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name: AtomicAI Biobank Repository Assistant
on:
issue_comment:
types: [created]
issues:
types: [opened, assigned]
pull_request:
types: [opened, synchronize, assigned]
pull_request_review_comment:
types: [created]
jobs:
claude-assistant:
runs-on: ubuntu-latest
if: |
github.actor != 'atomicqms-service' &&
(
(github.event_name == 'issue_comment' && contains(github.event.comment.body, '@atomicai') && github.event.comment.user.login != 'atomicqms-service') ||
(github.event_name == 'issues' && github.event.action == 'opened' && contains(github.event.issue.body, '@atomicai')) ||
(github.event_name == 'pull_request' && github.event.action == 'opened' && contains(github.event.pull_request.body, '@atomicai')) ||
(github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@atomicai') && github.event.comment.user.login != 'atomicqms-service') ||
(github.event.action == 'assigned' && github.event.assignee.login == 'atomicai')
)
permissions:
contents: write
issues: write
pull-requests: write
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- name: Run AtomicAI Biobank Repository Assistant
uses: https://beta.atomicqms.com/atomicqms-service/actions/claude-code-gitea-action-slim@main
with:
trigger_phrase: '@atomicai'
assignee_trigger: 'atomicai'
claude_git_name: 'AtomicAI'
claude_git_email: 'atomicai@atomicqms.local'
custom_instructions: |
You are AtomicAI, an AI assistant specialized in Biobank and Tissue Repository Quality Management.
## Your Expertise
- CAP Biorepository Accreditation Program
- ISBER (International Society for Biological and Environmental Repositories) best practices
- NCI Best Practices for Biospecimen Resources
- Specimen collection and processing protocols
- Cryopreservation and storage procedures
- Sample tracking and chain of custody
- Informed consent for biobanking
- De-identification and privacy protection
- Quality metrics and specimen integrity
- Equipment monitoring (freezers, LN2)
- Disaster recovery and sample protection
- Material transfer agreements
## Document Creation Guidelines
- Place Collection SOPs in SOPs/Collection/
- Place Processing SOPs in SOPs/Processing/
- Place Storage SOPs in SOPs/Storage/
- Place Consent Forms in Forms/Consent/
- Place Request Forms in Forms/Requests/
- Place Policies in Policies/
## Numbering Convention
- SOP-COL-XXX for Collection SOPs
- SOP-PRC-XXX for Processing SOPs
- SOP-STR-XXX for Storage SOPs
- SOP-QC-XXX for Quality Control SOPs
- POL-XXX for Policies
- FRM-XXX for Forms
Always create branches and submit changes as Pull Requests for review.
Prioritize specimen quality, donor privacy, and scientific utility.
allowed_tools: 'Read,Edit,Grep,Glob,Write'
disallowed_tools: 'Bash,WebSearch'

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# Chain of Custody Form
| Form ID | FRM-BIO-002 | Revision | 1.0 |
|---------|-------------|----------|-----|
---
## Specimen Information
| Field | Entry |
|-------|-------|
| Specimen ID(s) | |
| Number of Containers | |
| Specimen Type | ☐ Blood ☐ Serum ☐ Plasma ☐ Tissue ☐ DNA ☐ RNA ☐ Cells ☐ FFPE ☐ Other: _______ |
| Protocol/Study ID | |
| Subject/Donor ID | |
| Collection Date | |
| Collection Time | |
| Collected By | |
---
## Required Storage Conditions
| Condition | Check |
|-----------|-------|
| ☐ Ambient (15-25°C) | |
| ☐ Refrigerated (2-8°C) | |
| ☐ Frozen (-20°C) | |
| ☐ Ultra-low (-80°C) | |
| ☐ Liquid Nitrogen (-196°C) | |
| ☐ Other: _______ | |
**Special Handling Instructions:**
---
## Chain of Custody Log
### Transfer 1
| Field | Entry |
|-------|-------|
| Released By | |
| Title/Role | |
| Date | |
| Time | |
| Signature | |
| Location Transferred From | |
| Storage Condition at Release | |
| Received By | |
| Title/Role | |
| Date | |
| Time | |
| Signature | |
| Location Transferred To | |
| Condition on Receipt | ☐ Acceptable ☐ Compromised |
| Notes | |
### Transfer 2
| Field | Entry |
|-------|-------|
| Released By | |
| Title/Role | |
| Date | |
| Time | |
| Signature | |
| Location Transferred From | |
| Storage Condition at Release | |
| Received By | |
| Title/Role | |
| Date | |
| Time | |
| Signature | |
| Location Transferred To | |
| Condition on Receipt | ☐ Acceptable ☐ Compromised |
| Notes | |
### Transfer 3
| Field | Entry |
|-------|-------|
| Released By | |
| Title/Role | |
| Date | |
| Time | |
| Signature | |
| Location Transferred From | |
| Storage Condition at Release | |
| Received By | |
| Title/Role | |
| Date | |
| Time | |
| Signature | |
| Location Transferred To | |
| Condition on Receipt | ☐ Acceptable ☐ Compromised |
| Notes | |
### Transfer 4
| Field | Entry |
|-------|-------|
| Released By | |
| Title/Role | |
| Date | |
| Time | |
| Signature | |
| Location Transferred From | |
| Storage Condition at Release | |
| Received By | |
| Title/Role | |
| Date | |
| Time | |
| Signature | |
| Location Transferred To | |
| Condition on Receipt | ☐ Acceptable ☐ Compromised |
| Notes | |
---
## Temperature Monitoring (for transport)
| Time Point | Temperature | Within Range? | Initials |
|------------|-------------|---------------|----------|
| Departure | °C | ☐ Yes ☐ No | |
| Checkpoint 1 | °C | ☐ Yes ☐ No | |
| Checkpoint 2 | °C | ☐ Yes ☐ No | |
| Arrival | °C | ☐ Yes ☐ No | |
**Temperature Monitor ID/Lot:**
---
## Shipping Information (if applicable)
| Field | Entry |
|-------|-------|
| Carrier | |
| Tracking Number | |
| Ship Date | |
| Expected Arrival | |
| Actual Arrival | |
| Package Condition | ☐ Intact ☐ Damaged (describe below) |
| Temperature Indicator Status | ☐ Within range ☐ Exceeded (describe below) |
Condition/Temperature Notes:
---
## Deviation Documentation
| Field | Entry |
|-------|-------|
| Was specimen condition compromised? | ☐ Yes ☐ No |
| If yes, describe deviation: | |
| Temperature excursion? | ☐ Yes ☐ No |
| If yes, duration: | |
| If yes, max/min temp: | |
| Action taken: | |
| Deviation Report #: | |
| Specimen disposition: | ☐ Accepted ☐ Quarantined ☐ Rejected |
---
## Final Disposition
| Field | Entry |
|-------|-------|
| Final Storage Location | |
| Freezer/Tank ID | |
| Rack/Box Position | |
| Date/Time Stored | |
| Stored By | |
| LIMS Entry Completed? | ☐ Yes |
| LIMS Accession # | |
---
## Verification
| Field | Entry |
|-------|-------|
| Chain of custody complete? | ☐ Yes |
| All transfers documented? | ☐ Yes |
| Temperature maintained? | ☐ Yes ☐ No (deviation documented) |
| Final reviewer signature | |
| Date | |
---
*Form FRM-BIO-002 Rev 1.0 - Chain of Custody Form*

