Search / io.github.mims-harvard/tooluniverse
protogridL0· runs locally2,700+ scientific tools for AI scientists: life science, research, literature, and more.
v1.5.7 · active · repository · website · descriptor JSON · versions
{
"mcpServers": {
"tooluniverse": {
"command": "uvx",
"args": [
"tooluniverse==1.5.7",
"tooluniverse-smcp-stdio",
"--compact-mode",
"--categories"
],
"env": {
"OPENAI_API_KEY": "${OPENAI_API_KEY}",
"ANTHROPIC_API_KEY": "${ANTHROPIC_API_KEY}",
"GEMINI_API_KEY": "${GEMINI_API_KEY}",
"OPENROUTER_API_KEY": "${OPENROUTER_API_KEY}",
"AZURE_OPENAI_API_KEY": "${AZURE_OPENAI_API_KEY}",
"HF_TOKEN": "${HF_TOKEN}",
"NCBI_API_KEY": "${NCBI_API_KEY}",
"SEMANTIC_SCHOLAR_API_KEY": "${SEMANTIC_SCHOLAR_API_KEY}",
"BIOGRID_API_KEY": "${BIOGRID_API_KEY}",
"DISGENET_API_KEY": "${DISGENET_API_KEY}",
"OMIM_API_KEY": "${OMIM_API_KEY}",
"ONCOKB_API_TOKEN": "${ONCOKB_API_TOKEN}",
"NVIDIA_API_KEY": "${NVIDIA_API_KEY}",
"USPTO_API_KEY": "${USPTO_API_KEY}",
"UMLS_API_KEY": "${UMLS_API_KEY}",
"BRENDA_PASSWORD": "${BRENDA_PASSWORD}"
}
}
}
}claude mcp add tooluniverse -e "OPENAI_API_KEY=${OPENAI_API_KEY}" -e "ANTHROPIC_API_KEY=${ANTHROPIC_API_KEY}" -e "GEMINI_API_KEY=${GEMINI_API_KEY}" -e "OPENROUTER_API_KEY=${OPENROUTER_API_KEY}" -e "AZURE_OPENAI_API_KEY=${AZURE_OPENAI_API_KEY}" -e "HF_TOKEN=${HF_TOKEN}" -e "NCBI_API_KEY=${NCBI_API_KEY}" -e "SEMANTIC_SCHOLAR_API_KEY=${SEMANTIC_SCHOLAR_API_KEY}" -e "BIOGRID_API_KEY=${BIOGRID_API_KEY}" -e "DISGENET_API_KEY=${DISGENET_API_KEY}" -e "OMIM_API_KEY=${OMIM_API_KEY}" -e "ONCOKB_API_TOKEN=${ONCOKB_API_TOKEN}" -e "NVIDIA_API_KEY=${NVIDIA_API_KEY}" -e "USPTO_API_KEY=${USPTO_API_KEY}" -e "UMLS_API_KEY=${UMLS_API_KEY}" -e "BRENDA_PASSWORD=${BRENDA_PASSWORD}" -- uvx tooluniverse==1.5.7 tooluniverse-smcp-stdio --compact-mode --categories[mcp_servers.tooluniverse]
command = "uvx"
args = ["tooluniverse==1.5.7", "tooluniverse-smcp-stdio", "--compact-mode", "--categories"]
env = { "OPENAI_API_KEY" = "${OPENAI_API_KEY}", "ANTHROPIC_API_KEY" = "${ANTHROPIC_API_KEY}", "GEMINI_API_KEY" = "${GEMINI_API_KEY}", "OPENROUTER_API_KEY" = "${OPENROUTER_API_KEY}", "AZURE_OPENAI_API_KEY" = "${AZURE_OPENAI_API_KEY}", "HF_TOKEN" = "${HF_TOKEN}", "NCBI_API_KEY" = "${NCBI_API_KEY}", "SEMANTIC_SCHOLAR_API_KEY" = "${SEMANTIC_SCHOLAR_API_KEY}", "BIOGRID_API_KEY" = "${BIOGRID_API_KEY}", "DISGENET_API_KEY" = "${DISGENET_API_KEY}", "OMIM_API_KEY" = "${OMIM_API_KEY}", "ONCOKB_API_TOKEN" = "${ONCOKB_API_TOKEN}", "NVIDIA_API_KEY" = "${NVIDIA_API_KEY}", "USPTO_API_KEY" = "${USPTO_API_KEY}", "UMLS_API_KEY" = "${UMLS_API_KEY}", "BRENDA_PASSWORD" = "${BRENDA_PASSWORD}" }
{
"$schema": "https://opencode.ai/config.json",
"mcp": {
"tooluniverse": {
"type": "local",
"command": [
"uvx",
"tooluniverse==1.5.7",
"tooluniverse-smcp-stdio",
"--compact-mode",
"--categories"
],
"enabled": true,
