jean — Molecular Biology & Genomics

golden_gate_assemble

Assemble parts with a Type-IIS enzyme (Golden Gate / MoClo, DnaCauldron). Emits the first construct as a NEW record for downstream nodes.

Input Schema

TableJSON Schema

Name	Required	Description
`parts`	No	the parts to assemble — wire upstream `record` outputs here, or list library document names/ids.
`_files`	No	The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
`enzyme`	No	Type-IIS enzyme, or leave unset to let DnaCauldron pick one.
`_subject`	No	The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
`connectors`	No	candidate bridging LINKERS, a library distinct from `parts`. The engine reaches for one as a FALLBACK, where the parts alone do not close a construct, and names the ones it added in `warnings`; a candidate it does not need is silently unused.
`max_constructs`	No	cap on enumerated constructs. Advanced.
`include_subject`	No	also include the node's subject as a part.
`expected_constructs`	No	expect exactly this many constructs and fail when the count differs. Leave unset to enumerate every valid one.
`expect_no_unused_parts`	No	treat a part the assembly did not consume as an error, which is DnaCauldron's own default.

Output Schema

TableJSON Schema

Name	Required	Description
`enzyme`	Yes	the Type-IIS enzyme actually used
`errors`	Yes	assembly errors — the structured flaws DnaCauldron's errors spreadsheet is built from
`record`	Yes	the first assembled construct, as a record
`products`	Yes	every enumerated construct
`warnings`	Yes	assembly warnings
`overhangs`	Yes	the first construct’s junction overhangs, in assembly order: wire this into score_overhang_fidelity
`productCount`	Yes	number of constructs

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A3.8/5.0

Behavior4/5

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

Annotations already declare readOnlyHint=false, destructiveHint=false, and openWorldHint=false, so the safety profile is covered. The description adds useful behavioral context by stating it 'Emits the first construct as a NEW record for downstream nodes,' clarifying the write is constructive rather than destructive. It does not cover warnings, fallback linker behavior, or failure modes, which remain in the schema.

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

Conciseness5/5

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

Two tightly written sentences with no waste. The first sentence front-loads purpose and method; the second supplies the output side effect that matters for downstream nodes.

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

Completeness4/5

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

This is a complex nine-parameter assembly tool, but schema coverage is 100%, an output schema exists, and annotations cover safety. The description supplies purpose and output record creation, though it omits explicit sibling routing and when-to-use guidance.

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 all nine parameters already carry documentation and constraints. The description does not add parameter syntax, defaults, or format details beyond what the schema provides, so the baseline score applies.

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

Purpose5/5

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

States a specific verb ('Assemble'), resource ('parts'), and method (Type-IIS enzyme / Golden Gate / MoClo, DnaCauldron), plus the output behavior. This distinguishes it from sibling assembly tools such as gibson_assemble, recombine, and restriction_ligate by enzyme class.

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

Usage Guidelines2/5

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

The description never explicitly says when to use this tool versus alternatives, nor when not to use it. The enzyme class implies a Golden Gate context, but there is no routing to or away from gibson_assemble, restriction_ligate, recombine, or the upstream check_golden_gate_parts / downstream verify_construct tools.

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

All jean — Molecular Biology & Genomics tools Inspect

Try in Browser

One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

Glama MCP Gateway

Add one secure layer between your agents and this server.

Resources

Need Help?