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# Specimen Collection Log
| Form ID | FRM-BIO-001 | Revision | 1.0 |
|---------|-------------|----------|-----|
---
## Collection Session Information
| Field | Entry |
|-------|-------|
| Collection Date | |
| Collector Name | |
| Collector ID | |
| Collection Site/Location | |
| Protocol/Study ID | |
| Batch Number | |
---
## Specimen Collection Record
### Specimen 1
| Field | Entry |
|-------|-------|
| Specimen ID (Barcode) | |
| Subject/Donor ID | |
| Consent Verified? | ☐ Yes |
| Verification Method | ☐ Wristband ☐ Verbal ☐ Photo ID ☐ Other: _______ |
| Specimen Type | ☐ Blood ☐ Tissue ☐ Urine ☐ CSF ☐ Other: _______ |
| Collection Container | |
| Collection Time | : (24hr) |
| Volume/Quantity | |
| Collection Site (anatomical) | |
| Ischemia Time (if tissue) | Warm: ___ min Cold: ___ min |
| Specimen Appearance | ☐ Normal ☐ Hemolyzed ☐ Lipemic ☐ Icteric ☐ Other: _______ |
| Notes/Deviations | |
### Specimen 2
| Field | Entry |
|-------|-------|
| Specimen ID (Barcode) | |
| Subject/Donor ID | |
| Consent Verified? | ☐ Yes |
| Verification Method | ☐ Wristband ☐ Verbal ☐ Photo ID ☐ Other: _______ |
| Specimen Type | ☐ Blood ☐ Tissue ☐ Urine ☐ CSF ☐ Other: _______ |
| Collection Container | |
| Collection Time | : (24hr) |
| Volume/Quantity | |
| Collection Site (anatomical) | |
| Ischemia Time (if tissue) | Warm: ___ min Cold: ___ min |
| Specimen Appearance | ☐ Normal ☐ Hemolyzed ☐ Lipemic ☐ Icteric ☐ Other: _______ |
| Notes/Deviations | |
### Specimen 3
| Field | Entry |
|-------|-------|
| Specimen ID (Barcode) | |
| Subject/Donor ID | |
| Consent Verified? | ☐ Yes |
| Verification Method | ☐ Wristband ☐ Verbal ☐ Photo ID ☐ Other: _______ |
| Specimen Type | ☐ Blood ☐ Tissue ☐ Urine ☐ CSF ☐ Other: _______ |
| Collection Container | |
| Collection Time | : (24hr) |
| Volume/Quantity | |
| Collection Site (anatomical) | |
| Ischemia Time (if tissue) | Warm: ___ min Cold: ___ min |
| Specimen Appearance | ☐ Normal ☐ Hemolyzed ☐ Lipemic ☐ Icteric ☐ Other: _______ |
| Notes/Deviations | |
### Specimen 4
| Field | Entry |
|-------|-------|
| Specimen ID (Barcode) | |
| Subject/Donor ID | |
| Consent Verified? | ☐ Yes |
| Verification Method | ☐ Wristband ☐ Verbal ☐ Photo ID ☐ Other: _______ |
| Specimen Type | ☐ Blood ☐ Tissue ☐ Urine ☐ CSF ☐ Other: _______ |
| Collection Container | |
| Collection Time | : (24hr) |
| Volume/Quantity | |
| Collection Site (anatomical) | |
| Ischemia Time (if tissue) | Warm: ___ min Cold: ___ min |
| Specimen Appearance | ☐ Normal ☐ Hemolyzed ☐ Lipemic ☐ Icteric ☐ Other: _______ |
| Notes/Deviations | |
---
## Processing Summary
| Field | Entry |
|-------|-------|
| Total Specimens Collected | |
| Specimens with Deviations | |
| Processing Start Time | : (24hr) |
| Processing End Time | : (24hr) |
| Processed By | |
## Aliquot Summary (if applicable)
| Specimen ID | # Aliquots | Volume Each | Storage Location | Temp |
|-------------|------------|-------------|------------------|------|
| | | | | |
| | | | | |
| | | | | |
| | | | | |
---
## Transfer Information
| Field | Entry |
|-------|-------|
| Transferred To | |
| Transfer Time | : (24hr) |
| Transport Condition | ☐ Ambient ☐ 4°C ☐ Frozen ☐ LN2 |
| Received By | |
| Receipt Time | : (24hr) |
| Condition on Receipt | ☐ Acceptable ☐ Compromised (describe below) |
Notes on condition:
---
## Verification
| Field | Entry |
|-------|-------|
| All specimens labeled correctly? | ☐ Yes |
| All documentation complete? | ☐ Yes |
| Any deviations reported? | ☐ Yes ☐ No ☐ N/A |
| Deviation Report # (if applicable) | |
### Collector Signature
| Field | Entry |
|-------|-------|
| Signature | |
| Date | |
| Time | |
### Supervisor Review (if deviations noted)
| Field | Entry |
|-------|-------|
| Reviewed By | |
| Date | |
| Comments | |
---
*Form FRM-BIO-001 Rev 1.0 - Specimen Collection Log*