"environment": {
"OPENAI_API_KEY": "{env:OPENAI_API_KEY}",
"ANTHROPIC_API_KEY": "{env:ANTHROPIC_API_KEY}",
"GEMINI_API_KEY": "{env:GEMINI_API_KEY}",
"OPENROUTER_API_KEY": "{env:OPENROUTER_API_KEY}",
"AZURE_OPENAI_API_KEY": "{env:AZURE_OPENAI_API_KEY}",
"HF_TOKEN": "{env:HF_TOKEN}",
"NCBI_API_KEY": "{env:NCBI_API_KEY}",
"SEMANTIC_SCHOLAR_API_KEY": "{env:SEMANTIC_SCHOLAR_API_KEY}",
"BIOGRID_API_KEY": "{env:BIOGRID_API_KEY}",
"DISGENET_API_KEY": "{env:DISGENET_API_KEY}",
"OMIM_API_KEY": "{env:OMIM_API_KEY}",
"ONCOKB_API_TOKEN": "{env:ONCOKB_API_TOKEN}",
"NVIDIA_API_KEY": "{env:NVIDIA_API_KEY}",
"USPTO_API_KEY": "{env:USPTO_API_KEY}",
"UMLS_API_KEY": "{env:UMLS_API_KEY}",
"BRENDA_PASSWORD": "{env:BRENDA_PASSWORD}"
}
}
}
}{
"mcpServers": {
"tooluniverse": {
"command": "uvx",
"args": [
"tooluniverse==1.5.7",
"tooluniverse-smcp-stdio",
"--compact-mode",
"--categories"
],
"env": {
"OPENAI_API_KEY": "${OPENAI_API_KEY}",
"ANTHROPIC_API_KEY": "${ANTHROPIC_API_KEY}",
"GEMINI_API_KEY": "${GEMINI_API_KEY}",
"OPENROUTER_API_KEY": "${OPENROUTER_API_KEY}",
"AZURE_OPENAI_API_KEY": "${AZURE_OPENAI_API_KEY}",
"HF_TOKEN": "${HF_TOKEN}",
"NCBI_API_KEY": "${NCBI_API_KEY}",
"SEMANTIC_SCHOLAR_API_KEY": "${SEMANTIC_SCHOLAR_API_KEY}",
"BIOGRID_API_KEY": "${BIOGRID_API_KEY}",
"DISGENET_API_KEY": "${DISGENET_API_KEY}",
"OMIM_API_KEY": "${OMIM_API_KEY}",
"ONCOKB_API_TOKEN": "${ONCOKB_API_TOKEN}",
"NVIDIA_API_KEY": "${NVIDIA_API_KEY}",
"USPTO_API_KEY": "${USPTO_API_KEY}",
"UMLS_API_KEY": "${UMLS_API_KEY}",
"BRENDA_PASSWORD": "${BRENDA_PASSWORD}"
}
}
},
"deeplink": "cursor://anysphere.cursor-deeplink/mcp/install?name=tooluniverse&config=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"
}{
"servers": {
"tooluniverse": {
"type": "stdio",
"command": "uvx",
"args": [
"tooluniverse==1.5.7",
"tooluniverse-smcp-stdio",
"--compact-mode",
"--categories"
],
"env": {
"OPENAI_API_KEY": "${OPENAI_API_KEY}",
"ANTHROPIC_API_KEY": "${ANTHROPIC_API_KEY}",
"GEMINI_API_KEY": "${GEMINI_API_KEY}",
"OPENROUTER_API_KEY": "${OPENROUTER_API_KEY}",
"AZURE_OPENAI_API_KEY": "${AZURE_OPENAI_API_KEY}",
"HF_TOKEN": "${HF_TOKEN}",
"NCBI_API_KEY": "${NCBI_API_KEY}",
"SEMANTIC_SCHOLAR_API_KEY": "${SEMANTIC_SCHOLAR_API_KEY}",
"BIOGRID_API_KEY": "${BIOGRID_API_KEY}",
"DISGENET_API_KEY": "${DISGENET_API_KEY}",
"OMIM_API_KEY": "${OMIM_API_KEY}",
"ONCOKB_API_TOKEN": "${ONCOKB_API_TOKEN}",
"NVIDIA_API_KEY": "${NVIDIA_API_KEY}",
"USPTO_API_KEY": "${USPTO_API_KEY}",
"UMLS_API_KEY": "${UMLS_API_KEY}",
"BRENDA_PASSWORD": "${BRENDA_PASSWORD}"
}
}
}
}{
"mcpServers": {
"tooluniverse": {
"command": "uvx",
"args": [
"tooluniverse==1.5.7",
"tooluniverse-smcp-stdio",
"--compact-mode",
"--categories"
],
"env": {
"OPENAI_API_KEY": "${OPENAI_API_KEY}",
"ANTHROPIC_API_KEY": "${ANTHROPIC_API_KEY}",
"GEMINI_API_KEY": "${GEMINI_API_KEY}",
