Jean — Molecular Biology & Genomics

plan_master_mix

Read-only

Scale one PCR reaction into a master mix for N reactions plus overage. Starts from a vendor's own published reaction setup (scaled to any reaction volume in proportion to the vendor's columns, so every final concentration is the vendor's, with water making up the volume and the template added per tube), or from your own component list.

Input Schema

Name	Required	Description	Default
`setup`	No	the vendor reaction setup to scale. Ignored when `components` is given. Values: neb-phusion-m0530 (Phusion High-Fidelity DNA Polymerase (M0530)), takara-taq-r001a (TaKaRa Taq (R001A)), takara-ex-taq-rr001a (TaKaRa Ex Taq (RR001A)), takara-la-taq-rr002a (TaKaRa LA Taq (RR002A)), takara-ex-premier-rr370a (TaKaRa Ex Premier (RR370A)), primestar-gxl-r050a (PrimeSTAR GXL (R050A), standard protocol), primestar-gxl-r050a-rapid (PrimeSTAR GXL (R050A), rapid protocol), primestar-hs-r010a (PrimeSTAR HS (R010A)), primestar-max-r045a (PrimeSTAR Max (R045A)), primestar-longseq-r055a (PrimeSTAR LongSeq (R055S/R055A)), cloneamp-hifi-639298 (CloneAmp HiFi PCR Premix (639298)), speedstar-hs-rr070a (SpeedSTAR HS (RR070A)), terra-direct-639270 (Terra PCR Direct Polymerase Mix (639270)), titanium-taq-639208 (Titanium Taq DNA Polymerase (639208)), advantage-hd-639241 (Advantage HD Polymerase Mix (639241)), qiagen-taq-201203 (QIAGEN Taq DNA Polymerase (201203)), qiagen-hotstartaq-203203 (QIAGEN HotStarTaq DNA Polymerase (203203)). Only applies when components is not given.	neb-phusion-m0530
`_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.
`overage`	No	extra mix for pipetting loss, as a percent of the N-reaction volume. In %.
`_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.
`mg_final`	No	total Mg²⁺ in the reaction, mM, reached by adding the vendor's 25 mM MgCl2 on top of what the buffer holds. Unset uses the vendor's default. Offered by QIAGEN Taq DNA Polymerase (201203), QIAGEN HotStarTaq DNA Polymerase (203203). In mM. Only applies when setup is qiagen-taq-201203 or qiagen-hotstartaq-203203.
`reactions`	No	how many reactions the mix is for.
`components`	No	your own recipe instead of a vendor setup: objects of { name, perReaction (µl), fill (true on the one component that makes up the volume), perTube (true to add it to each tube instead of the mix) }. Advanced.
`include_dmso`	No	include the setup's optional DMSO (3% final). Offered by Phusion High-Fidelity DNA Polymerase (M0530); the setup's notes say when to use it. Only applies when setup is neb-phusion-m0530.
`primer_final`	No	final concentration of each primer, µM. Most vendors state primers as a range rather than a volume; unset uses the setup's own value (its single stated value, else the low end of its range). In µM. Only applies when setup is takara-taq-r001a or takara-ex-taq-rr001a or takara-la-taq-rr002a or takara-ex-premier-rr370a or primestar-gxl-r050a or primestar-gxl-r050a-rapid or primestar-hs-r010a or primestar-max-r045a or primestar-longseq-r055a or cloneamp-hifi-639298 or speedstar-hs-rr070a or terra-direct-639270 or advantage-hd-639241 or qiagen-taq-201203 or qiagen-hotstartaq-203203.
`primer_stock`	No	concentration of your primer stock, µM; each primer's volume is its final concentration diluted from this stock. In µM. Only applies when setup is takara-taq-r001a or takara-ex-taq-rr001a or takara-la-taq-rr002a or takara-ex-premier-rr370a or primestar-gxl-r050a or primestar-gxl-r050a-rapid or primestar-hs-r010a or primestar-max-r045a or primestar-longseq-r055a or cloneamp-hifi-639298 or speedstar-hs-rr070a or terra-direct-639270 or advantage-hd-639241 or qiagen-taq-201203 or qiagen-hotstartaq-203203.
`reaction_volume`	No	volume of one reaction, µl. Each vendor publishes its setup at one or two volumes (25, 50 or 100 µl; NEB's Phusion at 20 and 50); any volume scales from them. In µl.
`template_volume`	No	template DNA per reaction, µl, added to each tube rather than the mix. The vendor states an amount, not a volume (NEB Phusion: < 250 ng), so the volume is yours. In µl. Only applies when components is not given.
`include_q_solution`	No	include the setup's optional Q-Solution (1x (from the 5x stock) final). Offered by QIAGEN Taq DNA Polymerase (201203), QIAGEN HotStarTaq DNA Polymerase (203203); the setup's notes say when to use it. Only applies when setup is qiagen-taq-201203 or qiagen-hotstartaq-203203.

