Sync template from atomicqms-style deployment

.gitea/workflows/atomicai.yml

@@ -0,0 +1,78 @@
+name: AtomicAI Animal Facility 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 Animal Facility 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 Animal Research Facility Quality Management.
+
+            ## Your Expertise
+            - IACUC (Institutional Animal Care and Use Committee) protocols
+            - AAALAC International accreditation standards
+            - USDA Animal Welfare Act and regulations
+            - PHS Policy on Humane Care and Use of Laboratory Animals
+            - Animal housing and husbandry standards
+            - Veterinary care and monitoring protocols
+            - Pain and distress assessment and management
+            - Euthanasia methods and documentation
+            - Occupational health and safety for animal workers
+            - Breeding colony management
+            - Quarantine and biosecurity procedures
+
+            ## Document Creation Guidelines
+            - Place Animal Care SOPs in SOPs/Animal-Care/
+            - Place Veterinary Protocols in Protocols/Veterinary/
+            - Place IACUC Forms in Forms/IACUC/
+            - Place Training Records in Forms/Training/
+            - Place Safety SOPs in SOPs/Safety/
+            - Place Policies in Policies/
+
+            ## Numbering Convention
+            - SOP-AC-XXX for Animal Care SOPs
+            - SOP-VET-XXX for Veterinary SOPs
+            - SOP-BIO-XXX for Biosecurity SOPs
+            - PRO-XXX for Protocols
+            - POL-XXX for Policies
+            - FRM-XXX for Forms
+
+            Always create branches and submit changes as Pull Requests for review.
+            Prioritize animal welfare, regulatory compliance, and scientific validity.
+          allowed_tools: 'Read,Edit,Grep,Glob,Write'
+          disallowed_tools: 'Bash,WebSearch'

Forms/FRM-001-Document-Change-Request.md

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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*

Forms/FRM-003-CAPA-Form.md

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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*

Forms/FRM-006-Audit-Checklist.md

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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*

Forms/Health-Records/FRM-VET-001-Daily-Health-Check.md

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+# Daily Animal Health Check
+
+| Form ID | FRM-VET-001 | Revision | 1.0 |
+|---------|-------------|----------|-----|
+
+---
+
+## Room/Area Information
+
+| Field | Entry |
+|-------|-------|
+| Room Number | |
+| Species | |
+| Date | |
+| Observer Name | |
+| Observer Initials | |
+
+## Health Observation Checklist
+
+For each cage/pen, check off normal observations. Circle and note any abnormalities.
+
+### General Colony Status
+
+- [ ] All animals present and accounted for
+- [ ] No mortalities observed
+- [ ] HVAC functioning (temp/humidity in range)
+- [ ] Lighting on appropriate cycle
+- [ ] No unusual odors
+
+### Individual Cage Assessment
+
+| Cage # | Animals OK | Food OK | Water OK | Abnormalities Noted |
+|--------|------------|---------|----------|---------------------|
+| | ☐ | ☐ | ☐ | |
+| | ☐ | ☐ | ☐ | |
+| | ☐ | ☐ | ☐ | |
+| | ☐ | ☐ | ☐ | |
+| | ☐ | ☐ | ☐ | |
+| | ☐ | ☐ | ☐ | |
+| | ☐ | ☐ | ☐ | |
+| | ☐ | ☐ | ☐ | |
+
+## Abnormality Details
+
+If any abnormalities noted above, provide details:
+
+### Animal 1
+| Field | Entry |
+|-------|-------|
+| Cage # | |
+| Animal ID | |
+| Protocol # | |
+| PI Name | |
+| Clinical Signs Observed | |
+| Action Taken | |
+| Vet Notified? | ☐ Yes ☐ No |
+| Vet Name/Time | |
+
+### Animal 2
+| Field | Entry |
+|-------|-------|
+| Cage # | |
+| Animal ID | |
+| Protocol # | |
+| PI Name | |
+| Clinical Signs Observed | |
+| Action Taken | |
+| Vet Notified? | ☐ Yes ☐ No |
+| Vet Name/Time | |
+
+## Clinical Signs Reference
+
+Check all that apply for abnormal animals:
+
+**Appearance**
+- [ ] Rough/unkempt coat
+- [ ] Hunched posture
+- [ ] Piloerection
+- [ ] Lethargy
+- [ ] Weight loss visible
+
+**Respiratory**
+- [ ] Labored breathing
+- [ ] Nasal discharge
+- [ ] Open-mouth breathing
+
+**GI/Elimination**
+- [ ] Diarrhea
+- [ ] Blood in stool
+- [ ] Bloated abdomen
+
+**Neurological**
+- [ ] Circling
+- [ ] Head tilt
+- [ ] Seizures
+- [ ] Ataxia
+
+**Other**
+- [ ] Wounds/lesions
+- [ ] Eye abnormalities
+- [ ] Tumor growth
+- [ ] Other: _______________
+
+## Environmental Observations
+
+| Parameter | Reading | Normal Range | OK? |
+|-----------|---------|--------------|-----|
+| Temperature | °F/°C | Species-specific | ☐ |
+| Humidity | % | 30-70% | ☐ |
+| Light Cycle | :00 - :00 | Per protocol | ☐ |
+
+Environmental concerns noted:
+
+_______________________________________________
+
+## Completion Verification
+
+| Field | Entry |
+|-------|-------|
+| All cages checked? | ☐ Yes |
+| All abnormalities documented? | ☐ Yes ☐ N/A |
+| Vet notified of concerns? | ☐ Yes ☐ N/A |
+| Observer Signature | |
+| Time Completed | |
+
+## Supervisor Review (if abnormalities noted)
+
+| Field | Entry |
+|-------|-------|
+| Reviewed By | |
+| Date | |
+| Comments | |
+
+---
+
+*Form FRM-VET-001 Rev 1.0 - Daily Animal Health Check*