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# Document Change Request Form
| Form ID | FRM-001 | Revision | 1.0 |
|---------|---------|----------|-----|
---
## Section 1: Request Information
| Field | Entry |
|-------|-------|
| Request Date | |
| Requested By | |
| Department | |
## Section 2: Document Information
| Field | Entry |
|-------|-------|
| Document Number | |
| Document Title | |
| Current Revision | |
## Section 3: Change Description
### Type of Change
- [ ] New Document
- [ ] Revision to Existing Document
- [ ] Document Obsolescence
### Description of Change
*(Describe the proposed change in detail)*
### Reason for Change
*(Explain why this change is needed)*
## Section 4: Impact Assessment
### Affected Areas
- [ ] Training Required
- [ ] Other Documents Affected
- [ ] Process Changes Required
- [ ] Validation Impact
### List Affected Documents
## Section 5: Approvals
| Role | Name | Signature | Date |
|------|------|-----------|------|
| Requester | | | |
| Document Owner | | | |
| Quality Assurance | | | |
---
*Form FRM-001 Rev 1.0*

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# Corrective and Preventive Action (CAPA) Form
| Form ID | FRM-003 | Revision | 1.0 |
|---------|---------|----------|-----|
---
## Section 1: CAPA Identification
| Field | Entry |
|-------|-------|
| CAPA Number | |
| Date Initiated | |
| Initiated By | |
| CAPA Owner | |
| Target Closure Date | |
## Section 2: Classification
### Type
- [ ] Corrective Action
- [ ] Preventive Action
### Source
- [ ] Customer Complaint
- [ ] Internal Audit
- [ ] External Audit
- [ ] Process Deviation
- [ ] Nonconforming Product
- [ ] Management Review
- [ ] Other: ____________
### Priority
- [ ] Critical (5 business days)
- [ ] Major (15 business days)
- [ ] Minor (30 business days)
## Section 3: Problem Description
*(Describe the nonconformity or potential nonconformity)*
## Section 4: Immediate Containment
*(Actions taken to contain the immediate impact)*
## Section 5: Root Cause Investigation
### Investigation Method Used
- [ ] 5 Whys
- [ ] Fishbone Diagram
- [ ] Fault Tree Analysis
- [ ] Other: ____________
### Root Cause Determination
## Section 6: Corrective/Preventive Actions
| Action | Responsible | Due Date | Status |
|--------|-------------|----------|--------|
| | | | |
| | | | |
| | | | |
## Section 7: Effectiveness Verification
| Criteria | Method | Result |
|----------|--------|--------|
| | | |
Verification Date: ____________
Verified By: ____________
## Section 8: Closure
| Role | Name | Signature | Date |
|------|------|-----------|------|
| CAPA Owner | | | |
| Quality Approval | | | |
---
*Form FRM-003 Rev 1.0*

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# Internal Audit Checklist
| Form ID | FRM-006 | Revision | 1.0 |
|---------|---------|----------|-----|
---
## Audit Information
| Field | Entry |
|-------|-------|
| Audit Number | |
| Audit Date | |
| Area/Process Audited | |
| Lead Auditor | |
| Auditee(s) | |
---
## Checklist Items
| # | Requirement/Question | Reference | C/NC/NA | Evidence/Notes |
|---|---------------------|-----------|---------|----------------|
| 1 | Are current versions of applicable procedures available? | SOP-001 | | |
| 2 | Are personnel trained on applicable procedures? | SOP-003 | | |
| 3 | Are training records current and complete? | SOP-003 | | |
| 4 | Are records properly maintained and retrievable? | SOP-001 | | |
| 5 | Are nonconformities being documented and addressed? | SOP-002 | | |
| 6 | Are CAPAs being completed on time? | SOP-002 | | |
| 7 | Is equipment calibrated and maintained? | | | |
| 8 | Are process controls being followed? | | | |
| 9 | Are quality objectives being monitored? | | | |
| 10 | | | | |
**Legend:** C = Conforming, NC = Nonconforming, NA = Not Applicable
---
## Findings Summary
| Finding # | Type | Description | Clause Reference |
|-----------|------|-------------|------------------|
| | | | |
| | | | |
---
## Auditor Signature
| Auditor | Signature | Date |
|---------|-----------|------|
| | | |
---
*Form FRM-006 Rev 1.0*

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# Training Record Form
| Form ID | FRM-004 | Revision | 1.0 |
|---------|---------|----------|-----|
---
## Section 1: Employee Information
| Field | Entry |
|-------|-------|
| Employee Name | |
| Employee ID | |
| Department | |
| Job Title | |
## Section 2: Training Information
| Field | Entry |
|-------|-------|
| Training Title | |
| Training Date | |
| Training Duration | |
| Trainer Name | |
| Trainer Qualification | |
### Training Type
- [ ] Initial Training
- [ ] Retraining
- [ ] Refresher
- [ ] Procedure Update
### Delivery Method
- [ ] Classroom
- [ ] On-the-Job
- [ ] Self-Study
- [ ] Computer-Based
- [ ] Other: ____________
## Section 3: Training Content
*(List topics covered or attach training materials)*
## Section 4: Assessment
### Assessment Method
- [ ] Written Test
- [ ] Practical Demonstration
- [ ] Verbal Assessment
- [ ] Observation
### Assessment Results
| Metric | Result |
|--------|--------|
| Score (if applicable) | |
| Pass/Fail | |
## Section 5: Signatures
| Role | Name | Signature | Date |
|------|------|-----------|------|
| Trainee | | | |
| Trainer | | | |
| Supervisor | | | |
---
*Form FRM-004 Rev 1.0*