Output Schema

Name	Required	Description
`rows`	Yes	each component: name, µl per reaction, µl in the mix (null when added per tube)
`mixTotal`	Yes	µl of master mix to prepare
`multiplier`	Yes	reactions × (1 + overage/100)
`dispensePerTube`	Yes	µl of master mix to dispense into each tube

Schema Changelog

Changes observed during successful MCP inspections.

Changed9 schema fields changedOct 26, 2026

changedInput schema / properties / include_dmso / description

Previous value: -"include the setup's optional DMSO (3% final for Phusion). It lowers primer Tm, so lower the annealing temperature. Only applies when components is not given."New value: +"include the setup's optional DMSO (3% final). Offered by Phusion High-Fidelity DNA Polymerase (M0530); the setup's notes say when to use it. Only applies when setup is neb-phusion-m0530."

addedInput schema / properties / include_q_solution

Added value: +{
+  "default": false,
+  "description": "include the setup's optional Q-Solution (1x (from the 5x stock) final). Offered by QIAGEN Taq DNA Polymerase (201203), QIAGEN HotStarTaq DNA Polymerase (203203); the setup's notes say when to use it. Only applies when setup is qiagen-taq-201203 or qiagen-hotstartaq-203203.",
+  "type": "boolean"
+}

addedInput schema / properties / mg_final

Added value: +{
+  "description": "total Mg²⁺ in the reaction, mM, reached by adding the vendor's 25 mM MgCl2 on top of what the buffer holds. Unset uses the vendor's default. Offered by QIAGEN Taq DNA Polymerase (201203), QIAGEN HotStarTaq DNA Polymerase (203203). In mM. Only applies when setup is qiagen-taq-201203 or qiagen-hotstartaq-203203.",
+  "minimum": 0,
+  "type": "number"
+}

addedInput schema / properties / primer_final

Added value: +{
+  "description": "final concentration of each primer, µM. Most vendors state primers as a range rather than a volume; unset uses the setup's own value (its single stated value, else the low end of its range). In µM. Only applies when setup is takara-taq-r001a or takara-ex-taq-rr001a or takara-la-taq-rr002a or takara-ex-premier-rr370a or primestar-gxl-r050a or primestar-gxl-r050a-rapid or primestar-hs-r010a or primestar-max-r045a or primestar-longseq-r055a or cloneamp-hifi-639298 or speedstar-hs-rr070a or terra-direct-639270 or advantage-hd-639241 or qiagen-taq-201203 or qiagen-hotstartaq-203203.",
+  "minimum": 0,
+  "type": "number"
+}

addedInput schema / properties / primer_stock

Added value: +{
+  "default": 10,
+  "description": "concentration of your primer stock, µM; each primer's volume is its final concentration diluted from this stock. In µM. Only applies when setup is takara-taq-r001a or takara-ex-taq-rr001a or takara-la-taq-rr002a or takara-ex-premier-rr370a or primestar-gxl-r050a or primestar-gxl-r050a-rapid or primestar-hs-r010a or primestar-max-r045a or primestar-longseq-r055a or cloneamp-hifi-639298 or speedstar-hs-rr070a or terra-direct-639270 or advantage-hd-639241 or qiagen-taq-201203 or qiagen-hotstartaq-203203.",
+  "minimum": 0,
+  "type": "number"
+}

changedInput schema / properties / reaction_volume / description

Previous value: -"volume of one reaction, µl. NEB publishes the Phusion setup at 20 and 50 µl; any volume scales from them. In µl."New value: +"volume of one reaction, µl. Each vendor publishes its setup at one or two volumes (25, 50 or 100 µl; NEB's Phusion at 20 and 50); any volume scales from them. In µl."

