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jean — Molecular Biology & Genomics

design_rbs

Design a 5'UTR (Shine-Dalgarno + spacer) in front of a CDS to hit a target translation-initiation strength (SC-08 engine, Turner-2004 folding).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
cdsNothe CDS starting at its start codon; unset = the open record's sequence.
_filesNoThe 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.
_subjectNoThe 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.
upstreamNoupstream context 5' of the UTR (engine default when unset). Advanced.
target_strengthYestarget relative strength, on the model's own scale — 1 is as strong as its reference site, and real sites do score above it.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
sdYesthe Shine-Dalgarno core
utrYesthe designed 5'UTR
fullYesUTR + CDS
spacingYesSD→start spacing
onTargetYeswhether the target strength was reachable
relStrengthYesachieved relative strength

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

B3.3/5.0
Behavior3/5

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

Annotations declare readOnlyHint=false, destructiveHint=false, openWorldHint=false, so the agent knows this is a non-destructive mutation. The description usefully adds the engine and folding model used, but says nothing about whether it writes to the open record, requires an existing CDS, or how the cds default interacts with the open record.

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?

A single dense sentence, front-loaded with the action and objective and followed by the engine details. No filler or repetition; every clause carries information.

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?

An output schema exists and schema coverage is full, so return values and parameters are covered. However, for a non-destructive mutation tool with a nested _subject object and 5 parameters, the description omits what actually happens on success (does it write into the record, return a sequence, etc.) and how it relates to score_rbs.

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 target_strength's scale, the cds default, and the upstream context. The description adds no syntax or interpretation beyond what the schema states, so the baseline of 3 is appropriate.

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 and resource: 'Design a 5'UTR (Shine-Dalgarno + spacer) in front of a CDS' with the concrete goal of hitting a target translation-initiation strength, and it names the underlying engine (SC-08, Turner-2004). It is clearly distinct from the scoring counterpart score_rbs, but it never explicitly names that sibling to anchor the contrast.

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 states the goal (hit a target strength) but offers no when-to-use/when-not guidance, no mention of the obvious alternative score_rbs, and no prerequisites for invoking it. The agent must infer that this is the design counterpart to score_rbs entirely on its own.

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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