Jean by Melad Labs

gibson_assemble

Assemble fragments by terminal homology (Gibson / NEBuilder / In-Fusion, DnaCauldron).

Input Schema

Name	Required	Description	Default
`_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.
`max_tm`	No	optional ceiling on the same gate scale. 0 = no constraint. In °C. Advanced.
`min_tm`	No	optional floor on the junction's GATE value (DnaCauldron's naive A/T = 2, G/C = 4 sum, not a nearest-neighbour temperature). 0 = no constraint. In °C. Advanced.
`_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.
`topology`	No	product topology to enumerate. Values: circular (Circular), linear (Linear), both (Both).	circular
`fragments`	No	the fragments to assemble — wire upstream `record` outputs here, or list library document names/ids.
`max_constructs`	No	cap on how many distinct constructs are enumerated, so an ambiguous fragment set cannot run away. Advanced.
`include_subject`	No	also include the node's subject as a fragment.
`max_homology_bp`	No	longest terminal homology considered. The bound is EXCLUSIVE, as upstream's own `range(min, max)` is: a maximum of 40 rejects a 40 bp arm. In bp.
`min_homology_bp`	No	minimum terminal homology for two ends to join. In bp.
`expect_no_unused_parts`	No	treat a fragment left out of every construct as an error rather than a warning (upstream's own default).
`preserve_backbone_origin`	No	for circular products, rotate the origin to the start of the backbone fragment and name the product after it. Advanced.

Output Schema

Name	Required	Description
`errors`	Yes	assembly errors — the structured flaws DnaCauldron's errors spreadsheet is built from
`record`	Yes	the first assembled product, as a record
`products`	Yes	every enumerated product
`warnings`	Yes	assembly warnings
`productCount`	Yes	number of products (>1 = ambiguous assembly)

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

B3.2/5.0

Behavior2/5

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

Annotations already cover the safety profile (readOnlyHint=false, destructiveHint=false, openWorldHint=false), so the description's job is to add operational context — and it adds almost none. It never mentions that the tool enumerates multiple candidate constructs, that an unused fragment can be treated as an error, or how ambiguity is capped, all of which are meaningful behaviors buried only in parameter defaults.

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?

A single front-loaded sentence with no wasted words, and the key differentiator (terminal homology) appears first. It is arguably too terse for a 12-parameter, nested-schema tool, but it is not padded.

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?

The rich schema and the presence of an output schema offload most detail, so a one-liner is defensible. However, for an enumerative assembly tool with 12 parameters and a complex nested _subject, the absence of any note on combinatorial output, ambiguity handling, or relationship to other assembly tools leaves real gaps.

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 every parameter including the advanced TM gates, homology bounds, and topology enum is already documented in the schema. The description contributes no additional parameter meaning, so the baseline of 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 gives a specific verb (assemble), resource (fragments), and mechanism (terminal homology), and names the concrete chemistries (Gibson/NEBuilder/In-Fusion, DnaCauldron). That distinguishes it from sibling assembly tools like golden_gate_assemble or ligate_fragments by method, though it never names those siblings explicitly.

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

Usage Guidelines3/5

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

Naming Gibson/NEBuilder/In-Fusion implies the scenario (homology-based, scarless joining) without stating it outright. There is no explicit when-to-use/when-not guidance relative to the many competing assembly siblings, so the agent must infer the choice from method names alone.

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

All Jean by Melad Labs 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?