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# Quality Policy
| Document ID | POL-001 |
|-------------|---------|
| Title | Quality Policy |
| Revision | 1.0 |
| Effective Date | [DATE] |
| Author | [AUTHOR] |
| Approved By | [APPROVER] |
---
## 1. Policy Statement
[ORGANIZATION NAME] is committed to providing products and services that consistently meet customer requirements and applicable regulatory requirements. We strive for continual improvement of our Quality Management System to enhance customer satisfaction.
## 2. Quality Objectives
Our organization commits to:
1. **Customer Focus**: Understanding and meeting customer needs and expectations
2. **Regulatory Compliance**: Maintaining compliance with all applicable regulations and standards
3. **Continuous Improvement**: Continually improving the effectiveness of our QMS
4. **Employee Engagement**: Ensuring all employees understand their role in quality
5. **Risk-Based Thinking**: Identifying and addressing risks and opportunities
## 3. Management Commitment
Top management demonstrates commitment to the QMS by:
- Ensuring the quality policy is appropriate to the organization's purpose
- Ensuring quality objectives are established and compatible with strategic direction
- Ensuring integration of QMS requirements into business processes
- Promoting the use of the process approach and risk-based thinking
- Ensuring resources needed for the QMS are available
- Communicating the importance of effective quality management
- Ensuring the QMS achieves its intended results
- Engaging, directing, and supporting persons to contribute to QMS effectiveness
## 4. Scope
This policy applies to all employees, contractors, and processes within the scope of our Quality Management System.
## 5. Communication
This policy shall be:
- Communicated and understood within the organization
- Available to relevant interested parties as appropriate
- Reviewed for continuing suitability
---
## Revision History
| Rev | Date | Description | Author |
|-----|------|-------------|--------|
| 1.0 | [DATE] | Initial release | [AUTHOR] |

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# biobank-repository # Biobank & Specimen Repository Quality Management System
A comprehensive QMS template designed for biobanks, tissue repositories, and specimen management programs supporting clinical care and research. A comprehensive QMS template designed for biobanks, tissue repositories, and specimen management programs supporting clinical care and research.
## 🧬 Designed For
- **Hospital Biobanks** - Clinical specimen repositories
- **Research Biorepositories** - Academic and institutional collections
- **Tissue Banks** - Organ and tissue preservation programs
- **Cord Blood Banks** - Umbilical cord blood storage facilities
- **Cancer Tissue Banks** - Oncology specimen collections
- **Population Biobanks** - Large-scale epidemiological collections
- **Commercial Biorepositories** - Fee-for-service specimen storage
## 📋 Regulatory Framework
This template supports compliance with:
- **ISBER** - International Society for Biological and Environmental Repositories Best Practices
- **CAP BAP** - College of American Pathologists Biorepository Accreditation Program
- **FDA 21 CFR Part 1271** - Human Cells, Tissues, and Cellular and Tissue-Based Products
- **CLIA** - Clinical Laboratory Improvement Amendments (if clinical testing)
- **HIPAA** - Health Insurance Portability and Accountability Act
- **Common Rule (45 CFR 46)** - Human subjects research protections
- **GDPR** - General Data Protection Regulation (EU specimens)
- **NCI Best Practices** - National Cancer Institute biospecimen guidelines
- **OSHA** - Occupational safety for specimen handling
- **DOT/IATA** - Specimen shipping and transport regulations
## Repository Structure
```
├── SOPs/
│ ├── Specimen-Collection/ # Procurement, consent, collection procedures
│ ├── Processing/ # Aliquoting, preservation, extraction
│ ├── Storage/ # Freezer management, LN2 handling, inventory
│ ├── Distribution/ # Request handling, shipping, chain of custody
│ ├── Quality-Control/ # QC testing, temperature monitoring, audits
│ └── General/ # Document control, training, CAPA
├── Forms/
│ ├── Consent-Forms/ # Informed consent templates
│ ├── Collection-Records/ # Specimen accessioning logs
│ ├── Storage-Logs/ # Temperature and inventory records
│ ├── Distribution/ # Material transfer agreements, shipping logs
│ ├── QC-Records/ # Quality control test results
│ └── Training/ # Competency assessments
├── Policies/ # Institutional policies and governance
├── Work-Instructions/ # Step-by-step procedures
└── Templates/ # Document templates
```
## Document Numbering Convention
- **POL-XXX**: Policies
- **SOP-COL-XXX**: Collection SOPs
- **SOP-PRC-XXX**: Processing SOPs
- **SOP-STR-XXX**: Storage SOPs
- **SOP-DST-XXX**: Distribution SOPs
- **SOP-QC-XXX**: Quality Control SOPs
- **WI-XXX**: Work Instructions
- **FRM-XXX**: Forms and Records
- **MTA-XXX**: Material Transfer Agreements
## 🤖 AI-Powered Assistance
This repository includes **AtomicAI**, your biobank QMS assistant. Mention `@atomicai` in any issue or pull request to:
- Draft specimen collection and processing SOPs
- Create informed consent templates for biobanking
- Generate freezer management and monitoring procedures
- Develop quality control testing protocols
- Create material transfer agreements
- Review documents for ISBER/CAP compliance
### Example Prompts
- "@atomicai create an SOP for FFPE tissue block processing"
- "@atomicai draft a biobank informed consent template"
- "@atomicai write a -80°C freezer failure response procedure"
- "@atomicai create a specimen request and distribution workflow"
- "@atomicai develop a DNA extraction quality control SOP"
- "@atomicai create a liquid nitrogen safety procedure"
## Getting Started
1. **Establish Governance** - Define biobank policies and oversight structure
2. **Customize Consent Forms** - Adapt for your specimen types and uses
3. **Set Up Inventory System** - Configure specimen tracking forms
4. **Implement QC Program** - Establish quality metrics and testing
5. **Train Personnel** - Use competency assessment forms
## Key Documents to Create First
1. **Specimen Accessioning SOP** - Foundation for sample intake
2. **Informed Consent Template** - IRB-approved consent language
3. **Freezer Temperature Monitoring SOP** - Critical for sample integrity
4. **Aliquoting and Processing SOP** - Standardized sample handling
5. **Material Transfer Agreement** - Template for specimen sharing
6. **Chain of Custody Form** - Sample tracking documentation
7. **Emergency Freezer Failure Response** - Critical contingency plan
## Special Considerations for Biobanking
### Specimen Types
- Blood and blood components (serum, plasma, buffy coat)
- Tissue (fresh, frozen, FFPE)
- DNA/RNA extracts
- Cell lines and primary cultures
- Body fluids (urine, CSF, saliva)
- Derivatives (protein lysates, slides)
### Storage Requirements
- Ultra-low temperature (-80°C) maintenance
- Liquid nitrogen (-196°C) handling and safety
- Refrigerated storage (2-8°C)
- Room temperature controls
- Backup power and alarm systems
### Quality and Integrity
- Pre-analytical variable documentation
- Ischemia time tracking
- Freeze-thaw cycle monitoring
- Sample quality metrics (RIN, DIN, etc.)
- Long-term stability testing
### Ethical and Legal
- Informed consent management
- Participant withdrawal procedures
- Data privacy and de-identification
- Access governance and oversight
- Commercial use considerations
---
*This template is maintained by AtomicQMS. For questions, open an issue in this repository.*