changedInput schema / properties / setup / description

Previous value: -"the vendor reaction setup to scale. Ignored when `components` is given. Values: neb-phusion-m0530 (Phusion High-Fidelity DNA Polymerase (M0530)). Only applies when components is not given."New value: +"the vendor reaction setup to scale. Ignored when `components` is given. Values: neb-phusion-m0530 (Phusion High-Fidelity DNA Polymerase (M0530)), takara-taq-r001a (TaKaRa Taq (R001A)), takara-ex-taq-rr001a (TaKaRa Ex Taq (RR001A)), takara-la-taq-rr002a (TaKaRa LA Taq (RR002A)), takara-ex-premier-rr370a (TaKaRa Ex Premier (RR370A)), primestar-gxl-r050a (PrimeSTAR GXL (R050A), standard protocol), primestar-gxl-r050a-rapid (PrimeSTAR GXL (R050A), rapid protocol), primestar-hs-r010a (PrimeSTAR HS (R010A)), primestar-max-r045a (PrimeSTAR Max (R045A)), primestar-longseq-r055a (PrimeSTAR LongSeq (R055S/R055A)), cloneamp-hifi-639298 (CloneAmp HiFi PCR Premix (639298)), speedstar-hs-rr070a (SpeedSTAR HS (RR070A)), terra-direct-639270 (Terra PCR Direct Polymerase Mix (639270)), titanium-taq-639208 (Titanium Taq DNA Polymerase (639208)), advantage-hd-639241 (Advantage HD Polymerase Mix (639241)), qiagen-taq-201203 (QIAGEN Taq DNA Polymerase (201203)), qiagen-hotstartaq-203203 (QIAGEN HotStarTaq DNA Polymerase (203203)). Only applies when components is not given."

changedInput schema / properties / setup / enum

Previous value: -[
-  "neb-phusion-m0530"
-]New value: +[
+  "neb-phusion-m0530",
+  "takara-taq-r001a",
+  "takara-ex-taq-rr001a",
+  "takara-la-taq-rr002a",
+  "takara-ex-premier-rr370a",
+  "primestar-gxl-r050a",
+  "primestar-gxl-r050a-rapid",
+  "primestar-hs-r010a",
+  "primestar-max-r045a",
+  "primestar-longseq-r055a",
+  "cloneamp-hifi-639298",
+  "speedstar-hs-rr070a",
+  "terra-direct-639270",
+  "titanium-taq-639208",
+  "advantage-hd-639241",
+  "qiagen-taq-201203",
+  "qiagen-hotstartaq-203203"
+]

changedInput schema / properties / template_volume / description

Previous value: -"template DNA per reaction, µl, added to each tube rather than the mix. The vendor leaves it to you (NEB: < 250 ng). In µl. Only applies when components is not given."New value: +"template DNA per reaction, µl, added to each tube rather than the mix. The vendor states an amount, not a volume (NEB Phusion: < 250 ng), so the volume is yours. In µl. Only applies when components is not given."

AddedOct 25, 2026

TDQS

A4/5.0

Behavior4/5

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

Annotations already declare readOnlyHint, destructiveHint=false and openWorldHint=false, so the safety profile is covered. Beyond that, the description adds real behavioral detail: scaling is proportional to the vendor's published columns, water makes up the volume, and template is added per tube rather than into the mix. Nothing contradicts the annotations.

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?

Two sentences, with the core action front-loaded before the mode branching. The long parenthetical in the second sentence is dense but earns its place by explaining the scaling rule. Minor trimming possible but no filler.

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 13 parameters, nested objects, an output schema and full annotation coverage, the description supplies what is needed to choose a mode and understand scaling behavior. Optional vendor-specific additives (Mg, DMSO, Q-Solution) are left to the schema descriptions, which is acceptable given their per-setup scoping is documented there.

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 100%, so the baseline would be 3, but the description genuinely adds meaning: overage is described as covering pipetting loss on top of the N-reaction volume, and template volume is explained as a per-tube addition the vendor specifies in mass, not volume. That clarifies parameters the schema enumerates but does not motivate.

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 names a specific verb and resource: 'Scale one PCR reaction into a master mix for N reactions plus overage.' That is concrete and distinguishable from siblings such as plan_thermocycler_program or pcr_amplify. It stops short of explicitly naming an alternative tool, which keeps it at 4 rather than 5.

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?

It clearly defines the two entry paths — a vendor published setup or 'your own component list' — which is the key usage decision an agent must make. It does not state exclusions or point to sibling tools for adjacent tasks, so it sits at clear-context-but-no-exclusions.

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

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