aipoch/protocol-standardization

When to Use

• You have messy notes (chat logs, notebook fragments, bullet points) and need a formal, reproducible experimental protocol.
• You are preparing a lab SOP for standardization across multiple operators or sites.
• You need to convert exploratory/iterative experimental steps into a structured method for documentation or publication support.
• You are onboarding new team members and must clarify steps, parameters, and checkpoints without inventing missing information.
• You are auditing an existing method to identify missing critical parameters and quality-control points.

Key Features

• Converts fragmented experimental steps into a standardized protocol structure (prep → execution → closing).
• Enforces parameter completeness for reproducibility (e.g., temperature, time, concentration, volume, mixing/rotation speed).
• Prohibits fabrication: any unknown or uncertain information is explicitly labeled as "To be supplemented/Not provided".
• Unifies units, terminology, and step formatting for consistency.
• Adds operational checks: logical order, safety notes, and waste disposal requirements.
• Supports structured output using reusable templates (see assets/protocol_template.md).
• Provides format guidance and checklists via references/guide.md.

Dependencies

• None (documentation-only skill; no runtime dependencies specified).

Example Usage

Input (raw experimental notes)

Goal: Protein precipitation and cleanup (example)

Materials/Reagents

• Sample lysate: 200 µL
• Acetone (pre-chilled): volume not recorded
• Microcentrifuge tubes
• Centrifuge

Steps (as recorded)

1. Add acetone to lysate, mix.
2. Put at cold temperature for a while.
3. Spin down, remove supernatant.
4. Dry pellet, then resuspend.

Output (standardized protocol)

Title: Protein Precipitation by Cold Acetone (Standardized Protocol)

Purpose

• Precipitate proteins from lysate for downstream analysis.

Materials/Reagents

• Sample lysate: 200 µL
• Acetone (pre-chilled): To be supplemented/Not provided (final ratio/volume)
• Microcentrifuge tubes
• Centrifuge (model/rotor: To be supplemented/Not provided)

Equipment

• Microcentrifuge capable of: To be supplemented/Not provided (×g or rpm)
• Temperature control (ice bath / 4°C fridge / cold room): To be supplemented/Not provided

Procedure

A. Preparation

1. Label microcentrifuge tubes with sample IDs.
2. Pre-chill acetone to To be supplemented/Not provided (e.g., -20°C) and prepare a cold incubation environment (To be supplemented/Not provided).

B. Execution 3. Add pre-chilled acetone to 200 µL lysate at a ratio of To be supplemented/Not provided (e.g., 4:1 acetone:lysate). 4. Mix by To be supplemented/Not provided (vortex/inversion) for To be supplemented/Not provided (time). 5. Incubate at To be supplemented/Not provided (temperature) for To be supplemented/Not provided (time). 6. Centrifuge at To be supplemented/Not provided (×g or rpm) for To be supplemented/Not provided (time) at To be supplemented/Not provided (temperature). 7. Carefully remove and discard the supernatant without disturbing the pellet.

C. Closing 8. Air-dry pellet for To be supplemented/Not provided (time) until residual solvent is removed (do not overdry if resuspension is required). 9. Resuspend pellet in To be supplemented/Not provided (buffer type and volume) by To be supplemented/Not provided (pipetting/vortexing) for To be supplemented/Not provided (time).

Critical Parameters to Supplement

• Acetone:lysate ratio (or acetone volume)
• Incubation temperature and duration
• Centrifugation force/time/temperature
• Pellet drying time
• Resuspension buffer and volume

Quality Control / Checkpoints

• Pellet presence after centrifugation: Expected (yes/no criteria to be supplemented)
• Supernatant clarity: To be supplemented/Not provided
• Resuspension completeness: To be supplemented/Not provided

Safety & Waste Disposal

• Acetone handling: To be supplemented/Not provided (PPE/ventilation requirements)
• Solvent waste disposal route: To be supplemented/Not provided

Suggested Output Location

• outputs/ProteinPrecipitation_Acetone.txt (example naming)

Implementation Details

• Workflow Structure

  1. Step Review: Collect all steps/materials; classify into preparation, execution, and closing phases.
  2. Parameter Completion: Identify required parameters (time, temperature, concentration, volume, mixing/rotation speed, centrifugation force, etc.).
     • If missing/uncertain, do not infer; mark as "To be supplemented/Not provided" and list fields requiring supplementation.
  3. Standardization and Organization: Rewrite into a consistent protocol format; unify units and terminology.
  4. Output Check: Validate logical sequence and operability; add safety and waste disposal notes.

• Parameter Rules

  • Never fabricate values.
  • Use consistent units (e.g., °C, min, mL/µL, mM, ×g or rpm).
  • Explicitly surface “critical control points” (steps where parameter deviations affect outcomes).

• Templates and References

  • Protocol template: assets/protocol_template.md
  • Output formats, checklists, and key checkpoints: references/guide.md

• Output Path and Naming

  • Default output directory: outputs/
  • Naming convention: {Experiment_Info_Abbreviation}.txt