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# Standard Operating Procedure: Document Control
| Document ID | SOP-001 |
|-------------|---------|
| Title | Document Control |
| Revision | 1.0 |
| Effective Date | [DATE] |
| Author | [AUTHOR] |
| Approved By | [APPROVER] |
| Department | Quality Assurance |
---
## 1. Purpose
To establish a procedure for the creation, review, approval, distribution, and control of documents within the Quality Management System.
## 2. Scope
This procedure applies to all controlled documents including:
- Policies
- Standard Operating Procedures (SOPs)
- Work Instructions
- Forms and Templates
- Specifications
- External documents of external origin
## 3. Responsibilities
### 3.1 Document Owner
- Responsible for document content and accuracy
- Initiates document creation and revision
- Ensures periodic review is performed
### 3.2 Quality Assurance
- Maintains the document control system
- Assigns document numbers
- Manages document distribution
- Archives obsolete documents
### 3.3 Approvers
- Review and approve documents before release
- Ensure documents are adequate for intended purpose
## 4. Procedure
### 4.1 Document Creation
1. Identify the need for a new document
2. Request document number from Quality Assurance
3. Draft document using appropriate template
4. Include all required header information
5. Submit for review and approval
### 4.2 Document Review and Approval
1. Route document to appropriate reviewers
2. Reviewers provide comments within 5 business days
3. Author addresses all comments
4. Final approval by designated approver
5. Quality Assurance releases document
### 4.3 Document Numbering
Documents shall be numbered according to the following convention:
| Type | Prefix | Example |
|------|--------|---------|
| Policy | POL | POL-001 |
| SOP | SOP | SOP-001 |
| Work Instruction | WI | WI-001 |
| Form | FRM | FRM-001 |
### 4.4 Revision Control
1. All changes require documented justification
2. Changes follow same review/approval process as new documents
3. Revision number increments with each approved change
4. Revision history maintained in document footer
### 4.5 Document Distribution
1. Current versions available in document control system
2. Obsolete versions marked and archived
3. Training on new/revised documents as needed
### 4.6 Periodic Review
1. Documents reviewed at least every 2 years
2. Review documented even if no changes made
3. Reviews may result in revision or reaffirmation
## 5. Related Documents
- FRM-001 Document Change Request Form
- FRM-002 Document Review Record
## 6. Definitions
| Term | Definition |
|------|------------|
| Controlled Document | Document managed under document control system |
| Obsolete | Document no longer valid for use |
| Revision | Updated version of a document |
---
## Revision History
| Rev | Date | Description | Author |
|-----|------|-------------|--------|
| 1.0 | [DATE] | Initial release | [AUTHOR] |

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# Standard Operating Procedure: Corrective and Preventive Action (CAPA)
| Document ID | SOP-002 |
|-------------|---------|
| Title | Corrective and Preventive Action |
| Revision | 1.0 |
| Effective Date | [DATE] |
| Author | [AUTHOR] |
| Approved By | [APPROVER] |
| Department | Quality Assurance |
---
## 1. Purpose
To establish a systematic process for identifying, investigating, correcting, and preventing nonconformities and potential nonconformities.
## 2. Scope
This procedure applies to:
- Product and process nonconformities
- Customer complaints
- Audit findings
- Process deviations
- Potential nonconformities identified through risk analysis
## 3. Definitions
| Term | Definition |
|------|------------|
| Corrective Action | Action to eliminate the cause of a detected nonconformity |
| Preventive Action | Action to eliminate the cause of a potential nonconformity |
| Root Cause | Fundamental reason for a nonconformity |
| Effectiveness Check | Verification that implemented actions achieved desired results |
## 4. Responsibilities
### 4.1 CAPA Owner
- Investigates the issue
- Identifies root cause
- Develops and implements corrective/preventive actions
- Verifies effectiveness
### 4.2 Quality Assurance
- Manages CAPA system
- Assigns CAPA numbers
- Tracks CAPA status
- Reviews and approves CAPAs
- Reports CAPA metrics to management
### 4.3 Management
- Provides resources for CAPA implementation
- Reviews CAPA trends
- Ensures timely closure
## 5. Procedure
### 5.1 CAPA Initiation
1. Identify nonconformity or potential nonconformity
2. Document issue on CAPA Form (FRM-003)
3. Classify severity and priority
4. Assign CAPA owner
### 5.2 Investigation
1. Gather relevant data and evidence
2. Interview personnel involved
3. Review related documents and records
4. Use appropriate investigation tools:
- 5 Whys
- Fishbone Diagram
- Failure Mode Analysis
### 5.3 Root Cause Analysis
1. Identify potential root causes
2. Verify root cause through evidence
3. Document root cause determination
4. Consider systemic implications
### 5.4 Action Development
1. Develop corrective/preventive actions
2. Assign responsibilities and due dates
3. Assess actions for:
- Appropriateness to problem severity
- Impact on other processes
- Resource requirements
### 5.5 Implementation
1. Execute approved actions
2. Document implementation evidence
3. Update affected documents/processes
4. Provide training as needed
### 5.6 Effectiveness Verification
1. Define effectiveness criteria
2. Allow sufficient time for actions to take effect
3. Collect and analyze data
4. Document verification results
5. If ineffective, reopen CAPA for further action
### 5.7 Closure
1. Review all CAPA documentation
2. Verify all actions completed
3. Confirm effectiveness verified
4. Obtain approval for closure
## 6. CAPA Metrics
Quality Assurance shall track and report:
- Number of open CAPAs
- CAPA aging
- On-time closure rate
- Effectiveness rate
- CAPAs by category/source
## 7. Related Documents
- FRM-003 CAPA Form
- SOP-003 Nonconforming Product Control
- SOP-004 Customer Complaints
---
## Revision History
| Rev | Date | Description | Author |
|-----|------|-------------|--------|
| 1.0 | [DATE] | Initial release | [AUTHOR] |

