──────────────┐
│  Qwen Code   │ ← Command Line Interface & Reasoning
│              │
└──────┬───────┘
       │ MCP Protocol
       │
┌──────▼───────┐
│ ToolUniverse │ ← MCP Server
│   MCP Server │
└──────┬───────┘
       │
┌──────▼───────┐
│ 600+ Scientific Tools │
└───────────────────────┘

Benefits of Qwen Code Integration:

  • Command-Line Efficiency: Scriptable, terminal-first scientific workflows

  • Advanced Reasoning: Qwen Coder models optimized for code and tooling

  • Comprehensive Tools: Access 600+ scientific tools via ToolUniverse

  • Automated Execution: Natural language to tool execution

  • Batch Processing: Efficient multi-task research

Prerequisites

Before setting up Qwen Code integration, ensure you have:

  • Qwen Code: Installed and runnable (qwen –version)

  • ToolUniverse: Installed

  • UV Package Manager: For running the MCP server

  • System Requirements: macOS, Windows, or Linux with Python 3.10+

  • API Keys: For tools and optional summarization hooks

Installation and Setup

Command Legend

  • System terminal (your shell: zsh/bash): run installation and file editing commands

  • Qwen Code prompt (inside qwen): run slash commands like /mcp, /stats, /memory show

Step 1: Install Qwen Code

You can install Qwen Code via npm or Homebrew.

# From npm (requires Node.js >= 20)
npm install -g @qwen-code/qwen-code@latest
qwen --version

# Or install from source
git clone https://github.com/QwenLM/qwen-code.git
cd qwen-code
npm install
npm install -g .

# Or install with Homebrew (macOS/Linux)
brew install qwen-code

For details, see the official repository Qwen Code on GitHub.

Step 2: Install ToolUniverse

pip install tooluniverse

Verify installation:

python -c "import tooluniverse; print('ToolUniverse installed successfully')"

Step 3: Locate Qwen Code Configuration

Qwen Code reads settings from a home directory config at ~/.qwen/settings.json or from a project-local .qwen/settings.json.

Create or open your settings file:

# Global configuration
mkdir -p ~/.qwen
vim ~/.qwen/settings.json

# Or project-specific configuration
mkdir -p .qwen
vim .qwen/settings.json

Note: These commands are run in your system terminal.

Step 4: Configure ToolUniverse MCP Server

Add the ToolUniverse MCP server configuration to your Qwen settings settings.json.

Note: Edit the JSON in your system terminal/editor.

Basic Configuration:

{
  "mcpServers": {
    "tooluniverse": {
      "command": "uv",
      "args": [
        "--directory",
        "/path/to/your/qwen_running_env",
        "run",
        "tooluniverse-smcp-stdio"
      ]
    }
  }
}

Optimized Configuration for Research Users (Recommended):

{
  "mcpServers": {
    "tooluniverse": {
      "command": "uv",
      "args": [
        "--directory",
        "/path/to/your/qwen_running_env",
        "run",
        "tooluniverse-smcp-stdio",
        "--exclude-tool-types",
        "PackageTool",
        "--hook-type",
        "SummarizationHook"
      ],
      "env": {
        "AZURE_OPENAI_API_KEY": "your-azure-openai-api-key",
        "AZURE_OPENAI_ENDPOINT": "https://your-resource.openai.azure.com"
      }
    }
  }
}

Configuration Benefits:

  • --exclude-tool-types PackageTool: Saves context if you don’t need coding package tools

  • --hook-type SummarizationHook: Summarizes long outputs to fit context

  • AZURE_OPENAI_*: Required for SummarizationHook

Important Notes:

  • Replace /path/to/your/qwen_running_env with the absolute path to your Qwen working folder

  • Prefer absolute paths for reliability

Step 5: Configure Context File (QWEN.md)

You can provide project-specific research instructions to Qwen Code using a context file.

  1. Create QWEN.md in your project root:

    vim QWEN.md

  2. Add ToolUniverse-specific context:

    # ToolUniverse Scientific Research Project

## General Instructions

- Use ToolUniverse's scientific tools ecosystem for evidence-based research
- Prefer tools from the `tooluniverse` MCP server first
- Cross-validate findings across multiple sources
- Use appropriate scientific terminology

Step 6: Start Qwen Code and Verify MCP

  1. Start Qwen Code:

    qwen

    Note: Run this in your system terminal.

