MCP Server

io.github.mims-harvard/tooluniverse MCP Server

Name: io.github.mims-harvard/tooluniverse MCP Server
Author: io.github.mims-harvard

io.github.mims-harvard/tooluniverse

Repository Registry

What is the io.github.mims-harvard/tooluniverse MCP server?

1000+ scientific tools for AI scientists: life science, reserach, literature, and more.

How to install io.github.mims-harvard/tooluniverse

Copy-paste configuration for popular MCP clients.

transport: stdio

Config generated by PluginBench — verify against the source before use.

Environment / auth

OPENAI_API_KEY
secret
OpenAI API key for LLM-based tool finding and embedding features
ANTHROPIC_API_KEY
secret
Anthropic API key for Claude-based features
GEMINI_API_KEY
secret
Google Gemini API key for Gemini-based features
OPENROUTER_API_KEY
secret
OpenRouter API key for accessing 100+ LLM models
AZURE_OPENAI_API_KEY
secret
Azure OpenAI API key (alternative to OpenAI)
HF_TOKEN
secret
HuggingFace token for accessing models and datasets
NCBI_API_KEY
secret
NCBI/PubMed API key for higher rate limits (10 req/sec vs 3 req/sec). Register at https://www.ncbi.nlm.nih.gov/account/
SEMANTIC_SCHOLAR_API_KEY
secret
Semantic Scholar API key for higher rate limits (100 req/sec vs 1 req/sec). Register at https://www.semanticscholar.org/product/api
BIOGRID_API_KEY
secret
BioGRID API key for protein-protein interaction queries. Register free at https://webservice.thebiogrid.org/
DISGENET_API_KEY
secret
DisGeNET API key for gene-disease association data. Register free at https://www.disgenet.org/
OMIM_API_KEY
secret
OMIM API key for Mendelian disease data. Register at https://omim.org/api
ONCOKB_API_TOKEN
secret
OncoKB API token for precision oncology annotations. Register at https://www.oncokb.org/apiAccess
NVIDIA_API_KEY
secret
NVIDIA NIM API key for AlphaFold2 structure prediction, molecular docking, and genomics tools. Get key at https://build.nvidia.com
USPTO_API_KEY
secret
USPTO API key for patent data access. Register at https://developer.uspto.gov/
UMLS_API_KEY
secret
UMLS API key for medical terminology and concept mapping. Register at https://uts.nlm.nih.gov/uts/
BRENDA_EMAIL
BRENDA enzyme database login email. Register at https://www.brenda-enzymes.org/
BRENDA_PASSWORD
secret
BRENDA enzyme database login password

Claude Desktop

~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "tooluniverse": {
      "command": "uvx",
      "args": [
        "tooluniverse",
        "tooluniverse-smcp-stdio",
        "--compact-mode",
        "--categories"
      ],
      "env": {
        "OPENAI_API_KEY": "<YOUR_OPENAI_API_KEY>",
        "ANTHROPIC_API_KEY": "<YOUR_ANTHROPIC_API_KEY>",
        "GEMINI_API_KEY": "<YOUR_GEMINI_API_KEY>",
        "OPENROUTER_API_KEY": "<YOUR_OPENROUTER_API_KEY>",
        "AZURE_OPENAI_API_KEY": "<YOUR_AZURE_OPENAI_API_KEY>",
        "HF_TOKEN": "<YOUR_HF_TOKEN>",
        "NCBI_API_KEY": "<YOUR_NCBI_API_KEY>",
        "SEMANTIC_SCHOLAR_API_KEY": "<YOUR_SEMANTIC_SCHOLAR_API_KEY>",
        "BIOGRID_API_KEY": "<YOUR_BIOGRID_API_KEY>",
        "DISGENET_API_KEY": "<YOUR_DISGENET_API_KEY>",
        "OMIM_API_KEY": "<YOUR_OMIM_API_KEY>",
        "ONCOKB_API_TOKEN": "<YOUR_ONCOKB_API_TOKEN>",
        "NVIDIA_API_KEY": "<YOUR_NVIDIA_API_KEY>",
        "USPTO_API_KEY": "<YOUR_USPTO_API_KEY>",
        "UMLS_API_KEY": "<YOUR_UMLS_API_KEY>",
        "BRENDA_EMAIL": "<YOUR_BRENDA_EMAIL>",
        "BRENDA_PASSWORD": "<YOUR_BRENDA_PASSWORD>"
      }
    }
  }
}