Forms/Training/FRM-004-Training-Record.md

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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*

Policies/POL-001-Quality-Policy.md

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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] |

README.md

@@ -1,3 +1,134 @@
-# animal-facility
+# Animal Research Facility Quality Management System
 
 A comprehensive QMS template designed for animal research facilities, vivaria, and laboratory animal care programs supporting biomedical research.
+
+## 🐭 Designed For
+
+- **Academic Vivaria** - University and medical center animal facilities
+- **Pharmaceutical Research** - Drug discovery and preclinical testing facilities
+- **Contract Research Organizations (CROs)** - Animal study service providers
+- **Biotechnology Companies** - Research and development animal programs
+- **Government Research Facilities** - NIH, CDC, and agency research programs
+- **Veterinary Schools** - Teaching and research animal programs
+- **Breeding Colonies** - Specialized genetic model production facilities
+
+## 📋 Regulatory Framework
+
+This template supports compliance with:
+
+- **PHS Policy** - Public Health Service Policy on Humane Care and Use of Laboratory Animals
+- **USDA/AWA** - Animal Welfare Act and Regulations (9 CFR Parts 1-4)
+- **AAALAC** - Association for Assessment and Accreditation of Laboratory Animal Care International
+- **IACUC** - Institutional Animal Care and Use Committee requirements
+- **Guide for the Care and Use of Laboratory Animals** (8th Edition)
+- **AVMA Guidelines** - Euthanasia and veterinary care standards
+- **OLAW** - Office of Laboratory Animal Welfare requirements
+- **GLP** - Good Laboratory Practice for regulated studies (21 CFR Part 58)
+- **OSHA** - Occupational safety for animal handlers
+- **CDC/NIH BMBL** - Biosafety in Microbiological and Biomedical Laboratories
+
+## Repository Structure
+
+```
+├── SOPs/
+│   ├── Animal-Care/           # Daily care, feeding, environmental enrichment
+│   ├── Veterinary-Services/   # Health monitoring, treatments, euthanasia
+│   ├── Colony-Management/     # Breeding, genetics, census tracking
+│   ├── Facility-Operations/   # Sanitation, cage wash, environmental controls
+│   ├── Safety/                # Zoonosis, allergens, occupational health
+│   └── General/               # Document control, training, CAPA
+├── Forms/
+│   ├── IACUC-Protocols/       # Protocol submission and amendment forms
+│   ├── Health-Records/        # Veterinary treatment and observation logs
+│   ├── Census-Tracking/       # Animal inventory and disposition records
+│   ├── Environmental/         # Temperature, humidity, light cycle logs
+│   ├── Training/              # Competency assessments, certifications
+│   └── Incident-Reports/      # Adverse events, protocol deviations
+├── Policies/                  # Institutional policies and IACUC guidelines
+├── Work-Instructions/         # Step-by-step procedures
+└── Templates/                 # Document templates
+```
+
+## Document Numbering Convention
+
+- **POL-XXX**: Policies
+- **SOP-AC-XXX**: Animal Care SOPs
+- **SOP-VET-XXX**: Veterinary Services SOPs
+- **SOP-COL-XXX**: Colony Management SOPs
+- **SOP-FAC-XXX**: Facility Operations SOPs
+- **SOP-SAF-XXX**: Safety SOPs
+- **WI-XXX**: Work Instructions
+- **FRM-XXX**: Forms and Records
+- **PRO-XXX**: IACUC Protocol Templates
+
