Source: https://github.com/aipoch/medical-research-skills
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
When Not to Use
- Do not proceed when required input files, identifiers, parameters, or context are missing — ask the user to provide them first.
- Do not assume capabilities beyond this skill's declared scope when the user requests external operations or inferences.
- Do not proceed without user confirmation when overwriting existing results, executing high-cost batch operations, or expanding task scope.
Required Inputs
| Field |
Required |
Format/Source |
Example |
If Missing |
| User task description |
Yes |
Text |
Research question, writing goal, analysis objective |
Stop and ask user to provide |
| Primary input material |
Depends on task |
Text, file path, ID, table, or literature |
PMID, PDF, CSV, DOCX, keywords, etc. |
Specify which material type is missing |
| Output preference |
No |
Text |
Language, format, target journal, template |
Use skill default format |
Output Contract
- Primary output: Structured result or target file aligned with this skill's objective.
- Optional output: Intermediate check notes, issue list, supplementary suggestions, or generated file paths.
- Format requirement: Unless the user specifies otherwise, prefer stable, reviewable Markdown or JSON; if the skill's bundled script requires a fixed format, use that format.
- If partially complete: Must explicitly mark as PARTIAL and state which steps are completed and which remain.
Failure Handling
- Missing critical input: Explicitly state which fields, files, or identifiers are missing and pause.
- Script, template, or resource execution failure: Report the failing step, likely cause, and recovery suggestions — do not silently degrade.
- Partial completion only: Return the verified portion first, then list remaining blockers and suggested next steps.
User Checkpoints
- Before executing batch processing, overwriting files, long-running searches, or multi-stage generation, confirm scope and output format with the user.
- Before proceeding when a key judgment is ambiguous, evidence is insufficient, or the workflow is entering the next stage, confirm with the user.
Input Validation
This skill accepts requests that match the documented purpose of protocol-standardization and include enough context to complete the workflow safely.
Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:
protocol-standardization only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.
Quick Validation
- Check that key scripts, templates, or reference file paths this skill depends on exist.
- Check that the final output contains the core fields, sections, or files specified for this task.
- Check that results clearly mark assumptions, limitations, and incomplete items.
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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)
7
8
9## When to Use
10
11- You have messy notes (chat logs, notebook fragments, bullet points) and need a formal, reproducible experimental protocol.
12- You are preparing a lab SOP for standardization across multiple operators or sites.
13- You need to convert exploratory/iterative experimental steps into a structured method for documentation or publication support.
14- You are onboarding new team members and must clarify steps, parameters, and checkpoints without inventing missing information.
15- You are auditing an existing method to identify missing critical parameters and quality-control points.
16
17## Key Features
18
19- Converts fragmented experimental steps into a standardized protocol structure (prep → execution → closing).
20- Enforces parameter completeness for reproducibility (e.g., temperature, time, concentration, volume, mixing/rotation speed).
21- Prohibits fabrication: any unknown or uncertain information is explicitly labeled as **"To be supplemented/Not provided"**.
22- Unifies units, terminology, and step formatting for consistency.
23- Adds operational checks: logical order, safety notes, and waste disposal requirements.
24- Supports structured output using reusable templates (see `assets/protocol_template.md`).
25- Provides format guidance and checklists via `references/guide.md`.
26
27## Dependencies
28
29- None (documentation-only skill; no runtime dependencies specified).
30
31## Example Usage
32
33### Input (raw experimental notes)
34
35**Goal:** Protein precipitation and cleanup (example)
36
37**Materials/Reagents**
38- Sample lysate: 200 µL
39- Acetone (pre-chilled): volume not recorded
40- Microcentrifuge tubes
41- Centrifuge
42
43**Steps (as recorded)**
441. Add acetone to lysate, mix.
452. Put at cold temperature for a while.
463. Spin down, remove supernatant.
474. Dry pellet, then resuspend.
48
49### Output (standardized protocol)
50
51**Title:** Protein Precipitation by Cold Acetone (Standardized Protocol)
52
53**Purpose**
54- Precipitate proteins from lysate for downstream analysis.
55
56**Materials/Reagents**
57- Sample lysate: 200 µL
58- Acetone (pre-chilled): **To be supplemented/Not provided** (final ratio/volume)
59- Microcentrifuge tubes
60- Centrifuge (model/rotor: **To be supplemented/Not provided**)
61
62**Equipment**
63- Microcentrifuge capable of: **To be supplemented/Not provided** (×g or rpm)
64- Temperature control (ice bath / 4°C fridge / cold room): **To be supplemented/Not provided**
65
66**Procedure**
67
68**A. Preparation**
691. Label microcentrifuge tubes with sample IDs.
702. Pre-chill acetone to **To be supplemented/Not provided** (e.g., -20°C) and prepare a cold incubation environment (**To be supplemented/Not provided**).
71
72**B. Execution**
733. Add pre-chilled acetone to 200 µL lysate at a ratio of **To be supplemented/Not provided** (e.g., 4:1 acetone:lysate).