Cursor

~/.cursor/mcp.json

{
  "mcpServers": {
    "tooluniverse": {
      "command": "uvx",
      "args": [
        "tooluniverse",
        "tooluniverse-smcp-stdio",
        "--compact-mode",
        "--categories"
      ],
      "env": {
        "OPENAI_API_KEY": "<YOUR_OPENAI_API_KEY>",
        "ANTHROPIC_API_KEY": "<YOUR_ANTHROPIC_API_KEY>",
        "GEMINI_API_KEY": "<YOUR_GEMINI_API_KEY>",
        "OPENROUTER_API_KEY": "<YOUR_OPENROUTER_API_KEY>",
        "AZURE_OPENAI_API_KEY": "<YOUR_AZURE_OPENAI_API_KEY>",
        "HF_TOKEN": "<YOUR_HF_TOKEN>",
        "NCBI_API_KEY": "<YOUR_NCBI_API_KEY>",
        "SEMANTIC_SCHOLAR_API_KEY": "<YOUR_SEMANTIC_SCHOLAR_API_KEY>",
        "BIOGRID_API_KEY": "<YOUR_BIOGRID_API_KEY>",
        "DISGENET_API_KEY": "<YOUR_DISGENET_API_KEY>",
        "OMIM_API_KEY": "<YOUR_OMIM_API_KEY>",
        "ONCOKB_API_TOKEN": "<YOUR_ONCOKB_API_TOKEN>",
        "NVIDIA_API_KEY": "<YOUR_NVIDIA_API_KEY>",
        "USPTO_API_KEY": "<YOUR_USPTO_API_KEY>",
        "UMLS_API_KEY": "<YOUR_UMLS_API_KEY>",
        "BRENDA_EMAIL": "<YOUR_BRENDA_EMAIL>",
        "BRENDA_PASSWORD": "<YOUR_BRENDA_PASSWORD>"
      }
    }
  }
}

Windsurf

~/.codeium/windsurf/mcp_config.json

{
  "mcpServers": {
    "tooluniverse": {
      "command": "uvx",
      "args": [
        "tooluniverse",
        "tooluniverse-smcp-stdio",
        "--compact-mode",
        "--categories"
      ],
      "env": {
        "OPENAI_API_KEY": "<YOUR_OPENAI_API_KEY>",
        "ANTHROPIC_API_KEY": "<YOUR_ANTHROPIC_API_KEY>",
        "GEMINI_API_KEY": "<YOUR_GEMINI_API_KEY>",
        "OPENROUTER_API_KEY": "<YOUR_OPENROUTER_API_KEY>",
        "AZURE_OPENAI_API_KEY": "<YOUR_AZURE_OPENAI_API_KEY>",
        "HF_TOKEN": "<YOUR_HF_TOKEN>",
        "NCBI_API_KEY": "<YOUR_NCBI_API_KEY>",
        "SEMANTIC_SCHOLAR_API_KEY": "<YOUR_SEMANTIC_SCHOLAR_API_KEY>",
        "BIOGRID_API_KEY": "<YOUR_BIOGRID_API_KEY>",
        "DISGENET_API_KEY": "<YOUR_DISGENET_API_KEY>",
        "OMIM_API_KEY": "<YOUR_OMIM_API_KEY>",
        "ONCOKB_API_TOKEN": "<YOUR_ONCOKB_API_TOKEN>",
        "NVIDIA_API_KEY": "<YOUR_NVIDIA_API_KEY>",
        "USPTO_API_KEY": "<YOUR_USPTO_API_KEY>",
        "UMLS_API_KEY": "<YOUR_UMLS_API_KEY>",
        "BRENDA_EMAIL": "<YOUR_BRENDA_EMAIL>",
        "BRENDA_PASSWORD": "<YOUR_BRENDA_PASSWORD>"
      }
    }
  }
}