+## 🤖 AI-Powered Assistance
+
+This repository includes **AtomicAI**, your animal facility QMS assistant. Mention `@atomicai` in any issue or pull request to:
+
+- Draft species-specific SOPs for animal care and handling
+- Create IACUC protocol templates and amendments
+- Generate veterinary treatment and monitoring procedures
+- Develop environmental enrichment programs
+- Create biosafety and occupational health procedures
+- Review documents for regulatory compliance
+
+### Example Prompts
+
+- "@atomicai create an SOP for rodent health monitoring per the Guide"
+- "@atomicai draft a post-operative care procedure for surgical models"
+- "@atomicai write an environmental enrichment policy for NHPs"
+- "@atomicai create an IACUC annual review checklist"
+- "@atomicai develop a quarantine procedure for incoming animals"
+- "@atomicai create a controlled substance log for veterinary use"
+
+## Getting Started
+
+1. **Review IACUC Requirements** - Align policies with your institutional IACUC
+2. **Customize Species SOPs** - Adapt procedures for your animal models
+3. **Set Up Health Monitoring** - Configure veterinary observation forms
+4. **Establish Environmental Controls** - Implement monitoring logs
+5. **Train Personnel** - Use competency assessment forms
+
+## Key Documents to Create First
+
+1. **Animal Health Monitoring SOP** - Foundation for veterinary oversight
+2. **Euthanasia Policy** - AVMA-compliant methods by species
+3. **Environmental Enrichment Program** - Species-specific enrichment plans
+4. **IACUC Protocol Template** - Standardized protocol submission format
+5. **Post-Procedure Monitoring Form** - Observation and scoring records
+6. **Occupational Health Program** - Staff safety and zoonosis prevention
+7. **Sanitation and Cage Wash SOP** - Facility hygiene procedures
+
+## Special Considerations for Animal Research
+
+### Species-Specific Requirements
+- Housing density and cage dimensions
+- Environmental parameters (temp, humidity, lighting)
+- Dietary requirements and feeding schedules
+- Social housing and compatibility
+- Enrichment appropriate to natural behaviors
+
+### Veterinary Care
+- Regular health monitoring schedules
+- Pain and distress assessment scales
+- Anesthesia and analgesia protocols
+- Humane endpoints and euthanasia criteria
+- Emergency veterinary coverage
+
+### Regulatory Compliance
+- IACUC protocol approval and amendments
+- Annual protocol reviews and renewals
+- Semi-annual facility inspections
+- USDA annual reports (covered species)
+- Personnel training documentation
+
+### Biosafety and Occupational Health
+- Zoonotic disease prevention
+- Allergen exposure monitoring
+- Personal protective equipment
+- Hazardous agent handling (if applicable)
+- Medical surveillance program
+
+---
+
+*This template is maintained by AtomicQMS. For questions, open an issue in this repository.*

SOPs/General/SOP-001-Document-Control.md

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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] |

SOPs/General/SOP-002-CAPA.md

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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] |

SOPs/General/SOP-003-Training.md

@@ -0,0 +1,123 @@
+# 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] |

SOPs/General/SOP-004-Internal-Audit.md

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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] |

