MCP servers

Expose PraisonAIBio tools to Cursor, Claude Desktop, and other MCP clients.

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Servers

Server	Path	Scope
sysbio	mcp/sysbio-server/server.py	11 T2B simulation tools
biomodels	mcp/biomodels-server/server.py	Read-only search and metadata
Package	praisonai-bio-mcp	Same as sysbio (console entry point)
ClawBio bridge	mcp/clawbio-bridge/bridge.py	v2 — connect genomics context to pathway tools

Discovery tools

MCP servers expose the 11 Talk2BioModels tools. The extra 10 discovery tools (rank_models, sbml_validate, repro_export, etc.) are available via Python toolsets and YAML workflows, not MCP yet.

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Run locally

pip install -e "src/praisonai-bio[simulation]"
python -c "import praisonai_bio"
python mcp/sysbio-server/server.py

Read-only (no BASICO):

python mcp/biomodels-server/server.py

Health check:

praisonai-bio doctor mcp

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PraisonAI integration

praisonai mcp add   # register server in config
praisonai serve mcp

Workflow stub: workflows/platform/mcp_sysbio_server.yaml

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Resources and prompts

File	Purpose
mcp/sysbio-server/resources.md	biomodel://{id}, demo://glycolysis URIs
mcp/sysbio-server/prompts.md	Pre-built MCP prompts

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Cursor config example

{
  "mcpServers": {
    "praisonai-sysbio": {
      "command": "python",
      "args": ["/path/to/PraisonAIBio/mcp/sysbio-server/server.py"]
    }
  }
}

Run from repo root after pip install -e "src/praisonai-bio[simulation]".

See Tools reference for all 21 Python tools.