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ToolUniverse Claude skills

Harvard MIMS lab's Python SDK, MCP server and 556 skills that give agents access to thousands of scientific databases and tools for biomedical research.

mims-harvard/ToolUniverse 556 skills Science & academiaData & analytics
Our verdict Recommended

A large, actively maintained research toolkit from an academic lab with real code behind the skills and a stated no-telemetry policy; expect some setup and API keys.

4/5 Depth expertise shipped ! Security Broad access 2d Maintenance Updated 2 days ago 1.8K Adoption stars OK License Apache-2.0, commercial OK

What ToolUniverse does

ToolUniverse is a research platform for building "AI scientist" agents. The core is a Python package (tooluniverse on PyPI) that exposes a large catalog of tools, which the setup skill puts at more than 2,700, covering databases and services such as PubMed, UniProt, ChEMBL, FAERS and ClinicalTrials.gov. It can run as an MCP server, through a tu command-line tool with subcommands for listing, searching, running and testing tools, or as a Python SDK. In MCP mode it starts in a compact setup that exposes five core tools (list, grep, get info, execute, find) while keeping the rest reachable through execute_tool.

The repo's 556 skills are mostly workflow guides written for specific research tasks. Names in the sample include ACMG variant classification, ADMET prediction, adverse event detection, antibody engineering, binder discovery, cancer genomics with TCGA and biomedical fact lookup. They average about 14 KB, a number have reference files, and one skill, setup-tooluniverse, walks a user step by step through choosing between MCP, CLI and SDK, configuring more than a dozen clients, and adding API keys. There are about 40 eval files and CI.

Installation options include a Claude Code plugin marketplace, npx skills add, an MCP config using uvx, or pip-style installs through uv. Optional extras add local machine-learning and cheminformatics tools.

Good for

  • Biomedical and life-science researchers using an agent for literature, variant, drug and pathway questions
  • Teams building agent systems that need one gateway to many scientific APIs
  • Developers who want an MCP server plus matching workflow skills

Not for

  • General software work with no scientific data needs
  • Offline use, since most tools call remote databases

What's inside depth 4/5

556 skills averaging 14 KB with reference files in many, backed by a real SDK, CLI and MCP server with CI and about 40 eval files.

Skills
556
Reference docs
360
Scripts
149
Tests / evals
47
Templates
2
Avg SKILL.md
14 KB

Counted from the repository file tree. How we score depth.

Dependencies and costs

  • Python 3.10+ and uv (macOS 14+ on Apple Silicon for the vector-search extras)
  • API keys for some databases, walked through by the setup skill
  • Network access to the scientific services
  • Telemetry: The README says ToolUniverse runs locally and collects no telemetry or analytics, and that API keys stay local and are sent only to the services they belong to.

Security review

Broad access

This skill asks for more access than most, or sends data to another service. That is usually a design choice rather than bad intent, but you should know before you install it.

  • Loads instructions from a server at run timeFor the hosted ToolUniverse Connect service the skill tells the agent to call get_skill or list_skills on the mcp.aiscientist.tools server and follow the returned guide, doing the steps itself; the guide text is served at runtime and can change without a repo change. setup-tooluniverse/SKILL.md line 153 also suggests asking an agent to 'Read https://aiscientist.tools/setup.md and set up ToolUniverse'.plugin/skills/tooluniverse-connect/SKILL.md:65
  • Sends your keys or tokens to a third-party serviceFor hosted use the user is told to paste database API keys (OMIM, DisGeNET, UMLS, NCBI and others) into connect.aiscientist.tools, which stores them encrypted and applies them to tool calls; this is opt-in and the local install keeps keys in environment variables.plugin/skills/tooluniverse-database-logins/SKILL.md:39

A large set of scientific-database skills for ToolUniverse, with setup scripts and a few analysis pipelines. Local use runs the unpinned tooluniverse Python package and edits your MCP client configs. The optional hosted ToolUniverse Connect path has the agent fetch and follow guides from the vendor's server, pipes a vendor skills.sh into sh, and has you store database API keys on the vendor's website; the README says the local install collects no telemetry.

