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)
- Add acetone to lysate, mix.
- Put at cold temperature for a while.
- Spin down, remove supernatant.
- 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
- Label microcentrifuge tubes with sample IDs.
- 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
- Step Review: Collect all steps/materials; classify into preparation, execution, and closing phases.
- 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.
- Standardization and Organization: Rewrite into a consistent protocol format; unify units and terminology.
- 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
1---2name: protocol-standardization3description: Standardize fragmented experimental steps into reproducible protocol documents when you need method organization, lab SOP drafting, or cross-operator reproducibility; missing parameters must be explicitly marked as "To be supplemented/Not provided".4license: MIT5---6
7## When to Use
8
9- You have messy notes (chat logs, notebook fragments, bullet points) and need a formal, reproducible experimental protocol.
10- You are preparing a lab SOP for standardization across multiple operators or sites.
11- You need to convert exploratory/iterative experimental steps into a structured method for documentation or publication support.
12- You are onboarding new team members and must clarify steps, parameters, and checkpoints without inventing missing information.
13- You are auditing an existing method to identify missing critical parameters and quality-control points.
14
15## Key Features
16
17- Converts fragmented experimental steps into a standardized protocol structure (prep → execution → closing).
18- Enforces parameter completeness for reproducibility (e.g., temperature, time, concentration, volume, mixing/rotation speed).
19- Prohibits fabrication: any unknown or uncertain information is explicitly labeled as **"To be supplemented/Not provided"**.
20- Unifies units, terminology, and step formatting for consistency.
21- Adds operational checks: logical order, safety notes, and waste disposal requirements.
22- Supports structured output using reusable templates (see `assets/protocol_template.md`).
23- Provides format guidance and checklists via `references/guide.md`.
24
25## Dependencies
26
27- None (documentation-only skill; no runtime dependencies specified).
28
29## Example Usage
30
31### Input (raw experimental notes)
32
33**Goal:** Protein precipitation and cleanup (example)
34
35**Materials/Reagents**
36- Sample lysate: 200 µL
37- Acetone (pre-chilled): volume not recorded
38- Microcentrifuge tubes
39- Centrifuge
40
41**Steps (as recorded)**
421. Add acetone to lysate, mix.
432. Put at cold temperature for a while.
443. Spin down, remove supernatant.
454. Dry pellet, then resuspend.
46
47### Output (standardized protocol)
48
49**Title:** Protein Precipitation by Cold Acetone (Standardized Protocol)
50
51**Purpose**
52- Precipitate proteins from lysate for downstream analysis.
53
54**Materials/Reagents**
55- Sample lysate: 200 µL
56- Acetone (pre-chilled): **To be supplemented/Not provided** (final ratio/volume)
57- Microcentrifuge tubes
58- Centrifuge (model/rotor: **To be supplemented/Not provided**)
59
60**Equipment**
61- Microcentrifuge capable of: **To be supplemented/Not provided** (×g or rpm)
62- Temperature control (ice bath / 4°C fridge / cold room): **To be supplemented/Not provided**
63
64**Procedure**
65
66**A. Preparation**
671. Label microcentrifuge tubes with sample IDs.
682. Pre-chill acetone to **To be supplemented/Not provided** (e.g., -20°C) and prepare a cold incubation environment (**To be supplemented/Not provided**).
69
70**B. Execution**
713. Add pre-chilled acetone to 200 µL lysate at a ratio of **To be supplemented/Not provided** (e.g., 4:1 acetone:lysate).
724. Mix by **To be supplemented/Not provided** (vortex/inversion) for **To be supplemented/Not provided** (time).
735. Incubate at **To be supplemented/Not provided** (temperature) for **To be supplemented/Not provided** (time).
746. Centrifuge at **To be supplemented/Not provided** (×g or rpm) for **To be supplemented/Not provided** (time) at **To be supplemented/Not provided** (temperature).
757. Carefully remove and discard the supernatant without disturbing the pellet.
76
77**C. Closing**
788. Air-dry pellet for **To be supplemented/Not provided** (time) until residual solvent is removed (do not overdry if resuspension is required).
799. 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).
80
81**Critical Parameters to Supplement**
82- Acetone:lysate ratio (or acetone volume)
83- Incubation temperature and duration
84- Centrifugation force/time/temperature
85- Pellet drying time
86- Resuspension buffer and volume
87
88**Quality Control / Checkpoints**
89- Pellet presence after centrifugation: **Expected** (yes/no criteria to be supplemented)
90- Supernatant clarity: **To be supplemented/Not provided**
91- Resuspension completeness: **To be supplemented/Not provided**
92
93**Safety & Waste Disposal**
94- Acetone handling: **To be supplemented/Not provided** (PPE/ventilation requirements)
95- Solvent waste disposal route: **To be supplemented/Not provided**
96
97**Suggested Output Location**
98- `outputs/ProteinPrecipitation_Acetone.txt` (example naming)
99
100## Implementation Details
101
102- **Workflow Structure**
103 1. **Step Review:** Collect all steps/materials; classify into preparation, execution, and closing phases.
104 2. **Parameter Completion:** Identify required parameters (time, temperature, concentration, volume, mixing/rotation speed, centrifugation force, etc.).
105 - If missing/uncertain, do **not** infer; mark as **"To be supplemented/Not provided"** and list fields requiring supplementation.
106 3. **Standardization and Organization:** Rewrite into a consistent protocol format; unify units and terminology.
107 4. **Output Check:** Validate logical sequence and operability; add safety and waste disposal notes.
108
109- **Parameter Rules**
110 - Never fabricate values.
111 - Use consistent units (e.g., °C, min, mL/µL, mM, ×g or rpm).
112 - Explicitly surface “critical control points” (steps where parameter deviations affect outcomes).
113
114- **Templates and References**
115 - Protocol template: `assets/protocol_template.md`
116 - Output formats, checklists, and key checkpoints: `references/guide.md`
117
118- **Output Path and Naming**
119 - Default output directory: `outputs/`
120 - Naming convention: `{Experiment_Info_Abbreviation}.txt`
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