"OPENROUTER_API_KEY": "${OPENROUTER_API_KEY}",
"AZURE_OPENAI_API_KEY": "${AZURE_OPENAI_API_KEY}",
"HF_TOKEN": "${HF_TOKEN}",
"NCBI_API_KEY": "${NCBI_API_KEY}",
"SEMANTIC_SCHOLAR_API_KEY": "${SEMANTIC_SCHOLAR_API_KEY}",
"BIOGRID_API_KEY": "${BIOGRID_API_KEY}",
"DISGENET_API_KEY": "${DISGENET_API_KEY}",
"OMIM_API_KEY": "${OMIM_API_KEY}",
"ONCOKB_API_TOKEN": "${ONCOKB_API_TOKEN}",
"NVIDIA_API_KEY": "${NVIDIA_API_KEY}",
"USPTO_API_KEY": "${USPTO_API_KEY}",
"UMLS_API_KEY": "${UMLS_API_KEY}",
"BRENDA_PASSWORD": "${BRENDA_PASSWORD}"
}
}
}
}extensions:
"tooluniverse":
enabled: true
name: "tooluniverse"
type: stdio
cmd: "uvx"
args:
- "tooluniverse==1.5.7"
- "tooluniverse-smcp-stdio"
- "--compact-mode"
- "--categories"
envs:
"OPENAI_API_KEY": "${OPENAI_API_KEY}"
"ANTHROPIC_API_KEY": "${ANTHROPIC_API_KEY}"
"GEMINI_API_KEY": "${GEMINI_API_KEY}"
"OPENROUTER_API_KEY": "${OPENROUTER_API_KEY}"
"AZURE_OPENAI_API_KEY": "${AZURE_OPENAI_API_KEY}"
"HF_TOKEN": "${HF_TOKEN}"
"NCBI_API_KEY": "${NCBI_API_KEY}"
"SEMANTIC_SCHOLAR_API_KEY": "${SEMANTIC_SCHOLAR_API_KEY}"
"BIOGRID_API_KEY": "${BIOGRID_API_KEY}"
"DISGENET_API_KEY": "${DISGENET_API_KEY}"
"OMIM_API_KEY": "${OMIM_API_KEY}"
"ONCOKB_API_TOKEN": "${ONCOKB_API_TOKEN}"
"NVIDIA_API_KEY": "${NVIDIA_API_KEY}"
"USPTO_API_KEY": "${USPTO_API_KEY}"
"UMLS_API_KEY": "${UMLS_API_KEY}"
"BRENDA_PASSWORD": "${BRENDA_PASSWORD}"
timeout: 300
Placeholders to fill from your own secret store: ${OPENAI_API_KEY}, ${ANTHROPIC_API_KEY}, ${GEMINI_API_KEY}, ${OPENROUTER_API_KEY}, ${AZURE_OPENAI_API_KEY}, ${HF_TOKEN}, ${NCBI_API_KEY}, ${SEMANTIC_SCHOLAR_API_KEY}, ${BIOGRID_API_KEY}, ${DISGENET_API_KEY}, ${OMIM_API_KEY}, ${ONCOKB_API_TOKEN}, ${NVIDIA_API_KEY}, ${USPTO_API_KEY}, ${UMLS_API_KEY}, ${BRENDA_PASSWORD}. The registry never accepts secret values.
This is a local package: the command runs on your machine.
Not scored: fewer than three checks apply, usually because no remote answered a credential-free probe or the server is a local package.
protocol.modern, protocol.stateless, protocol.transport, protocol.list_ttlno remote answered a protocol handshake (not probed yet, unreachable, or local-only)auth.prm, auth.as_metadata, auth.cimdno remote uses OAuthauth.secret_in_urlno templated URLtools.descriptions, tools.description_length, tools.schemas, tools.annotations, tools.directory_hints, tools.token_cost, tools.api_dumptool list unknown (behind auth, not probed, or empty)stability.changes, stability.rug_pulltool list unknownNo tool definition changes recorded. A server's first observation is its baseline; later probes record what changes.
Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed. How it is computed.
+repository +namespace-matches-repo +website ~liveness-unmeasured +updated-7d-ago
Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed. How it is computed.