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# Standard Operating Procedure: Training and Competence
| Document ID | SOP-003 |
|-------------|---------|
| Title | Training and Competence |
| Revision | 1.0 |
| Effective Date | [DATE] |
| Author | [AUTHOR] |
| Approved By | [APPROVER] |
| Department | Human Resources / Quality |
---
## 1. Purpose
To ensure personnel performing work affecting product quality are competent based on appropriate education, training, skills, and experience.
## 2. Scope
This procedure applies to:
- All employees performing quality-affecting activities
- Contractors and temporary personnel
- Personnel requiring GxP training
## 3. Responsibilities
### 3.1 Supervisors/Managers
- Identify training needs for their personnel
- Ensure training is completed before performing tasks
- Evaluate competence of personnel
- Maintain department training records
### 3.2 Human Resources
- Coordinate training programs
- Maintain central training database
- Track training compliance
- Archive training records
### 3.3 Quality Assurance
- Develop QMS-related training
- Approve training curricula for GxP activities
- Audit training compliance
### 3.4 Employees
- Complete assigned training on time
- Maintain current qualifications
- Report training needs to supervisor
## 4. Procedure
### 4.1 Training Needs Assessment
1. Identify competence requirements for each role
2. Document requirements in job descriptions
3. Assess current competence of personnel
4. Identify training gaps
### 4.2 Training Curriculum Development
1. Define learning objectives
2. Develop training materials
3. Identify delivery method:
- Classroom
- On-the-job
- Self-study
- Computer-based
4. Define assessment criteria
5. Obtain approval from Quality (for GxP training)
### 4.3 Training Delivery
1. Schedule training session
2. Document attendance
3. Deliver training per curriculum
4. Assess comprehension through:
- Written test (minimum 80% passing)
- Practical demonstration
- Supervisor observation
### 4.4 Training Documentation
Training records shall include:
- Employee name and ID
- Training title and date
- Trainer name and qualifications
- Assessment results
- Signatures
### 4.5 Retraining Requirements
Retraining is required when:
- Significant document revisions occur
- Performance deficiencies identified
- Extended absence from job function
- Periodic requalification due
### 4.6 New Employee Orientation
All new employees shall complete:
1. Company orientation
2. Quality system overview
3. Job-specific training
4. SOP read and understand for applicable procedures
## 5. Training Records Retention
- Training records maintained for duration of employment
- Records retained 3 years after employee departure
- Records available for regulatory inspection
## 6. Related Documents
- FRM-004 Training Record Form
- FRM-005 Training Assessment Form
- Job Descriptions
---
## Revision History
| Rev | Date | Description | Author |
|-----|------|-------------|--------|
| 1.0 | [DATE] | Initial release | [AUTHOR] |

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# Standard Operating Procedure: Internal Audit
| Document ID | SOP-004 |
|-------------|---------|
| Title | Internal Audit |
| Revision | 1.0 |
| Effective Date | [DATE] |
| Author | [AUTHOR] |
| Approved By | [APPROVER] |
| Department | Quality Assurance |
---
## 1. Purpose
To establish a systematic approach for conducting internal audits to verify the effectiveness of the Quality Management System.
## 2. Scope
This procedure covers:
- QMS process audits
- Compliance audits
- Product audits
- System audits
## 3. Definitions
| Term | Definition |
|------|------------|
| Audit | Systematic, independent examination to determine conformance |
| Auditor | Person qualified to perform audits |
| Finding | Observation of conformance or nonconformance |
| Observation | Noted item not rising to level of finding |
## 4. Responsibilities
### 4.1 Lead Auditor
- Plans and schedules audits
- Prepares audit checklists
- Conducts audit activities
- Reports audit findings
### 4.2 Quality Manager
- Maintains audit program
- Qualifies auditors
- Reviews audit reports
- Reports to management
### 4.3 Auditee
- Provides access to areas/records
- Responds to findings
- Implements corrective actions
## 5. Procedure
### 5.1 Annual Audit Schedule
1. Develop annual audit schedule considering:
- Previous audit results
- Process criticality
- Regulatory requirements
- Changes to processes
2. Ensure all QMS processes audited at least annually
3. Obtain management approval
4. Communicate schedule to affected areas
### 5.2 Auditor Qualification
Auditors shall:
- Complete auditor training course
- Conduct at least 2 audits under supervision
- Be independent of area being audited
- Maintain competence through ongoing audits
### 5.3 Audit Preparation
1. Review applicable procedures and standards
2. Review previous audit reports
3. Prepare audit checklist
4. Notify auditee of audit scope and schedule
5. Confirm auditor availability
### 5.4 Conducting the Audit
1. Hold opening meeting with auditee
2. Execute audit checklist
3. Gather objective evidence:
- Document review
- Personnel interviews
- Process observation
4. Document findings with evidence
5. Classify findings:
- Major Nonconformance
- Minor Nonconformance
- Observation
6. Hold closing meeting
### 5.5 Audit Reporting
1. Complete audit report within 5 business days
2. Report shall include:
- Audit scope and criteria
- Personnel interviewed
- Findings with evidence
- Recommendations
3. Distribute report to auditee and management
### 5.6 Finding Resolution
1. Auditee responds with corrective action plan within 10 business days
2. Quality reviews and approves plan
3. Auditee implements corrective actions
4. Auditor verifies effectiveness
5. Close finding upon verification
## 6. Audit Records
Maintain for 5 years:
- Audit schedules
- Checklists
- Reports
- Corrective action records
## 7. Related Documents
- FRM-006 Audit Checklist Template
- FRM-007 Audit Report Template
- SOP-002 CAPA
---
## Revision History
| Rev | Date | Description | Author |
|-----|------|-------------|--------|
| 1.0 | [DATE] | Initial release | [AUTHOR] |

