# run_research_cell

Run a bounded re-analysis cell for a DeepTrace entity investigation. Queries existing DeepTrace state through parallel branches (evidence gap analysis, counter-hypothesis, dimension coverage, source diversification) to surface gaps and weaknesses. Does NOT acquire new external evidence — use due-diligence orchestrator for that. Triggers when confidence is low, coverage is sparse, or operator requests deeper analysis. Returns merged findings in standard DeepTrace format with receipts and dimension profile.

Agent View of the PolicyLayer registry record for `run_research_cell`. HTML page: https://policylayer.com/tools/io-github-homenshum-nodebench/run-research-cell

## Facts

- Tool: `run_research_cell`
- Server: Nodebench (`nodebench-mcp`) — https://policylayer.com/tools/io-github-homenshum-nodebench.md
- Install: `npx -y nodebench-mcp`
- Homepage: https://github.com/HomenShum/nodebench-ai
- Risk category: Execute (High risk)
- Registry record: grade F, identity unverified
- Server rate-limited: no
- Parameters: 0
- Recommended policy verdict: Rate-limited

## Example call (MCP tools/call, JSON-RPC 2.0)

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "run_research_cell",
    "arguments": {}
  }
}
```

## Why run_research_cell is rated High

This tool executes analysis logic across multiple branches (evidence gap analysis, counter-hypothesis, dimension coverage, source diversification) to process and re-analyze existing data. While it does not acquire new external evidence or modify underlying state, it runs bounded computational procedures that execute analysis code paths determined by input parameters.

From the tool's own definition: "'Run a bounded re-analysis cell' and 'Queries existing DeepTrace state through parallel branches' indicate active code/query execution."

## Use case

AI agents invoke run_research_cell to trigger actions in Nodebench. What it does depends on the arguments the agent supplies, and its effects often reach beyond the immediate call: builds kicked off, notifications sent, workflows started.

## Recommended policy (PolicyLayer)

Verdict: **Rate-limited**. Enforced by the PolicyLayer MCP gateway (https://policylayer.com/mcp-gateway) before a call reaches Nodebench:

```json
{
  "version": "1",
  "default": "deny",
  "tools": {
    "run_research_cell": {
      "limits": [
        {
          "counter": "run_research_cell_rate",
          "window": "minute",
          "max": 10,
          "scope": "grant"
        }
      ]
    }
  }
}
```

## Other tools on Nodebench (823)

- `abandon_cycle` — Destructive — https://policylayer.com/tools/io-github-homenshum-nodebench/abandon-cycle.md
- `archiveDocument` — Destructive — https://policylayer.com/tools/io-github-homenshum-nodebench/archivedocument.md
- `cleanup_stale_runs` — Destructive — https://policylayer.com/tools/io-github-homenshum-nodebench/cleanup-stale-runs.md
- `deeptrace_revoke_passport` — Destructive — https://policylayer.com/tools/io-github-homenshum-nodebench/deeptrace-revoke-passport.md
- `delete_learning` — Destructive — https://policylayer.com/tools/io-github-homenshum-nodebench/delete-learning.md
- `delete_sandbox_policy` — Destructive — https://policylayer.com/tools/io-github-homenshum-nodebench/delete-sandbox-policy.md
- `deleteAgentMemory` — Destructive — https://policylayer.com/tools/io-github-homenshum-nodebench/deleteagentmemory.md
- `removeDocumentFromFolder` — Destructive — https://policylayer.com/tools/io-github-homenshum-nodebench/removedocumentfromfolder.md
- `share_revoke_packet_link` — Destructive — https://policylayer.com/tools/io-github-homenshum-nodebench/share-revoke-packet-link.md
- `unload_toolset` — Destructive — https://policylayer.com/tools/io-github-homenshum-nodebench/unload-toolset.md
- `benchmark_models` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/benchmark-models.md
- `bootstrap_parallel_agents` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/bootstrap-parallel-agents.md
- `build_banking_packet` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/build-banking-packet.md
- `build_company_profile_starter` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/build-company-profile-starter.md
- `build_founder_operating_model` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/build-founder-operating-model.md
- `build_research_digest` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/build-research-digest.md
- `build_shared_context_subscription` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/build-shared-context-subscription.md
- `build_shared_context_subscription_manifest` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/build-shared-context-subscription-manifest.md
- `build_submission_export` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/build-submission-export.md
- `build_temporal_graph` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/build-temporal-graph.md
- `burst_capture` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/burst-capture.md
- `call_driver_tool` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/call-driver-tool.md
- `call_llm` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/call-llm.md
- `call_openclaw_skill` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/call-openclaw-skill.md
- `call_webmcp_tool` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/call-webmcp-tool.md
- `capture_surface_stats` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/capture-surface-stats.md
- `capture_ui_screenshot` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/capture-ui-screenshot.md
- `compile_decision_packet` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/compile-decision-packet.md
- `compile_scenarios` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/compile-scenarios.md
- `compile_tension_model` — Execute — https://policylayer.com/tools/io-github-homenshum-nodebench/compile-tension-model.md
- …and 793 more: https://policylayer.com/tools/io-github-homenshum-nodebench.md

## For agents

This record is a snapshot. Live verdicts and the full registry:

- Check every server in your MCP config at once: `npx -y policylayer stack`
- Vet a server before you add it: install the mcp-precheck skill — `npx skills add https://policylayer.com` (skill text: https://policylayer.com/skill.md)
- Query the registry over MCP: endpoint `https://api.policylayer.com/mcp` — tools `check_mcp_server`, `check_mcp_stack`, `check_tool`, `search_registry`, `get_change_events`

---

Source: the PolicyLayer MCP registry — one continuously verified record per MCP server. Full record: https://policylayer.com/registry?q=io-github-homenshum-nodebench · API: https://policylayer.com/registry/api · Policy library: https://policylayer.com/policies/io-github-homenshum-nodebench