Claude Code¶

Building AI Scientists with Claude Code and ToolUniverse

Overview¶

Claude Code integration enables powerful IDE- or terminal-based scientific research through the Model Context Protocol (MCP). This approach provides a developer-friendly interface for research while leveraging Claude’s advanced reasoning and ToolUniverse’s 1000+ scientific tools.

┌─────────────────┐
│   Claude Code   │ ← IDE/CLI Interface & Reasoning
│                 │
└─────────┬───────┘
          │ MCP Protocol
          │
┌─────────▼───────┐
│ ToolUniverse     │ ← MCP Server
│   MCP Server     │
└─────────┬───────┘
          │
┌─────────▼───────┐
│ 1000+ Scientific │ ← Scientific Tools Ecosystem
│     Tools       │
└─────────────────┘

Benefits of Claude Code Integration:

Developer Workflow: Use Claude inside VS Code/JetBrains or terminal
Advanced Reasoning: Claude’s strong multi-step reasoning
Comprehensive Tools: Access to 1000+ ToolUniverse tools
Automated Execution: Natural-language to tools, directly in your editor
Batch & Iteration: Run multi-step research loops effectively

Prerequisites¶

Before setting up Claude Code integration, ensure you have:

Claude Code: Installed in your IDE or CLI
Python 3.10+: macOS, Windows, or Linux
API Keys (optional): For specific tools or hooks (e.g., Azure OpenAI for summarization)

Installation and Setup¶

Step 0: Install Claude Code¶

Install Claude Code in your terminal (any OS with Node.js 18+):

# Standard (recommended)
npm install -g @anthropic-ai/claude-code

Verify and diagnose your installation:

claude doctor

Native installer (beta) alternatives:

# macOS/Linux/WSL: stable
curl -fsSL https://claude.ai/install.sh | bash
# latest
curl -fsSL https://claude.ai/install.sh | bash -s latest

On Windows PowerShell:

irm https://claude.ai/install.ps1 | iex

After installation, you can start Claude Code in a project:

cd your-project
claude

For details, see: Anthropic — Set up Claude Code.

For Windows installation, see: Anthropic — Windows setup.

Step 1: Install ToolUniverse¶

# Using pip
pip install tooluniverse

# Or using uv (faster)
uv pip install tooluniverse

Step 2: Add ToolUniverse to Claude Code¶

claude mcp add --transport stdio tooluniverse -- tooluniverse-smcp-stdio --compact-mode

# Verify it was added successfully
claude mcp list

You should see tooluniverse in the list of MCP servers. The --compact-mode flag optimizes tool descriptions for better context efficiency.

Step 3: Verify in IDE/CLI¶

After saving the configuration, verify connectivity:

Terminal (Claude Code CLI) - Launch in your project:
cd /path/to/your-project claude
- In the chat, ask: “What ToolUniverse tools are available?”
- If issues occur, run diagnostics:
```
claude doctor
```
- For terminal configuration, see: Claude Code CLI reference
VS Code - Restart VS Code, then open Command Palette and run: “Claude: Open Chat” - Ask: “What ToolUniverse tools are available?” - If tools don’t appear, check .claude/settings.local.json and reload window - For VS Code setup, see: Add Claude Code to your IDE
JetBrains (IntelliJ/PyCharm/etc.) - Restart IDE → open the Claude tool window - Ask: “What ToolUniverse tools are available?” - If tools don’t appear, review Tools → Claude Code → MCP Servers settings - For JetBrains setup, see: Add Claude Code to your IDE

Scientific Research Capabilities¶

Drug Discovery and Development¶

Claude Code with ToolUniverse enables comprehensive drug discovery workflows:

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

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

Genomics and Molecular Biology¶

Access comprehensive genomics tools for molecular research:

Gene Analysis: - Gene information from UniProt - Protein structure analysis - Expression pattern analysis - Pathway involvement

Molecular Interactions: - Protein-protein interactions - Drug-target interactions - Pathway analysis - Functional annotation

Literature Research and Analysis¶

Comprehensive literature search and analysis capabilities:

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

Content Analysis: - Abstract summarization - Key finding extraction - Gap identification

Multi-Step Research Workflows¶

Claude Code excels at complex, multi-step research workflows:

Hypothesis-Driven Research: 1. Formulate a hypothesis 2. Design an approach and select tools 3. Gather supporting evidence 4. Validate findings 5. Generate conclusions

Advanced Configuration¶

Tool Selection¶

Load only specific tools for focused research domains:

# Add ToolUniverse with specific tools only
claude mcp add --transport stdio tooluniverse -- tooluniverse-smcp-stdio --compact-mode --include-tools EuropePMC_search_articles,ChEMBL_search_similar_molecules,openalex_literature_search

Summarization Hook¶

Enable automatic summarization for long outputs (requires Azure OpenAI):

claude mcp add --transport stdio tooluniverse --env AZURE_OPENAI_API_KEY=your-key --env AZURE_OPENAI_ENDPOINT=https://your-resource.openai.azure.com -- tooluniverse-smcp-stdio --compact-mode --hook-type SummarizationHook

Multiple Instances¶

Run separate instances for different purposes:

# Literature research instance
claude mcp add --transport stdio tooluniverse-literature -- tooluniverse-smcp-stdio --compact-mode --include-tools EuropePMC_search_articles,openalex_literature_search

# Drug analysis instance
claude mcp add --transport stdio tooluniverse-drugs -- tooluniverse-smcp-stdio --compact-mode --include-tools ChEMBL_search_similar_molecules,search_clinical_trials

# List all servers
claude mcp list

# Remove a server
claude mcp remove tooluniverse-literature

Troubleshooting¶

MCP Server Not Loading:

Verify ToolUniverse is installed: python -c "import tooluniverse; print('OK')"
Check server status: claude mcp list
Run diagnostics: claude doctor

No Tools Discovered:

Check if tool filters are too restrictive
Verify the command works: tooluniverse-smcp-stdio --help

Tools Not Executing:

Provide required API keys via --env flags
Verify network connectivity

For more help, see: Claude Code troubleshooting.