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PCR / qPCR master mix

pcr_master_mix
Read-onlyIdempotent

Use when someone sets up a PCR or qPCR reaction mix for several wells. Calculates volume of each component per reaction and for the whole mix with excess, with water filling the remaining volume. Give each component a stock and final concentration (molar, ng/µL, x buffer, %), an amount per reaction (e.g. 1.25 U polymerase from 5 U/µL, 10 ng template from ng/µL), or a fixed volume. Template can be added per well separately. Do not list water; it is calculated.

Input Schema

NameRequiredDescriptionDefault
reactionsNoNumber of reactions (wells), including controls.
componentsNoMaster mix components except water (water fills the remaining volume). Give each either a stock and final concentration (or amount per reaction), or a fixed volume per reaction.
reactionNameNoName for the master mix, e.g. 'IL-6 qPCR plate 2'.
excessPercentNoExtra master mix to cover pipetting loss, as a percent of the reactions.
reactionVolumeNoTotal volume of one reaction, including template.
templateVolumeNoTemplate volume added to each well separately (not in the master mix).
reactionVolumeUnitNouL
templateVolumeUnitNoDefaults to the reaction volume unit.

Output Schema

NameRequiredDescriptionDefault
cardNoWhat the Verbex card draws; same values as the notebook entry.
toolYes
resultNo
humanUrlNo
warningsNo
safetyNotesNo
toolVersionNo
notebookEntryNoMarkdown entry to paste into a lab notebook.
validationErrorsNo

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.3/5.0
Behavior4/5

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

Annotations already cover safety (readOnly, idempotent, non-destructive, closed-world), so the bar is lower. The description adds real behavioral context beyond that: the calculator fills leftover volume with water, applies an excess factor, and excludes template from the mix — all of which determine what the result actually contains.

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?

Front-loaded with the triggering condition, then the calculation rule, then input modes, then the two exclusions. Dense but every sentence carries information; the 'Give each component...' sentence is long but earns its length via examples.

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?

Output schema exists, so return values needn't be explained, and an output schema means the description only has to cover inputs and behavior — which it does for the component modes and water rule. Minor gaps: no mention of how excessPercent interacts with fixed-volume components, or what happens when per-reaction volumes exceed reactionVolume.

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

Parameters4/5

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

Schema coverage is already 88%, so baseline is 3, but the description goes further by explaining the three mutually exclusive ways to specify a component (stock + final concentration, amount per reaction such as '1.25 U from 5 U/µL', or a fixed volume) and the accepted unit families. That is the key disambiguation the flat enum lists cannot convey.

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 (calculates volume of each component) and resource (PCR/qPCR reaction master mix) and scopes it to 'several wells', which separates it from single-solution siblings such as solution_prep and serial_dilution. The water-fills-remainder rule makes the output shape unambiguous.

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?

'Use when someone sets up a PCR or qPCR reaction mix for several wells' gives a clear triggering condition, and 'Do not list water; it is calculated' plus 'Template can be added per well separately' give concrete usage rules. No alternative tool is named for the single-reaction or non-PCR case, so it stops short of explicit routing.

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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