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Tooluniverse MCP server

by mims-harvard·io.github.mims-harvard/tooluniverse·v1.5.0
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2,500+ scientific tools for AI scientists: life science, research, literature, and more.

C69/100grade C
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Safety scan
C69/100

full report

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1.7k stars7.0k downloads/wk

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Tooluniverse tools (10, 5 write)

write = sends, deletes, buys or posts

Read from the package source without running it. The installed server may list more.

  • boltz2_dockingwrite action

    Run the Boltz2 docking tool. Args: sequence: Protein sequence using single-letter amino acid codes. ligands: Ligand dictionaries with id and smiles fields. Returns dict: A dictionary containing the docking results with the following structure: - predicted_structure (str): The predicted protein-ligand complex structure in CIF format - structure_format (str): Format of the structure file (typically

  • compute_depmap24q2_gene_correlationswrite action

    Run one bounded DepMap lookup without blocking the MCP event loop.

  • find_tools

    Find and search available ToolUniverse tools using AI-powered search.

  • get_abstract_from_patent_app_number

    Retrieve the abstract of a patent application by its application number. Args: applicationNumberText: An 8- to 16-digit USPTO application number. Returns dict: A dictionary containing the abstract text under the 'result' key or an error message under the 'error' key if the document could not be retrieved.

  • get_claims_from_patent_app_number

    Retrieve the claims of a patent application by its application number. Args: applicationNumberText: An 8- to 16-digit USPTO application number. Returns dict: A dictionary containing the claims text under the 'result' key or an error message under the 'error' key if the document could not be retrieved.

  • get_full_text_from_patent_app_number

    Retrieve the full text of a patent application by its application number. Args: applicationNumberText: An 8- to 16-digit USPTO application number. Returns dict: A dictionary containing the full text under the 'result' key or an error message under the 'error' key if the document could not be retrieved.

  • run_compass_predictionwrite action

    Predict ICI response for one provider-rooted COMPASS TPM table.

  • run_pinnacle_ppi_retrievalwrite action

    Retrieve embeddings without blocking the MCP event loop.

  • run_transcriptformer_embedding_retrievalwrite action

    Retrieve embeddings without blocking the MCP event loop.

  • search_tools

Public scan report

scanner v0.1.8 · 2026-09-19 · same rubric, same numbers if you re-run it

2 medium
  • Code scan1500 source files scanned15/25
  • –Live reliabilityno gateway calls yet and no remote to proben/a
  • –Tool poisoningtools not inspected (local package is not executed); not countedn/a
  • Auth qualitystatic API keys via environment variables6/15
  • Maintenancelast push 0 days ago15/15
  • Maintainer identityregistry namespace matches repository owner; GitHub account older than a year9/10

Findings (2)

  • mediumNetwork call to a raw IP addressnet.raw-ip
    tooluniverse-1.5.0/src/tooluniverse/cellmarker_tool.py: …_files/file/Cell_marker_All.xlsx", "http://117.50.127.228/CellMarker/CellMarker_download_files/fil…
  • mediumeval / new Function usedexec.eval
    tooluniverse-1.5.0/src/tooluniverse/cellpose_tool.py: …nt is needed. masks = model.eval(img, diameter=diameter, channels=channel…
Overall 69/100. Components that don't apply are left out of the denominator. Any critical finding is an F.RubricAppeal a findingJSON

Grade history

  • 2026-09-19restoreD → Cscore 69: Network call to a raw IP address; eval / new Function used

Install directly

claude mcp add tooluniverse -- uvx tooluniverse
Add to Cursor

Tooluniverse: common questions

Is Tooluniverse MCP server safe?
With care: it is graded C, so read the findings first (69/100). Read the Tooluniverse safety report
How do I install Tooluniverse?
It runs on your machine. Copy the Claude Code, Claude Desktop or Cursor config from the install section.
Does Tooluniverse need an API key?
Yes. The registry entry asks for OPENAI_API_KEY, ANTHROPIC_API_KEY, GEMINI_API_KEY, OPENROUTER_API_KEY and 12 more.
Is Tooluniverse maintained?
The last commit was in the last day (2026-09-19). The latest release is v1.5.0.

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