SOPs/General/SOP-005-Management-Review.md

@@ -0,0 +1,114 @@
+# 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] |

SOPs/Safety/.gitkeep

@@ -0,0 +1 @@
+# Placeholder

SOPs/Veterinary-Services/SOP-VET-001-Health-Monitoring.md

@@ -0,0 +1,157 @@
+# Standard Operating Procedure: Animal Health Monitoring
+
+| Document ID | SOP-VET-001 |
+|-------------|-------------|
+| Title | Daily and Weekly Animal Health Monitoring |
+| Revision | 1.0 |
+| Effective Date | [DATE] |
+| Author | [AUTHOR] |
+| Approved By | [APPROVER] |
+| Department | Veterinary Services |
+
+---
+
+## 1. Purpose
+
+To establish standardized procedures for monitoring the health and welfare of laboratory animals in accordance with the Guide for the Care and Use of Laboratory Animals and IACUC requirements.
+
+## 2. Scope
+
+This procedure applies to all laboratory animals housed in the facility, including:
+- Rodents (mice, rats, hamsters, guinea pigs)
+- Rabbits
+- Large animals (as applicable)
+- All other species maintained under approved protocols
+
+## 3. Responsibilities
+
+### 3.1 Animal Care Staff
+- Perform daily health observations
+- Document abnormal findings
+- Report concerns to veterinary staff immediately
+
+### 3.2 Veterinary Technician
+- Conduct weekly detailed health assessments
+- Provide treatments as directed
+- Maintain health records
+
+### 3.3 Attending Veterinarian
+- Review health reports
+- Prescribe treatments
+- Make euthanasia decisions when necessary
+- Report to IACUC as required
+
+## 4. Definitions
+
+| Term | Definition |
+|------|------------|
+| BCS | Body Condition Score - assessment of nutritional status |
+| Clinical Sign | Observable indication of disease or abnormality |
+| Humane Endpoint | Predetermined point at which animal is euthanized to prevent suffering |
+
+## 5. Equipment and Materials
+
+- Health observation forms
+- Weighing scale (appropriate for species)
+- Flashlight for cage inspection
+- PPE (gloves, gown, mask as required)
+- Body condition score reference charts
+
+## 6. Procedure
+
+### 6.1 Daily Health Observations
+
+Performed by animal care staff during routine husbandry:
+
+1. **General Appearance**
+   - [ ] Coat condition (smooth, groomed, no lesions)
+   - [ ] Posture (normal stance, no hunching)
+   - [ ] Activity level (appropriate for species/time of day)
+   - [ ] Respiration (no labored breathing)
+
+2. **Food and Water**
+   - [ ] Food consumption (evidence of eating)
+   - [ ] Water consumption (bottle/sipper functioning)
+   - [ ] No evidence of dehydration
+
+3. **Cage Environment**
+   - [ ] Normal fecal output
+   - [ ] No evidence of diarrhea
+   - [ ] No blood in cage
+   - [ ] Bedding condition adequate
+
+4. **Documentation**
+   - Record any abnormalities on Daily Health Check form
+   - Notify veterinary staff of concerns immediately
+   - Do not wait until end of shift for urgent findings
+
+### 6.2 Weekly Health Assessments
+
+Performed by veterinary technician:
+
+1. **Individual Animal Examination**
+   - Body weight (compare to baseline)
+   - Body condition score (1-5 scale)
+   - Eyes, ears, nose examination
+   - Skin and coat assessment
+   - Palpation as appropriate
+
+2. **Colony Health Review**
+   - Mortality/morbidity trends
+   - Sentinel animal results (if applicable)
+   - Environmental monitoring review
+   - Protocol-specific assessments
+
+### 6.3 Body Condition Scoring
+
+| Score | Description | Action |
+|-------|-------------|--------|
+| 1 | Emaciated - Bones prominent | Immediate vet consult |
+| 2 | Underconditioned | Increase monitoring, consider intervention |
+| 3 | Well-conditioned (ideal) | Continue routine care |
+| 4 | Overconditioned | Dietary review |
+| 5 | Obese | Dietary intervention required |
+
+### 6.4 Clinical Signs Requiring Immediate Veterinary Notification
+
+- Respiratory distress
+- Severe lethargy or non-responsiveness
+- Bleeding or open wounds
+- Seizures
+- Prolapsed organs
+- Severe weight loss (>20% of baseline)
+- Tumor burden exceeding protocol limits
+- Signs of pain not controlled by protocol analgesia
+
+### 6.5 Humane Endpoint Assessment
+
+When clinical signs indicate potential endpoint:
+
+1. Assess against protocol-specific humane endpoints
+2. Calculate combined clinical score if applicable
+3. Consult veterinarian immediately
+4. Document assessment and decision
+5. Proceed with euthanasia if criteria met
+
+## 7. Documentation
+
+All health observations must be documented:
+- **Daily observations**: FRM-VET-001 Daily Health Check
+- **Weekly assessments**: FRM-VET-002 Weekly Health Assessment
+- **Abnormal findings**: FRM-VET-003 Veterinary Treatment Record
+- **Euthanasia**: FRM-VET-004 Euthanasia Record
+
+## 8. References
+
+- Guide for the Care and Use of Laboratory Animals (8th Edition)
+- AVMA Guidelines for the Euthanasia of Animals
+- Institutional IACUC policies
+- Species-specific husbandry guides
+
+---
+
+## Revision History
+
+| Rev | Date | Description | Author |
+|-----|------|-------------|--------|
+| 1.0 | [DATE] | Initial release | [AUTHOR] |

Templates/SOP-Template.md

@@ -0,0 +1,62 @@
+# 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] |

Work Instructions/WI-001-Template.md

@@ -0,0 +1,68 @@
+# 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] |