A local MCP server called Deepmap MCP. It starts a Python command and is configured to use a CRISPR gene-effect dataset, which contains experimental information about how genes affect cells.

Running Deepmap MCP with Python and pointing it to the configured dataset file.

It lets an agent access this locally configured server and dataset, but the supplied details do not say what questions or operations it supports.

deepmap-mcp — MCP server by Saurabhsing21

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods

npx agentmods add mcp/saurabhsing21/deepmap-mcp/deepmap-mcp

Clone the repo

git clone --depth 1 https://github.com/Saurabhsing21/Deepmap-mcp

Made for: Claude Code, Codex, Cursor.

Per session not measured What this adds to a session before it is invoked.

When invoked not measured Not applicable: nothing here is loaded into a session.

Security scan A 0 findings. Scan, not verified.

Origin original No closer match found in the catalogue.

Security

Grade A, and why

deepmap-mcp scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured yesterday.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

examples/claude_desktop_config.json · 15 lines

What it actually says

{
  "deepmap-mcp": {
    "command": "python3",
    "args": [
      "-m",
      "deepmap_mcp.cli",
      "--transport",
      "stdio"
    ],
    "env": {
      "PYTHONPATH": "/Users/apple/Projects/Agent4agent/deepmap-mcp/src",
      "DEEPMAP_MCP_DATASET_PATH": "/Users/apple/.cache/deepmap-mcp/CRISPRGeneEffect.csv"
    }
  }
}

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

yesterday First seen · 15 lines scan A 093cb89b633c

Subscribe to this mod's changes

deepmap-mcp is an MCP server published in the GitHub repository Saurabhsing21/Deepmap-mcp (1 stars, last pushed 6mo ago), licensed MIT. Its token cost is not measured: an MCP server costs its tool schemas, not its config file. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

Data and AI Languages agent deepmapping mcp mcp-server

deepmap-mcp

Getting it into your agent

Grade A, and why

Nothing flagged

What it actually says

What this file has done since we first saw it

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