Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare it is a write operation (readOnlyHint=false) that is not destructive, so the safety profile is covered. The description adds nothing beyond that: it does not say what side effects the run triggers, what permissions are needed, or whether the template defaults are mutated versus overridden (only implied via schema).

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Is the description appropriately sized, front-loaded, and free of redundancy?

A single, front-loaded sentence with no filler or redundancy. It is efficient, though the brevity comes at the cost of the details that would aid invocation.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

This is a mutation tool with four parameters, a nested parameterValues object, and no output schema. The description never indicates what is returned (e.g., a run ID to feed into get_protocol_run / pause_protocol_run), nor what state the new run starts in, which is important context for a create-style tool.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so id, kernelId, sampleIds, and parameterValues are already documented in the schema. The description's phrase 'on a specific kernel with given parameter values' mirrors the schema without adding format or constraint detail, so the baseline of 3 applies.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Does the description clearly state what the tool does and how it differs from similar tools?

The description gives a specific verb (Instantiate) and resource (a protocol template as a run) plus a scope qualifier (on a specific kernel). It clearly states what is produced, but it does not distinguish itself from close siblings like start_protocol_run, create_protocol, or fork_protocol, leaving the agent to infer the boundary.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Does the description explain when to use this tool, when not to, or what alternatives exist?

There is no when-to-use guidance, no prerequisites, and no mention of alternatives. With a sibling literally named start_protocol_run, the absence of any routing rule is a real gap for the agent.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.