  2. Verify MCP Server Connection:

    In the Qwen Code prompt, run:

    /mcp

  3. Verify context loading:

    Enter In the Qwen Code prompt, run:

    /memory show

For authentication methods (OAuth and API keys), see: Authorization (Qwen Code README).

This will display connection status, available ToolUniverse tools, configuration details, and any errors.

Step 7: Verify Integration

Try these prompts inside Qwen Code:

List available tools:

What scientific tools are available?

Execute a simple tool:

Search for information about Alzheimer's disease

Perform literature search:

Find recent papers about CRISPR gene editing in cancer therapy

Scientific Research Capabilities

Drug Discovery and Development

With ToolUniverse, Qwen Code supports comprehensive drug discovery workflows:

Target Identification: - Disease analysis and EFO ID lookup - Target discovery and validation - Literature-based assessment

Drug Analysis: - Drug information retrieval - Safety profile analysis - Drug interaction checking - Clinical trial data access

Genomics and Molecular Biology

Access genomics tools for molecular research:

Gene Analysis: - Gene information from UniProt - Protein structure analysis - Expression patterns and pathways

Molecular Interactions: - Protein-protein and drug-target interactions - Pathway analysis and functional annotation

Literature Research and Analysis

Perform literature search and analysis:

Literature Search: - PubMed, Europe PMC, Semantic Scholar - Citation analysis and filtering

Content Analysis: - Abstract summarization and key finding extraction - Trend analysis and gap identification

Settings and Configuration

Tool Selection Strategies

Optimize tool usage:

Selective Tool Loading:

{
  "mcpServers": {
    "tooluniverse": {
      "command": "uv",
      "args": [
        "--directory",
        "/path/to/your/qwen_running_env",
        "run",
        "tooluniverse-smcp-stdio"
      ],
      "includeTools": [
        "EuropePMC_search_articles",
        "ChEMBL_search_similar_molecules",
        "openalex_literature_search",
        "search_clinical_trials"
      ]
    }
  }
}

Multiple MCP Servers

Run multiple ToolUniverse instances for different purposes:

{
  "mcpServers": {
    "tooluniverse-research": {
      "command": "uv",
      "args": [
        "--directory",
        "/path/to/your/qwen_running_env",
        "run",
        "tooluniverse-smcp-stdio"
      ],
      "timeout": 30000
    },
    "tooluniverse-analysis": {
      "command": "uv",
      "args": [
        "--directory",
        "/path/to/your/qwen_running_env",
        "run",
        "tooluniverse-smcp-stdio"
      ],
      "timeout": 45000
    }
  }
}

Troubleshooting

Common Issues and Solutions

MCP Server Not Loading: - Verify ToolUniverse installation path - Check UV package manager installation - Ensure proper JSON syntax in configuration - Use /stats to confirm session info and limits

No Tools Discovered: - Verify the ToolUniverse MCP server is working - Check if your includeTools or excludeTools filter is too restrictive - Ensure all ToolUniverse dependencies are installed

Tools Not Executing: - Check your env configuration for needed API keys - Verify network connectivity - Increase the timeout value

Debug and Session Management

Qwen Code provides built-in session commands:

  • /compress: Compress conversation history to stay within token limits

  • /clear: Clear history and start fresh

  • /stats: Show current session token usage and limits

Authentication Options

Qwen Code supports multiple authentication methods.

1. Qwen OAuth (Recommended)

Start Qwen Code and follow the browser-based login.

qwen

Benefits include generous free-tier quotas and automatic credential management. See Qwen Code on GitHub.

2. OpenAI-Compatible API

Configure environment variables or a project .env file:

export OPENAI_API_KEY="your_api_key_here"
export OPENAI_BASE_URL="your_api_endpoint"
export OPENAI_MODEL="your_model_choice"

For regional guidance and provider options (Bailian, ModelScope, ModelStudio, OpenRouter), refer to the repository docs: Qwen Code on GitHub.

Tips

Tool Selection: Use includeTools to load only necessary tools.

Status Check: Use /mcp to confirm server status and available tools.

Session Control: Use /compress and /stats to manage token usage.

References