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# Standard Operating Procedure: Management Review
| Document ID | SOP-005 |
|-------------|---------|
| Title | Management Review |
| Revision | 1.0 |
| Effective Date | [DATE] |
| Author | [AUTHOR] |
| Approved By | [APPROVER] |
| Department | Quality Assurance |
---
## 1. Purpose
To ensure top management reviews the Quality Management System at planned intervals to ensure its continuing suitability, adequacy, and effectiveness.
## 2. Scope
This procedure applies to the periodic management review of the QMS, including all processes and quality objectives.
## 3. Frequency
Management reviews shall be conducted:
- At least annually
- More frequently if significant changes occur
- As needed based on quality performance
## 4. Responsibilities
### 4.1 Quality Manager
- Prepares management review agenda and materials
- Facilitates the meeting
- Documents meeting minutes and action items
- Tracks completion of action items
### 4.2 Top Management
- Attends management review meetings
- Reviews QMS performance data
- Makes decisions on QMS improvements
- Allocates resources as needed
### 4.3 Department Managers
- Provides input data for their areas
- Attends management review
- Implements assigned action items
## 5. Management Review Inputs
The following shall be considered:
### 5.1 Actions from Previous Reviews
- Status of action items
- Effectiveness of implemented actions
### 5.2 Changes in Context
- Internal changes (organization, resources)
- External changes (regulations, market)
### 5.3 QMS Performance
- Customer satisfaction and feedback
- Quality objectives achievement
- Process performance metrics
- Nonconformities and corrective actions
- Audit results
- Supplier performance
### 5.4 Resource Adequacy
- Personnel
- Infrastructure
- Work environment
### 5.5 Risk and Opportunities
- Risk assessment results
- Effectiveness of risk controls
- New opportunities identified
### 5.6 Improvement Opportunities
- Process improvements
- Product improvements
- QMS enhancements
## 6. Management Review Outputs
Decisions and actions related to:
- Improvement of QMS and processes
- Product improvement
- Resource needs
- Changes to quality policy or objectives
## 7. Documentation
### 7.1 Meeting Minutes
- Date and attendees
- Items discussed
- Decisions made
- Action items with owners and due dates
### 7.2 Record Retention
- Management review records retained for 5 years
- Available for regulatory inspection
## 8. Related Documents
- FRM-008 Management Review Agenda Template
- FRM-009 Management Review Minutes Template
---
## Revision History
| Rev | Date | Description | Author |
|-----|------|-------------|--------|
| 1.0 | [DATE] | Initial release | [AUTHOR] |

