benchos-pcr-calculator

name	benchos-pcr-calculator
description	Calculate BenchOS 50 µL PCR reactions, plasmid dilution guidance, and optional master-mix volumes. Use when the user wants a BenchOS CLI or agent-driven version of the PCR Calculator tool.
license	Proprietary
compatibility	Requires BenchOS agent runtime with `labbook_cli`, `benchos-cli`, and the curated `python-basic` capability pack.
metadata	{"author":"benchos","version":"1"}
allowed-tools	labbook_cli

BenchOS PCR Calculator

Use this skill when the user wants to:

• calculate the BenchOS 50 µL PCR reaction from plasmid DNA or cDNA
• generate the current dilution instruction for concentrated plasmid template
• prepare a multi-reaction master mix using the current BenchOS calculator convention

Browser Tool

BenchOS also exposes this workflow in the website Tools page as PCR Calculator. Use the browser tool for quick interactive setup; use this skill for terminal, agent, or workflow execution.

Default Workflow

1. Confirm template type, plasmid concentration when relevant, and the number of reactions for the master mix if needed.
2. Install the capability pack:

{ "args": ["capabilities", "install", "--name", "python-basic"] }

3. Run the shared script:

{
  "args": [
    "exec",
    "--capability",
    "python-basic",
    "--cwd",
    ".",
    "--",
    "/opt/benchos/shared-skills/benchos-pcr-calculator/scripts/pcr_calculator_cli.py",
    "--template-type",
    "plasmid",
    "--plasmid-concentration",
    "500",
    "--master-mix-reactions",
    "6",
    "--output-dir",
    "artifacts/pcr/run-001",
    "--json"
  ]
}

4. Read pcr-calculation.json and report the single-reaction volumes, dilution instruction, and master-mix recipe when present.

Outputs

• pcr-calculation.json: structured result payload
• pcr-calculation.txt: human-readable recipe summary

Notes

• This preserves the current BenchOS public calculator behavior, including the +0.5 reaction master-mix overage and the current master-mix component convention.