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三域医研 · 科研算法引擎 (SanYu Research Engine)

Molecular cloning design / 克隆方案设计

cloning_design
Read-only

Molecular cloning design / 克隆方案设计 | USE WHEN: design a plasmid construct: homology arms, primers, assembly strategy | ALIASES: 分子克隆, 构建质粒, 同源臂, cloning, Gibson, 酶切连接, 引物设计克隆 | RETURNS: 克隆方案与引物

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "insert_seq": "<insert_seq>",
      "vector_seq": "<vector_seq>"
    },
    "name": "cloning_design"
  }
}

Input Schema

NameRequiredDescriptionDefault
methodNoGibson / Golden Gate / 酶切连接
insert_seqYes插入片段序列(≥40bp)
vector_seqYes载体序列

Schema Changelog

Changes observed during successful MCP inspections.

  1. Added

TDQS

A3.6/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false, and openWorldHint=false, so the safety profile is fully covered by structured data and the description need not restate it. The description contributes the 'RETURNS: 克隆方案与引物' line, which substitutes for the absent output schema, but says nothing about what the plan contains, whether an omitted 'method' falls back to a default, or what the ≥40bp insert constraint implies for failure modes.

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

Conciseness4/5

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

The pipe-delimited layout is front-loaded and scannable, with the action verb appearing in the first segment. The bilingual title repetition and the long alias list (including 引物设计克隆, which overlaps a sibling's territory) consume space without improving invocation decisions.

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

Completeness3/5

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

For a compact 3-parameter computational tool with a fully described schema and a stand-in RETURNS line, the essentials are present. Gaps remain around what the returned plan looks like, how 'method' behaves if omitted (it is not required), and why the two sequence inputs are needed together, which matters given there is no output schema.

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

Parameters3/5

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

Schema description coverage is 100%, so the schema already documents all three parameters including the Gibson / Golden Gate / 酶切连接 options for 'method'. The description only echoes those same method names in the ALIASES list, adding no new meaning about defaults, format, or interaction between insert_seq and vector_seq; baseline 3 applies.

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

Purpose4/5

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

The description names a specific verb and resource — design a plasmid construct — and enumerates the concrete outputs (homology arms, primers, assembly strategy), which is far more specific than the bare tool name. It does not, however, differentiate from closely related siblings such as plasmid_map, pcr_primer_design, restriction_sites, or primer_tm, which an agent could reasonably confuse with this one.

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

Usage Guidelines4/5

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

The 'USE WHEN' clause gives an explicit triggering condition ('design a plasmid construct'), so an agent knows the situation that selects this tool. It stops short of a when-not clause or naming an alternative sibling (e.g., 'for primer Tm only, use primer_tm'), so the routing is clear but not fully disambiguated.

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

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