[email protected] PyPIthis version is not known to the dependency resolver
Dependency graphs from deps.dev; advisories from OSV.dev, including the GitHub Advisory Database and the PyPI Advisory Database; all CC BY 4.0. The graph is what a clean install of this version resolves today; nothing was installed or run. How it is checked.
| package | registry | version | runtime | secrets |
|---|---|---|---|---|
tooluniverse | pypi | 1.5.7 | uvx | OPENAI_API_KEY, ANTHROPIC_API_KEY, GEMINI_API_KEY, OPENROUTER_API_KEY, AZURE_OPENAI_API_KEY, HF_TOKEN, NCBI_API_KEY, SEMANTIC_SCHOLAR_API_KEY, BIOGRID_API_KEY, DISGENET_API_KEY, OMIM_API_KEY, ONCOKB_API_TOKEN, NVIDIA_API_KEY, USPTO_API_KEY, UMLS_API_KEY, BRENDA_PASSWORD |
No tools observed. Local packages are never executed by the registry.
Schemas: list_tools.
{
"name": "io.github.mims-harvard/tooluniverse",
"_meta": {},
"$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
"version": "1.5.7",
"packages": [
{
"version": "1.5.7",
"transport": {
"type": "stdio"
},
"identifier": "tooluniverse",
"runtimeHint": "uvx",
"registryType": "pypi",
"registryBaseUrl": "https://pypi.org",
"packageArguments": [
{
"type": "positional",
"value": "tooluniverse-smcp-stdio"
},
{
"type": "positional",
"value": "--compact-mode",
"description": "Compact mode enabled by default: only exposes 5 core tools (tool finder, tool executor, etc.) to prevent context window overflow. All 2,700+ tools remain accessible via the execute_tool function."
},
{
"name": "--categories",
"type": "named",
"valueHint": "CATEGORY",
"isRepeated": true,
"description": "Specific tool categories to load (e.g., uniprot ChEMBL opentarget pubmed). Omit to load all tools. See full list: https://zitniklab.hms.harvard.edu/ToolUniverse/tools/tools_config_index.html"
}
],
"environmentVariables": [
{
"name": "OPENAI_API_KEY",
"isSecret": true,
"description": "OpenAI API key for LLM-based tool finding and embedding features"
},
{
"name": "ANTHROPIC_API_KEY",
"isSecret": true,
"description": "Anthropic API key for Claude-based features"
},
{
"name": "GEMINI_API_KEY",
"isSecret": true,
"description": "Google Gemini API key for Gemini-based features"
},
{
"name": "OPENROUTER_API_KEY",
"isSecret": true,
"description": "OpenRouter API key for accessing 100+ LLM models"
},
{
"name": "AZURE_OPENAI_API_KEY",
"isSecret": true,
"description": "Azure OpenAI API key (alternative to OpenAI)"
},
{
"name": "HF_TOKEN",
"isSecret": true,
"description": "HuggingFace token for accessing models and datasets"
},
{
"name": "NCBI_API_KEY",
"isSecret": true,
"description": "NCBI/PubMed API key for higher rate limits (10 req/sec vs 3 req/sec). Register at https://www.ncbi.nlm.nih.gov/account/"
},
{
"name": "SEMANTIC_SCHOLAR_API_KEY",
"isSecret": true,
"description": "Semantic Scholar API key for higher rate limits (100 req/sec vs 1 req/sec). Register at https://www.semanticscholar.org/product/api"
},
{
"name": "BIOGRID_API_KEY",
"isSecret": true,
"description": "BioGRID API key for protein-protein interaction queries. Register free at https://webservice.thebiogrid.org/"
},
{
"name": "DISGENET_API_KEY",
"isSecret": true,
"description": "DisGeNET API key for gene-disease association data. Register free at https://www.disgenet.org/"
},
{
"name": "OMIM_API_KEY",
"isSecret": true,
"description": "OMIM API key for Mendelian disease data. Register at https://omim.org/api"
},
{
"name": "ONCOKB_API_TOKEN",
"isSecret": true,
"description": "OncoKB API token for precision oncology annotations. Register at https://www.oncokb.org/apiAccess"
},
{
"name": "NVIDIA_API_KEY",
"isSecret": true,
"description": "NVIDIA NIM API key for AlphaFold2 structure prediction, molecular docking, and genomics tools. Get key at https://build.nvidia.com"
},
{
"name": "USPTO_API_KEY",
"isSecret": true,
"description": "USPTO API key for patent data access. Register at https://developer.uspto.gov/"
},
{
"name": "UMLS_API_KEY",
"isSecret": true,
"description": "UMLS API key for medical terminology and concept mapping. Register at https://uts.nlm.nih.gov/uts/"
},
{
"name": "BRENDA_EMAIL",
"description": "BRENDA enzyme database login email. Register at https://www.brenda-enzymes.org/"
},
{
"name": "BRENDA_PASSWORD",
"isSecret": true,
"description": "BRENDA enzyme database login password"
}
]
}
],
"repository": {
"url": "https://github.com/mims-harvard/ToolUniverse",
"source": "github"
},
"websiteUrl": "https://aiscientist.tools",
"description": "2,700+ scientific tools for AI scientists: life science, research, literature, and more."
}