Worth knowing

  • Installs with curl | shConnect setup for Claude Code and Codex runs 'curl -fsSL https://connect.aiscientist.tools/skills.sh | sh' (vendor host) after 'claude mcp add --scope user'; many setup docs also pipe https://astral.sh/uv/install.sh into sh (setup-tooluniverse/SKILL.md line 51, README.md line 64).plugin/skills/tooluniverse-connect/SKILL.md:42
  • Runs remote code at an unpinned versionDefault MCP server is 'uvx tooluniverse' with no version pin, auto-installed from PyPI; installs also use unpinned 'pip install tooluniverse'.plugin/skills/setup-tooluniverse/SKILL.md:435
  • Installs packages or toolsSetup installs uv, the tooluniverse Python package and optional extras (sentence_transformers, cellxgene_census, biopython, rdkit).plugin/skills/setup-tooluniverse/SKILL.md:99
  • Changes files outside your projectSetup edits MCP client config files outside the project (~/.cursor/mcp.json, Claude Desktop config, ~/.claude.json, ~/.gemini/settings.json) and can add a user-scope MCP server; diagnose_setup.py only reads them.plugin/skills/setup-tooluniverse/SKILL.md:219
  • Makes network requestsDownloads DepMap CRISPR files from depmap.org into a temp cache; ToolUniverse tools send query arguments to many public scientific databases and the Connect service.plugin/skills/tooluniverse-cell-line-profiling/scripts/depmap_gene_dependency.py:35
  • Relies on a CLI or package we could not reviewScripts and skills depend on the tooluniverse package and its tooluniverse-smcp-stdio, tooluniverse-http-api and tu commands, which are not in the files we have (including its python_code_executor and python_script_runner tools).plugin/skills/setup-tooluniverse/scripts/verify_installation.py:1

What we checked

The repository (9958 files) on Oct 29, 2026. Not a full review: 9803 of 9958 files were not downloaded (large repository; we reviewed the skill folders); we read 10 of 26 code files; it relies on code outside the repository: PyPI package tooluniverse (the real ToolUniverse implementation, installed by uvx or pip; includes code-executor tools); hosted services mcp.aiscientist.tools and connect.aiscientist.tools, including skills.sh and the guides returned by get_skill; https://aiscientist.tools/setup.md and the uv installer from astral.sh.

NVIDIA SkillSpector static scan: 168 pattern hits (MCP Rug Pull 58, Tool Misuse 28, Data Exfiltration 23, Supply Chain 14, Agent Snooping 10, Privilege Escalation 10). Most of the 168 SkillSpector hits are documentation: unpinned uvx mentions, sudo/apt and rm -rf cleanup commands in troubleshooting docs, MCP config file paths, and example URLs. The hits that mattered were the curl-to-sh installers and the hosted-guide flow, which are recorded as flags. The scripts I opened contain no obfuscation or credential reads.

A review, not a certification. Skills change after we check them — read the files before installing.

License

Apache-2.0 — commercial use allowed.

Can it run unattended?

Yes. The README describes async operations for long-running tasks such as docking and simulations with progress tracking, and the SDK is meant for building autonomous research pipelines.

Alternatives to ToolUniverse

Scientific Agent Skills

K-Dense-AI/scientific-agent-skills

K-Dense's library of 177 science skills covering bioinformatics, chemistry, clinical research, data analysis, lab tooling and scientific writing.

With caveats Broad access Depth 4/5

AI Research Skills (Orchestra)

Orchestra-Research/AI-Research-SKILLs

98 skills for AI research and ML engineering, plus an autoresearch orchestrator that runs a two-loop experiment and synthesis cycle.

With caveats Broad access Depth 4/5

Hugging Face Skills

huggingface/skills

Official Hugging Face skills led by hf-cli, a Hub CLI reference generated from your local install, plus AWS/SageMaker deployment and operations skills.

Recommended Check first Depth 3/5

FAQ

What is ToolUniverse?

ToolUniverse is an open-source ecosystem from Harvard's MIMS lab that connects language-model agents to thousands of scientific tools and databases through an MCP server, a CLI and a Python SDK. The repo also ships 556 skills for research workflows.

How do I install ToolUniverse in Claude Code?

Run claude plugin marketplace add mims-harvard/ToolUniverse and then claude plugin install tooluniverse@tooluniverse. You can also add the MCP config with uvx or run npx skills add mims-harvard/ToolUniverse.

Is ToolUniverse safe, and does it collect data?

The README states it runs locally with no telemetry or analytics, and API keys go only to the services they belong to. The package is unpinned by default in the suggested MCP config, so consider pinning a version for reproducible work.

ToolUniverse vs scientific-agent-skills: which should I use?

ToolUniverse supplies a tool runtime (MCP, CLI, SDK) with a very large database catalog plus skills on top. K-Dense's scientific-agent-skills is a skills library that relies more on the agent's own code and packages, so it fits you if you do not want a separate runtime.

Sources: GitHub repository (stars, license, file tree, last push Oct 27, 2026). Review based on the README and SKILL.md files as published.