Claude Code#

Claude Code is Anthropic’s terminal-based AI coding agent. ToolUniverse ships an official Claude Code plugin that auto-configures the MCP server, ~115 specialized research skills, slash commands, and a research agent — all in two commands.

The plugin is the recommended way to use ToolUniverse with Claude Code. A manual-MCP fallback is documented at the bottom of this page.

Quickstart — install the plugin#

Prerequisites (one-time check):

uv --version       # if missing:  curl -LsSf https://astral.sh/uv/install.sh | sh
claude --version   # if missing:  https://claude.com/claude-code

Install (two commands):

# 1. Register the ToolUniverse marketplace from GitHub
claude plugin marketplace add mims-harvard/ToolUniverse

# 2. Install the plugin
claude plugin install tooluniverse@tooluniverse

Restart Claude Code. The MCP server auto-starts via uvx tooluniverse on first use (~30 s cold start, instant after).

Tip

Recommended: turn on auto-update. Third-party marketplaces default to no auto-update, so new skills and fixes only reach you when you remember to run claude plugin update yourself. Turn it on once:

python3 -c "
import json, pathlib, sys
p = pathlib.Path.home() / '.claude/plugins/known_marketplaces.json'
d = json.loads(p.read_text())
if 'tooluniverse' not in d:
    sys.exit('Run the marketplace add command above first')
d['tooluniverse']['autoUpdate'] = True
p.write_text(json.dumps(d, indent=2))
print('autoUpdate enabled for tooluniverse')
"

Equivalent interactive path: /plugin → Marketplaces → tooluniverse → Enable auto-update. With this on, Claude Code checks for updates in the background after each session start (up to a ~10 min random delay) and updates the installed plugin automatically — no more manual claude plugin update.

Note

Pin to a specific version (optional):

claude plugin marketplace add mims-harvard/ToolUniverse#v1.2.0
claude plugin install tooluniverse@tooluniverse

Replace v1.2.0 with any released tag from the releases page.

Verify it worked#

claude plugin list
# Expect to see:  tooluniverse  (enabled)

Inside Claude Code, ask naturally — no command prefix needed; the router skill auto-dispatches:

What are the top mutated genes in breast cancer?
Research the drug metformin.
Run DESeq2 on my CD4 vs CD14 RNA-seq data in this folder.
How many indels are in the MDR sample VCF?

What you get#

Component	What it does	How to invoke
MCP server	1000+ scientific tools via `find_tools`, `get_tool_info`, `execute_tool`	Auto-loaded; no action needed
Slash commands	Discipline-enforcing prompts for common research tasks	Type `/tooluniverse:<command>`
`/tooluniverse:research`	Drive a multi-database investigation inline in this chat — same rigor as the `researcher` agent, but stays in your conversation so you see each step and can refine	Slash command
`/tooluniverse:translate-id`	Resolve an ID across all relevant namespaces (HGNC ↔ Ensembl ↔ UniProt ↔ NCBI ↔ ChEMBL ↔ PubChem)	Slash command
`/tooluniverse:cross-validate`	Verify a claim across 3+ independent databases	Slash command
`/tooluniverse:compare`	N-way side-by-side comparison with domain-appropriate columns	Slash command
`/tooluniverse:literature-sweep`	Graded mini-review across PubMed + EuropePMC + Semantic Scholar	Slash command
`/tooluniverse:verify-references`	Check that cited references are real and accurately described, including retraction status	Slash command
`/tooluniverse:self-review`	Generate weighted success criteria for a task and check work against them (what’s missing / done well)	Slash command
`/tooluniverse:setup-keys`	Configure ToolUniverse API keys	Slash command
`/tooluniverse:researcher`	Same investigation as `research`, delegated to a forked-context subagent that returns one summary (use when you don’t want intermediate tool-call output in your main thread)	Slash command
~115 research skills	Structured workflows for genomics, drug discovery, clinical analysis, statistical modeling, phylogenetics, CRISPR screens, variant interpretation, etc.	Auto-activate when the question matches

Update / uninstall#

If you enabled auto-update above, updates happen automatically in the background — no action needed. Otherwise, update manually:

# Update to the latest plugin release
claude plugin update tooluniverse

# Refresh the MCP server's tool cache (recommended after updates)
uv cache clean tooluniverse

# Restart Claude Code

# Uninstall
claude plugin uninstall tooluniverse
claude plugin marketplace remove tooluniverse

Optional — add API keys#

Most tools work without keys. For enhanced access (NCBI, OncoKB, NVIDIA, etc.), edit the plugin’s .mcp.json. Locate the installed plugin directory with:

# See plugin component inventory + on-disk location:
claude plugin details tooluniverse

# Or find the .mcp.json directly:
find ~/.claude/plugins -name '.mcp.json' -path '*tooluniverse*'

After install via the GitHub marketplace, the file is typically at: ~/.claude/plugins/cache/tooluniverse/tooluniverse/<version>/.mcp.json.

Add keys under the env block:

{
  "mcpServers": {
    "tooluniverse": {
      "command": "uvx",
      "args": ["tooluniverse"],
      "env": {
        "PYTHONIOENCODING": "utf-8",
        "NCBI_API_KEY": "your_key",
        "NVIDIA_API_KEY": "your_key",
        "ONCOKB_API_TOKEN": "your_token"
      }
    }
  }
}

Full API-key reference is in the bundled setup-tooluniverse skill — ask Claude Code: “Show me the ToolUniverse API keys reference.”

Alternative install paths#

Clone + local install (air-gapped / fork):

git clone https://github.com/mims-harvard/ToolUniverse.git
cd ToolUniverse
claude plugin marketplace add ./
claude plugin install tooluniverse@tooluniverse

Download the release zip (no git needed):

Grab tooluniverse-plugin-vX.Y.Z.zip from Releases, unzip, then:

claude plugin marketplace add /path/to/unzipped-dir
claude plugin install tooluniverse@tooluniverse

Troubleshooting#

Symptom	Fix
`marketplace add` fails with “no marketplace.json”	Use `mims-harvard/ToolUniverse` (owner/repo), not the plugin subdir.
`uvx: command not found`	Install `uv` (see Prerequisites), reopen terminal.
MCP server won’t start	Test in terminal: `uvx tooluniverse`. If it fails there, it’s a `uv`/Python issue.
Plugin installs but tools missing	Restart Claude Code. First launch downloads the package (~30 s).
`requires-python >= 3.10`	`uv python install 3.12`
Tools feel outdated	`uv cache clean tooluniverse` then restart Claude Code.
Skills don’t auto-dispatch	If you previously installed global ToolUniverse skills (`~/.claude/skills/tooluniverse-`), remove them: `rm -rf ~/.claude/skills/tooluniverse- ~/.claude/skills/setup-tooluniverse`. The plugin includes all skills; global copies interfere with routing.

Still stuck: open an issue.

Fallback — manual MCP setup (without the plugin)#

If you prefer not to use the plugin (e.g., custom MCP config or non-Claude clients sharing the same .mcp.json), you can configure Claude Code with the generic MCP setup. Open Claude Code and run:

Read https://aiscientist.tools/setup.md and set up ToolUniverse for me.

This walks you through MCP configuration, API keys, and validation step by step. See also: MCP Support and Anthropic’s official MCP setup guide.