benchos-grafix-simulator

name	benchos-grafix-simulator
description	Simulate GraFix-style migration distances for protein complexes across configurable sucrose gradients and rotor presets. Use when the user wants a quick comparative sedimentation-style simulation from complex sizes, rotor choice, spin rate, and run time.
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 GraFix Simulator

Use this skill when the user wants to:

• compare likely final migration distances for multiple protein complexes
• run the supplied GraFix simulator model from complex sizes, rotor speed, gradient parameters, and run time
• save a plot and JSON result into the BenchOS workspace

Quick Rules

• Treat this as a comparative simulator based on the provided lab script, not a calibrated physical prediction engine.
• Use the shared CLI wrapper instead of rewriting the equations inline.
• Install python-basic before running the script.
• Prefer writing outputs under artifacts/grafix/<run-name>/.
• Accept sizes in kDa rather than Da.
• Prefer rotor presets instead of freeform rotor assumptions.

Browser Tool

BenchOS also exposes this tool in the website Tools page as an interactive popup application. The browser app supports line-by-line kDa entry, rotor selection, configurable gradients, and fast or slow suggestion presets. Use the website when the user wants a fast visual run; use this skill when they want agent-driven execution, saved artifacts, or workspace automation.

Default Workflow

1. Confirm the complex sizes in kDa, rotor preset, rotor speed in RPM, run time in hours, and gradient range and length.
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-grafix-simulator/scripts/grafix_simulator_cli.py",
    "--mw-kda",
    "150",
    "--mw-kda",
    "300",
    "--mw-kda",
    "550",
    "--rotor",
    "sw60-ti",
    "--rotor-speed",
    "45000",
    "--run-time-hours",
    "16",
    "--gradient-start-percent",
    "10",
    "--gradient-end-percent",
    "30",
    "--gradient-length-cm",
    "6",
    "--output-dir",
    "artifacts/grafix/run-001",
    "--json"
  ]
}

4. Read the JSON result and report the final distances.
5. If the user wants the plot or summary persisted elsewhere in BenchOS, attach or append the generated files through the normal entry or registry APIs.

Outputs

• grafix-results.json: structured result payload
• grafix-final-distances.png: scatter plot preview

Rotor Presets

• sw60-ti
• sw55-ti
• sw41-ti
• sw40-ti
• tls-55

Suggestion Guidance

• For a fast exploratory run, prefer higher RPM with a shallower gradient and shorter run time.
• For a slow 16 hour run, prefer a broader gradient and lower RPM for better comparative separation.
• Treat these as BenchOS heuristics, not instrument-calibrated protocol recommendations.

Notes

• The simulator uses the supplied GraFix model with BenchOS rotor geometry presets and configurable gradient bounds.
• Molecular weights are accepted as repeated --mw-kda arguments in kDa.