benchos-buffer-calculator

name	benchos-buffer-calculator
description	Calculate BenchOS buffer recipes from preset or custom stock-solution inputs and export the resulting recipe. Use when the user wants a BenchOS CLI or agent-driven version of the Buffer 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 Buffer Calculator

Use this skill when the user wants to:

• calculate a BenchOS buffer recipe from the stock solution table
• start from a preset such as lysis, wash, elution, dialysis, storage, or complex buffer
• export a copyable recipe block and structured JSON summary into the BenchOS workspace

Browser Tool

BenchOS also exposes this workflow in the website Tools page as Buffer Calculator. Use the browser tool for interactive editing; use this skill for repeatable CLI or agent runs.

Quick Rules

• Use --preset for the standard BenchOS buffers when possible.
• Use repeated --component "Stock Name|FinalConcentration|Unit" arguments for custom recipes.
• Keep outputs under artifacts/buffers/<run-name>/ when possible.

Default Workflow

1. Confirm whether the user wants a preset or a custom buffer.
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-buffer-calculator/scripts/buffer_calculator_cli.py",
    "--preset",
    "lysis",
    "--output-dir",
    "artifacts/buffers/run-001",
    "--json"
  ]
}

Custom example:

{
  "args": [
    "exec",
    "--capability",
    "python-basic",
    "--cwd",
    ".",
    "--",
    "/opt/benchos/shared-skills/benchos-buffer-calculator/scripts/buffer_calculator_cli.py",
    "--buffer-name",
    "SEC Buffer",
    "--final-volume",
    "500",
    "--volume-unit",
    "mL",
    "--component",
    "HEPES-NaOH (pH 7.5)|20|mM",
    "--component",
    "NaCl|150|mM",
    "--output-dir",
    "artifacts/buffers/sec-buffer-001",
    "--json"
  ]
}

4. Read buffer-recipe.json and report the stock volumes plus the water balance.

Outputs

• buffer-recipe.json: structured result payload
• buffer-recipe.txt: copyable recipe text

Notes

• Unsupported unit conversions are rejected explicitly instead of silently generating invalid recipes.