VS Code

.vscode/mcp.json

{
  "servers": {
    "tooluniverse": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "tooluniverse",
        "tooluniverse-smcp-stdio",
        "--compact-mode",
        "--categories"
      ],
      "env": {
        "OPENAI_API_KEY": "<YOUR_OPENAI_API_KEY>",
        "ANTHROPIC_API_KEY": "<YOUR_ANTHROPIC_API_KEY>",
        "GEMINI_API_KEY": "<YOUR_GEMINI_API_KEY>",
        "OPENROUTER_API_KEY": "<YOUR_OPENROUTER_API_KEY>",
        "AZURE_OPENAI_API_KEY": "<YOUR_AZURE_OPENAI_API_KEY>",
        "HF_TOKEN": "<YOUR_HF_TOKEN>",
        "NCBI_API_KEY": "<YOUR_NCBI_API_KEY>",
        "SEMANTIC_SCHOLAR_API_KEY": "<YOUR_SEMANTIC_SCHOLAR_API_KEY>",
        "BIOGRID_API_KEY": "<YOUR_BIOGRID_API_KEY>",
        "DISGENET_API_KEY": "<YOUR_DISGENET_API_KEY>",
        "OMIM_API_KEY": "<YOUR_OMIM_API_KEY>",
        "ONCOKB_API_TOKEN": "<YOUR_ONCOKB_API_TOKEN>",
        "NVIDIA_API_KEY": "<YOUR_NVIDIA_API_KEY>",
        "USPTO_API_KEY": "<YOUR_USPTO_API_KEY>",
        "UMLS_API_KEY": "<YOUR_UMLS_API_KEY>",
        "BRENDA_EMAIL": "<YOUR_BRENDA_EMAIL>",
        "BRENDA_PASSWORD": "<YOUR_BRENDA_PASSWORD>"
      }
    }
  }
}

Claude Code

claude mcp add tooluniverse --env OPENAI_API_KEY=<YOUR_OPENAI_API_KEY> --env ANTHROPIC_API_KEY=<YOUR_ANTHROPIC_API_KEY> --env GEMINI_API_KEY=<YOUR_GEMINI_API_KEY> --env OPENROUTER_API_KEY=<YOUR_OPENROUTER_API_KEY> --env AZURE_OPENAI_API_KEY=<YOUR_AZURE_OPENAI_API_KEY> --env HF_TOKEN=<YOUR_HF_TOKEN> --env NCBI_API_KEY=<YOUR_NCBI_API_KEY> --env SEMANTIC_SCHOLAR_API_KEY=<YOUR_SEMANTIC_SCHOLAR_API_KEY> --env BIOGRID_API_KEY=<YOUR_BIOGRID_API_KEY> --env DISGENET_API_KEY=<YOUR_DISGENET_API_KEY> --env OMIM_API_KEY=<YOUR_OMIM_API_KEY> --env ONCOKB_API_TOKEN=<YOUR_ONCOKB_API_TOKEN> --env NVIDIA_API_KEY=<YOUR_NVIDIA_API_KEY> --env USPTO_API_KEY=<YOUR_USPTO_API_KEY> --env UMLS_API_KEY=<YOUR_UMLS_API_KEY> --env BRENDA_EMAIL=<YOUR_BRENDA_EMAIL> --env BRENDA_PASSWORD=<YOUR_BRENDA_PASSWORD> -- uvx tooluniverse tooluniverse-smcp-stdio --compact-mode --categories