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Jean — Molecular Biology & Genomics

plan_serial_dilution

Read-only

Plan a serial dilution: the same fold dilution repeated tube after tube from a stock, each tube made to one volume.

Input Schema

NameRequiredDescriptionDefault
foldNothe dilution at each step, as a fold (1:10 is 10).
stepsNohow many dilutions to make.
_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.
tube_volumeYesthe volume of each dilution after mixing (transfer plus diluent).
tube_volume_unitNothe unit of the tube volume.µL
stock_concentrationYesconcentration of the stock the series starts from.
stock_concentration_unitNothe unit of the stock concentration, which every tube is reported in.mM

Output Schema

NameRequiredDescriptionDefault
finalYesthe last tube's concentration, in the stock's unit
tubesYeseach tube: step, concentration, cumulative fold, volume left after its transfer
diluentYesdiluent in each tube, in the tube volume's unit
transferYesvolume moved into each tube, in the tube volume's unit

Schema Changelog

Changes observed during successful MCP inspections.

  1. Added

TDQS

B3.4/5.0
Behavior3/5

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

The annotations already state readOnlyHint=true, openWorldHint=false, and destructiveHint=false, so the safety profile is clear. The description adds the serial pattern and one-volume-per-tube behavior, but does not explain calculation details, output behavior, or why the generic _subject and _files parameters are present.

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?

It is one front-loaded sentence that defines the operation and its repeated tube-to-tube scope without filler. No unnecessary wording or repetition is present.

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?

With an output schema and full schema description coverage, return values and parameter details do not need to be repeated in the description. The description sufficiently covers the core planning semantics, though it leaves generic project/record parameters and sibling routing to the schema and usage context.

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%, including unit enums and defaults, so the baseline is 3. The description only reinforces concepts like stock, fold, and one volume; it adds no parameter syntax or meaning beyond what the schema already provides.

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 ('Plan') and resource ('serial dilution') and defines the repeated tube-to-tube pattern from a stock. It does not name or contrast a sibling such as solve_dilution, so the agent must infer that this is for multi-tube serial plans rather than a single dilution.

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?

There is no explicit when-to-use or when-not-to-use guidance, and no alternative tool is mentioned. The agent must infer from the phrase 'serial dilution' that solve_dilution or plan_master_mix might be alternatives.

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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