Sync template from atomicqms-style deployment

.gitea/workflows/atomicai.yml

@@ -0,0 +1,81 @@
+name: AtomicAI Laboratory Science 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 Laboratory Science 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 Laboratory Science Quality Management.
+            
+            ## Your Expertise
+            - Good Laboratory Practice (GLP) principles
+            - OSHA Laboratory Standard (29 CFR 1910.1450)
+            - Chemical, biological, and radiation safety protocols
+            - Equipment calibration and maintenance procedures
+            - Sample handling, storage, and chain of custody
+            - Laboratory data management and FAIR principles
+            - NIH Guidelines for Research
+            - Institutional Biosafety Committee (IBC) requirements
+            
+            ## Document Creation Guidelines
+            - Place Equipment SOPs in SOPs/Equipment/
+            - Place Sample Handling SOPs in SOPs/Sample-Handling/
+            - Place Safety SOPs in SOPs/Safety/
+            - Place Data Management SOPs in SOPs/Data-Management/
+            - Place General SOPs in SOPs/General/
+            - Place Equipment logs in Forms/Equipment-Logs/
+            - Place Training records in Forms/Training/
+            - Place Inventory tracking in Forms/Inventory/
+            - Place Work Instructions in Work-Instructions/
+            
+            ## Numbering Convention
+            - POL-XXX for Policies
+            - SOP-EQ-XXX for Equipment SOPs
+            - SOP-SH-XXX for Sample Handling SOPs
+            - SOP-SAF-XXX for Safety SOPs
+            - SOP-DM-XXX for Data Management SOPs
+            - SOP-GEN-XXX for General SOPs
+            - WI-XXX for Work Instructions
+            - FRM-XXX for Forms
+            - LOG-XXX for Equipment & Maintenance Logs
+            
+            Always create branches and submit changes as Pull Requests for review.
+            Include regulatory references (GLP, OSHA, NIH) where applicable.
+          allowed_tools: 'Read,Edit,Grep,Glob,Write'
+          disallowed_tools: 'Bash,WebSearch'

README.md

@@ -1,3 +1,75 @@
-# laboratory-science-template
+# Laboratory Science Quality Management System
 
-This repository contains template documents for implementing a Quality Management System (QMS) specifically designed for **Basic Science and Research Laboratories**.
+This repository contains template documents for implementing a Quality Management System (QMS) specifically designed for **Basic Science and Research Laboratories**.
+
+## 🔬 Designed For
+
+- Academic Research Laboratories
+- University Core Facilities
+- Biomedical Research Labs
+- Chemistry & Biochemistry Labs
+- Molecular Biology Labs
+- Cell Culture Facilities
+- Microscopy & Imaging Centers
+- Proteomics/Genomics Core Labs
+
+## Repository Structure
+
+```
+laboratory-science-template/
+├── Policies/                  # Lab policies and safety commitment
+├── SOPs/                      # Standard Operating Procedures
+│   ├── Equipment/             # Instrument operation & maintenance
+│   ├── Sample-Handling/       # Sample receipt, storage, processing
+│   ├── Safety/                # Chemical, biological, radiation safety
+│   ├── Data-Management/       # Lab notebooks, data backup, FAIR principles
+│   └── General/               # General lab operations
+├── Work Instructions/         # Detailed protocols
+├── Forms/                     # Record forms and templates
+│   ├── Equipment-Logs/        # Maintenance & calibration logs
+│   ├── Training/              # Training records
+│   └── Inventory/             # Reagent & supply tracking
+└── Templates/                 # Document templates
+```
+
+## Document Numbering Convention
+
+- **POL-XXX**: Policies
+- **SOP-EQ-XXX**: Equipment SOPs
+- **SOP-SH-XXX**: Sample Handling SOPs
+- **SOP-SAF-XXX**: Safety SOPs
+- **SOP-DM-XXX**: Data Management SOPs
+- **SOP-GEN-XXX**: General SOPs
+- **WI-XXX**: Work Instructions / Protocols
+- **FRM-XXX**: Forms and Records
+- **LOG-XXX**: Equipment & Maintenance Logs
+
+## 🤖 AI-Powered Document Creation
+
+This template includes **AtomicAI** integration. Create an issue and mention `@atomicai` to:
+- Generate new SOPs for equipment or procedures
+- Create safety protocols (chemical, biological, radiation)
+- Draft training documentation
+- Develop data management plans
+- Create equipment maintenance schedules
+
+## Getting Started
+
+1. Create a new repository using this template
+2. Customize documents with your lab's information
+3. Create issues with `@atomicai` to generate new documents
+4. Review and approve AI-generated content via Pull Requests
+
+## Compliance & Best Practices
+
+These templates support compliance with:
+- **Good Laboratory Practice (GLP)** principles
+- **OSHA** Laboratory Standard (29 CFR 1910.1450)
+- **NIH Guidelines** for Research
+- **Institutional Biosafety** (IBC) requirements
+- **IACUC** protocols (animal research)
+- **FAIR Data Principles** (Findable, Accessible, Interoperable, Reusable)
+- **Research Data Management** best practices
+
+---
+*Powered by AtomicQMS - AI-Enhanced Laboratory Quality Management*