compute_transition_matrix · Cellrank MCP: Risk & Policy

WHAT IT DOES

What compute_transition_matrix does on Cellrank

AI agents invoke compute_transition_matrix to trigger actions in Cellrank. 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.

WHY IT NEEDS A POLICY

Why compute_transition_matrix needs a policy

This tool performs a computational operation (computing a transition matrix) that runs a numerical algorithm on genomic data. It doesn't merely read existing data but actively processes and transforms it, fitting the Execute category. It doesn't write persistent data or delete anything, but triggers an external computation whose effects depend on the kernel and parameters provided.

From the tool's definition Compute transition matrix for a specified kernel using appropriate parameters

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

compute_transition_matrix Rate-limited

compute_transition_matrix stays usable, but rate-capped — a runaway agent can't fire it dozens of times a minute. Everything else on the server is denied unless you say otherwise.

View as policy code

policy.json

{
  "version": "1",
  "default": "deny",
  "tools": {
    "compute_transition_matrix": {
      "limits": [
        {
          "counter": "compute_transition_matrix_rate",
          "window": "minute",
          "max": 10,
          "scope": "grant"
        }
      ]
    }
  }
}

RATE-LIMIT THIS TOOL →

Instant setup, no code required.

PolicyLayer is an MCP gateway: every tool call is checked against your rule before it reaches Cellrank, so you can run agents against it safely.

FAQ

Questions about compute_transition_matrix

What does the compute_transition_matrix tool do? +

Compute transition matrix for a specified kernel using appropriate parameters. It is categorised as a Execute tool in the Cellrank MCP Server, which means it can trigger actions or run processes. Use rate limits and argument validation.

How do I enforce a policy on compute_transition_matrix? +

Register the Cellrank MCP server in PolicyLayer and add a rule for compute_transition_matrix: allow, deny, rate-limit, or require approval. Point your MCP client at the PolicyLayer proxy URL and the rule is enforced on every call, before it reaches Cellrank. Nothing to install.

What risk level is compute_transition_matrix? +

compute_transition_matrix is a Execute tool with high risk. Execute tools should be rate-limited and have argument validation enabled.

Can I rate-limit compute_transition_matrix? +

Yes. Add a rate_limit block to the compute_transition_matrix rule in your PolicyLayer policy. For example, setting max: 10 and window: 60 limits the tool to 10 calls per minute. Rate limits are tracked per agent session and reset automatically.

How do I block compute_transition_matrix completely? +

Set action: deny in the PolicyLayer policy for compute_transition_matrix. The AI agent will receive a policy violation error and cannot call the tool. You can also include a reason field to explain why the tool is blocked.

What MCP server provides compute_transition_matrix? +

compute_transition_matrix is provided by the Cellrank MCP server (scmcphub/cellrank-mcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.