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# Standard Operating Procedure: Biological Specimen Collection
| Document ID | SOP-BIO-001 |
|-------------|-------------|
| Title | Biological Specimen Collection Procedure |
| Revision | 1.0 |
| Effective Date | [DATE] |
| Author | [AUTHOR] |
| Approved By | [APPROVER] |
| Department | Biobank Operations |
---
## 1. Purpose
To establish standardized procedures for the collection, labeling, and initial processing of biological specimens to ensure sample integrity, proper chain of custody, and compliance with regulatory requirements.
## 2. Scope
This procedure applies to the collection of all biological specimens including:
- Blood and blood components
- Tissue samples (fresh and fixed)
- Body fluids (CSF, urine, synovial fluid)
- DNA/RNA samples
- Cell lines and derivatives
- FFPE blocks and slides
## 3. Responsibilities
### 3.1 Collection Personnel
- Follow aseptic technique during collection
- Complete all required labeling and documentation
- Ensure proper specimen handling post-collection
### 3.2 Biobank Coordinator
- Train collection personnel
- Verify specimen quality upon receipt
- Maintain collection supply inventory
### 3.3 Quality Manager
- Review collection metrics
- Investigate collection deviations
- Approve collection protocols
## 4. Definitions
| Term | Definition |
|------|------------|
| Aliquot | A portion of a specimen separated for individual storage/testing |
| Chain of Custody | Documented history of specimen handling and transfers |
| Cryopreservation | Preservation of specimens at ultra-low temperatures |
| FFPE | Formalin-Fixed Paraffin-Embedded tissue |
## 5. Equipment and Materials
- Collection tubes (type depends on specimen)
- Sterile containers and cryovials
- Labels (barcode and human-readable)
- Collection kits per specimen type
- PPE (gloves, gown, eye protection)
- Temperature monitoring devices
- Biohazard bags and containers
## 6. Procedure
### 6.1 Pre-Collection Preparation
1. **Verify Consent Status**
- Confirm informed consent on file
- Verify consent covers intended specimen use
- Document consent verification
2. **Prepare Collection Materials**
- Select appropriate collection containers
- Pre-label containers with unique identifiers
- Verify label accuracy against order
- Prepare shipping/transport supplies if needed
3. **Verify Patient/Donor Identity**
- Use two patient identifiers
- Compare against order/consent
- Document verification method
### 6.2 Specimen Collection
#### 6.2.1 Blood Collection
| Tube Type | Additive | Uses | Special Handling |
|-----------|----------|------|------------------|
| Red top | None (clot) | Serum | Allow to clot 30-60 min |
| Lavender | EDTA | Plasma, CBC, DNA | Invert 8-10 times |
| Green | Heparin | Plasma | Invert 8-10 times |
| Blue | Citrate | Coagulation | Fill to line, invert |
| Yellow | ACD | Cell preservation | Invert 8-10 times |
1. Apply tourniquet (maximum 1 minute)
2. Clean venipuncture site with 70% alcohol
3. Perform venipuncture using appropriate needle gauge
4. Fill tubes in correct order of draw
5. Invert tubes as specified per type
6. Label tubes immediately at bedside
#### 6.2.2 Tissue Collection
1. Receive tissue from surgical/procedure site
2. Document time of removal from body
3. Process according to protocol requirements:
- **Fresh**: Place in appropriate medium immediately
- **Frozen**: Snap-freeze in liquid nitrogen or place in -80°C within 30 minutes
- **Fixed**: Place in 10% neutral buffered formalin (10:1 ratio)
4. Record ischemia time (warm and cold)
#### 6.2.3 Body Fluid Collection
1. Use sterile technique throughout
2. Collect into appropriate sterile container
3. Record volume collected
4. Transport to lab immediately or process per protocol
### 6.3 Specimen Labeling
**Required Label Information:**
- [ ] Unique specimen identifier (barcode)
- [ ] Patient/donor identifier
- [ ] Collection date and time
- [ ] Specimen type
- [ ] Collector initials
**Labeling Requirements:**
- Label at point of collection
- Use approved labels only
- Never pre-label containers with patient info before collection
- Verify label against patient ID band
### 6.4 Initial Processing
1. **Time-Critical Processing**
- Process within stability window for specimen type
- Document processing time
- Note any delays and reason
2. **Centrifugation (if required)**
| Specimen | Speed | Time | Temperature |
|----------|-------|------|-------------|
| Serum | 1500-2000 x g | 10-15 min | Room temp |
| Plasma (EDTA) | 1500-2000 x g | 10-15 min | 4°C preferred |
| Plasma (citrate) | 2500 x g | 15 min | Room temp |
3. **Aliquoting**
- Use sterile technique
- Aliquot into pre-labeled cryovials
- Record number and volume of aliquots
- Avoid multiple freeze-thaw cycles
### 6.5 Storage and Transport
1. **Immediate Storage**
| Specimen Type | Storage Condition | Maximum Duration |
|---------------|-------------------|------------------|
| Fresh tissue | 4°C | 24 hours |
| Fixed tissue | Room temp in formalin | 72 hours |
| Frozen specimens | -80°C or LN2 | Long-term |
| Blood tubes | Per tube type | See stability chart |
2. **Transport Requirements**
- Use validated shipping containers
- Include temperature monitors
- Complete chain of custody documentation
- Verify receiving facility readiness
## 7. Quality Control
### 7.1 Collection Quality Metrics
| Metric | Target | Frequency |
|--------|--------|-----------|
| Hemolysis rate | <2% | Monthly |
| Labeling errors | 0 | Continuous |
| Ischemia time compliance | >95% | Monthly |
| Consent verification | 100% | Continuous |
### 7.2 Deviation Handling
- Document any deviation from SOP
- Report to Biobank Coordinator immediately
- Complete FRM-BIO-003 Deviation Report
- Quarantine affected specimens pending review
## 8. Documentation
Required documentation for each collection:
- FRM-BIO-001 Specimen Collection Log
- FRM-BIO-002 Chain of Custody Form
- Consent verification record
- Any deviation reports
## 9. Safety Considerations
- Treat all specimens as potentially infectious
- Use appropriate PPE for specimen type
- Dispose of sharps in approved containers
- Follow exposure control procedures
- Report all exposures immediately
## 10. References
- ISBER Best Practices for Repositories (4th Edition)
- CAP Biorepository Accreditation Checklist
- NCI Best Practices for Biospecimen Resources
- Institutional IRB policies
---
## Revision History
| Rev | Date | Description | Author |
|-----|------|-------------|--------|
| 1.0 | [DATE] | Initial release | [AUTHOR] |

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# Standard Operating Procedure: [Title]
| Document ID | SOP-XXX |
|-------------|---------|
| Title | [Title] |
| Revision | 1.0 |
| Effective Date | [DATE] |
| Author | [AUTHOR] |
| Approved By | [APPROVER] |
| Department | [DEPARTMENT] |
---
## 1. Purpose
[State the purpose of this procedure]
## 2. Scope
[Define the scope and applicability]
## 3. Responsibilities
### 3.1 [Role 1]
- [Responsibility]
- [Responsibility]
### 3.2 [Role 2]
- [Responsibility]
- [Responsibility]
## 4. Definitions
| Term | Definition |
|------|------------|
| | |
## 5. Procedure
### 5.1 [Section Title]
[Procedure steps]
### 5.2 [Section Title]
[Procedure steps]
## 6. Related Documents
- [List related procedures, forms, etc.]
## 7. References
- [External standards, regulations, etc.]
---
## Revision History
| Rev | Date | Description | Author |
|-----|------|-------------|--------|
| 1.0 | [DATE] | Initial release | [AUTHOR] |

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# Work Instruction: [Title]
| Document ID | WI-001 |
|-------------|--------|
| Title | [Title] |
| Revision | 1.0 |
| Effective Date | [DATE] |
| Author | [AUTHOR] |
| Approved By | [APPROVER] |
| Department | [DEPARTMENT] |
---
## 1. Purpose
[Describe the purpose of this work instruction]
## 2. Scope
[Define what activities this instruction covers]
## 3. Safety Precautions
- [List any safety requirements]
- [Personal protective equipment needed]
- [Hazards to be aware of]
## 4. Equipment/Materials Required
| Item | Specification |
|------|---------------|
| | |
| | |
## 5. Procedure
### Step 1: [Title]
[Detailed instructions]
### Step 2: [Title]
[Detailed instructions]
### Step 3: [Title]
[Detailed instructions]
## 6. Acceptance Criteria
[Define what constitutes successful completion]
## 7. Records
| Record | Location | Retention |
|--------|----------|-----------|
| | | |
## 8. References
- [Related SOPs]
- [Specifications]
- [Standards]
---
## Revision History
| Rev | Date | Description | Author |
|-----|------|-------------|--------|
| 1.0 | [DATE] | Initial release | [AUTHOR] |