744. Mix by **To be supplemented/Not provided** (vortex/inversion) for **To be supplemented/Not provided** (time).
755. Incubate at **To be supplemented/Not provided** (temperature) for **To be supplemented/Not provided** (time).
766. Centrifuge at **To be supplemented/Not provided** (×g or rpm) for **To be supplemented/Not provided** (time) at **To be supplemented/Not provided** (temperature).
777. Carefully remove and discard the supernatant without disturbing the pellet.
78
79**C. Closing**
808. Air-dry pellet for **To be supplemented/Not provided** (time) until residual solvent is removed (do not overdry if resuspension is required).
819. 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).
82
83**Critical Parameters to Supplement**
84- Acetone:lysate ratio (or acetone volume)
85- Incubation temperature and duration
86- Centrifugation force/time/temperature
87- Pellet drying time
88- Resuspension buffer and volume
89
90**Quality Control / Checkpoints**
91- Pellet presence after centrifugation: **Expected** (yes/no criteria to be supplemented)
92- Supernatant clarity: **To be supplemented/Not provided**
93- Resuspension completeness: **To be supplemented/Not provided**
94
95**Safety & Waste Disposal**
96- Acetone handling: **To be supplemented/Not provided** (PPE/ventilation requirements)
97- Solvent waste disposal route: **To be supplemented/Not provided**
98
99**Suggested Output Location**
100- `outputs/ProteinPrecipitation_Acetone.txt` (example naming)
101
102## Implementation Details
103
104- **Workflow Structure**
105 1. **Step Review:** Collect all steps/materials; classify into preparation, execution, and closing phases.
106 2. **Parameter Completion:** Identify required parameters (time, temperature, concentration, volume, mixing/rotation speed, centrifugation force, etc.).
107 - If missing/uncertain, do **not** infer; mark as **"To be supplemented/Not provided"** and list fields requiring supplementation.
108 3. **Standardization and Organization:** Rewrite into a consistent protocol format; unify units and terminology.
109 4. **Output Check:** Validate logical sequence and operability; add safety and waste disposal notes.
110
111- **Parameter Rules**
112 - Never fabricate values.
113 - Use consistent units (e.g., °C, min, mL/µL, mM, ×g or rpm).
114 - Explicitly surface “critical control points” (steps where parameter deviations affect outcomes).
115
116- **Templates and References**
117 - Protocol template: `assets/protocol_template.md`
118 - Output formats, checklists, and key checkpoints: `references/guide.md`
119
120- **Output Path and Naming**
121 - Default output directory: `outputs/`
122 - Naming convention: `{Experiment_Info_Abbreviation}.txt`
123
124## When Not to Use
125
126- Do not proceed when required input files, identifiers, parameters, or context are missing — ask the user to provide them first.
127- Do not assume capabilities beyond this skill's declared scope when the user requests external operations or inferences.
128- Do not proceed without user confirmation when overwriting existing results, executing high-cost batch operations, or expanding task scope.
129
130## Required Inputs
131
132| Field | Required | Format/Source | Example | If Missing |
133|---|---|---|---|---|
134| User task description | Yes | Text | Research question, writing goal, analysis objective | Stop and ask user to provide |
135| Primary input material | Depends on task | Text, file path, ID, table, or literature | PMID, PDF, CSV, DOCX, keywords, etc. | Specify which material type is missing |
136| Output preference | No | Text | Language, format, target journal, template | Use skill default format |
137
138## Output Contract
139
140- Primary output: Structured result or target file aligned with this skill's objective.
141- Optional output: Intermediate check notes, issue list, supplementary suggestions, or generated file paths.
142- Format requirement: Unless the user specifies otherwise, prefer stable, reviewable Markdown or JSON; if the skill's bundled script requires a fixed format, use that format.
143- If partially complete: Must explicitly mark as PARTIAL and state which steps are completed and which remain.
144
145## Failure Handling
146
147- Missing critical input: Explicitly state which fields, files, or identifiers are missing and pause.
148- Script, template, or resource execution failure: Report the failing step, likely cause, and recovery suggestions — do not silently degrade.
149- Partial completion only: Return the verified portion first, then list remaining blockers and suggested next steps.
150
151## User Checkpoints
152
153- Before executing batch processing, overwriting files, long-running searches, or multi-stage generation, confirm scope and output format with the user.
154- Before proceeding when a key judgment is ambiguous, evidence is insufficient, or the workflow is entering the next stage, confirm with the user.
155
156
157## Input Validation
158
159This skill accepts requests that match the documented purpose of `protocol-standardization` and include enough context to complete the workflow safely.
160
161Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:
162
163> `protocol-standardization` only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.
164
165## Quick Validation
166
167- Check that key scripts, templates, or reference file paths this skill depends on exist.
168- Check that the final output contains the core fields, sections, or files specified for this task.
169- Check that results clearly mark assumptions, limitations, and incomplete items.
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