Tooluniverse Sdk

A Python SDK for building AI research systems that need to orchestrate scientific tools across proteins, drugs, genomics, and literature databases. You get three calling patterns (portable dict API, function API, or direct instantiation), built-in caching for deterministic calls, and batch execution for parallel workflows. The tool discovery is embedding-based, which is helpful when you're not sure which of the 100+ tools you actually need. Main gotcha is remembering to call load_tools() before anything else, and tool names are case-sensitive. Best for building reproducible research pipelines or benchmarking systems where you need programmatic access to UniProt, ChEMBL, PubMed, AlphaFold predictions, and similar scientific APIs without writing individual integrations yourself.

skills.sh installs: 399
GitHub stars: 1.8K
last updated: Aug 21, 2026

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Install

$ npx -y skills add mims-harvard/tooluniverse --skill tooluniverse-sdk --agent claude-code

Installs into .claude/skills of the current project.

Files

ToolUniverse Python SDK

3 calling patterns -- start with pattern 1:

tu.run({"name": ..., "arguments": ...}) -- single tool call, dict API (most portable)
tu.tools.ToolName(param=value) -- function API (recommended for interactive use)
Direct class instantiation -- advanced, bypasses caching/hooks

Installation

pip install tooluniverse              # Standard
pip install tooluniverse[embedding]   # Embedding search (GPU)
pip install tooluniverse[all]         # All features

export OPENAI_API_KEY="sk-..."  # Required for LLM tool search
export NCBI_API_KEY="..."       # Optional

Quick Start

from tooluniverse import ToolUniverse

tu = ToolUniverse()
tu.load_tools()  # REQUIRED before any tool call

# Find tools
tools = tu.run({"name": "Tool_Finder_Keyword", "arguments": {"description": "protein structure", "limit": 10}})

# Execute (dict API)
result = tu.run({"name": "UniProt_get_entry_by_accession", "arguments": {"accession": "P05067"}})

# Execute (function API)
result = tu.tools.UniProt_get_entry_by_accession(accession="P05067")