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Add standard repository documentation and templates
Add comprehensive documentation to complete GitHub repository setup: - CONTRIBUTING.md: Detailed contribution guidelines with development workflow, coding standards, testing guidelines, and pull request process - CODE_OF_CONDUCT.md: Community guidelines based on Contributor Covenant with scientific integrity and clinical responsibility standards - SECURITY.md: Security policy covering vulnerability reporting, medical device considerations, data privacy (HIPAA/GDPR), and compliance - CONTRIBUTORS.md: Contributor recognition with attribution guidelines, acknowledgment of scientific foundations, and contribution types - .github/ISSUE_TEMPLATE/: Four issue templates for structured reporting * bug_report.md: Comprehensive bug reporting template * feature_request.md: Feature request with scientific justification * documentation.md: Documentation improvement template * question.md: Question template with resource checklist * config.yml: Links to discussions and security reporting - .github/PULL_REQUEST_TEMPLATE.md: Comprehensive PR template with testing, validation, documentation, and quality checklists These standard files improve community engagement, establish clear contribution processes, and provide proper attribution for the scientific work underlying this cardiovascular modeling platform.
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‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: Bug Report
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about: Report a bug or unexpected behavior
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title: '[BUG] '
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labels: 'bug'
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assignees: ''
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---
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## Bug Description
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A clear and concise description of what the bug is.
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## To Reproduce
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Steps to reproduce the behavior:
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1. Go to '...'
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2. Run command '...'
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3. Use parameters '...'
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4. See error
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## Expected Behavior
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A clear and concise description of what you expected to happen.
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## Actual Behavior
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A clear and concise description of what actually happened.
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## Error Messages
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```
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Paste any error messages, stack traces, or relevant output here
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```
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## Environment
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**System Information:**
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- OS: [e.g., Ubuntu 22.04, macOS 14.0, Windows 11]
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- Python Version: [e.g., 3.10.5]
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- NumPy Version: [e.g., 1.24.0]
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- Git Commit/Branch: [e.g., main, commit abc123]
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**Optional (if relevant):**
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- D Compiler Version: [e.g., ldc2 1.35.0]
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- Hardware: [if using Primal Logic Processor or QUANT]
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## Code Sample
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```python
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# Minimal code sample that reproduces the issue
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from src.cardiac import VanDerPolOscillator
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model = VanDerPolOscillator()
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# ... rest of the code
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```
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## Screenshots
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If applicable, add screenshots or plots to help explain the problem.
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## Additional Context
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Add any other context about the problem here:
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- Does this happen consistently or intermittently?
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- Did this work in a previous version?
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- Any relevant configuration files or parameters?
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- Related issues or pull requests?
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## Possible Solution
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If you have ideas on how to fix the bug, please describe them here.
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## Checklist
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- [ ] I have searched existing issues to avoid duplicates
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- [ ] I am using the latest version of the code
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- [ ] I have included all relevant information above
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- [ ] I have provided a minimal code sample to reproduce the issue
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- [ ] I have included error messages and stack traces

‎.github/ISSUE_TEMPLATE/config.yml‎

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blank_issues_enabled: true
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contact_links:
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- name: GitHub Discussions
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url: https://github.com/STLNFTART/Multi-Heart-Model/discussions
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about: For general questions, ideas, and community discussions
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- name: Documentation
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url: https://github.com/STLNFTART/Multi-Heart-Model/tree/main/docs
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about: Comprehensive technical documentation and guides
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- name: Security Vulnerability
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url: https://github.com/STLNFTART/Multi-Heart-Model/security/advisories
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about: Report security vulnerabilities privately

‎.github/ISSUE_TEMPLATE/documentation.md‎

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---
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name: Documentation Improvement
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about: Suggest improvements to documentation, tutorials, or examples
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title: '[DOCS] '
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labels: 'documentation'
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assignees: ''
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---
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## Documentation Issue
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**What documentation needs improvement?**
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- [ ] README.md
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- [ ] API documentation (docstrings)
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- [ ] Technical documentation (docs/)
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- [ ] Tutorial or example
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- [ ] Jupyter notebook
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- [ ] CLAUDE.md (developer guide)
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- [ ] Other: _______________
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**Specific file(s) or section(s):**
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- File: `path/to/file.md`
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- Section: "Section Name"
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- Line numbers (if applicable): Lines 123-145
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## Problem Description
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**What is unclear, missing, or incorrect?**
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A clear and concise description of the documentation issue.
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**Current documentation:**
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```markdown
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# Quote or describe the current documentation
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Current text or state...
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```
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**What's wrong with it:**
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- Information is missing
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- Explanation is unclear
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- Example doesn't work
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- Information is outdated
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- Contains errors
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- Other: _______________
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## Suggested Improvement
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**What should the documentation say instead?**
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```markdown
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# Proposed improved version
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Your suggested documentation text...
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```
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**Why is this better?**
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Explain how your suggestion improves the documentation.
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## Context
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**Who would benefit from this improvement?**
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- [ ] New users getting started
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- [ ] Developers contributing code
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- [ ] Researchers using the models
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- [ ] Clinical educators
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- [ ] Students
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- [ ] Other: _______________
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**What were you trying to do when you noticed this issue?**
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Describe the task or question that led you to notice the documentation problem.
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## Examples or References
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**Are there good examples elsewhere?**
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- Similar documentation from other projects
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- Relevant tutorials or guides
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- Scientific papers that could be referenced
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- Useful diagrams or visualizations
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**Links or references:**
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- [Example 1](URL)
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- [Example 2](URL)
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## Scope
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**What needs to be updated?**
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- [ ] One file/section only
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- [ ] Multiple related files
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- [ ] Tutorial/example code
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- [ ] API docstrings
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- [ ] All of the above
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**Estimated scope:**
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- [ ] Quick fix (typo, clarification)
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- [ ] Medium update (rewrite section)
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- [ ] Major update (new tutorial, significant rewrite)
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## Additional Context
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**Screenshots, diagrams, or mockups:**
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If applicable, add visual aids to help explain the issue or solution.
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**Related issues or PRs:**
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- #123
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- #456
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## Willingness to Contribute
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- [ ] I can submit a pull request to fix this
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- [ ] I can provide feedback on proposed changes
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- [ ] I am reporting the issue but cannot contribute the fix
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## Checklist
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- [ ] I have identified the specific documentation that needs improvement
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- [ ] I have described what's wrong and why it's a problem
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- [ ] I have suggested a concrete improvement
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- [ ] I have explained who would benefit from this change
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- [ ] I have checked for related documentation issues

‎.github/ISSUE_TEMPLATE/feature_request.md‎

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---
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name: Feature Request
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about: Suggest a new feature or enhancement
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title: '[FEATURE] '
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labels: 'enhancement'
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assignees: ''
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---
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## Feature Description
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A clear and concise description of the feature you'd like to see.
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## Motivation
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**What problem does this feature solve?**
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Describe the use case or problem this feature would address.
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**Why is this important?**
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Explain why this feature would be valuable to the project and its users.
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## Proposed Solution
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**How would this feature work?**
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Describe your proposed implementation or approach.
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```python
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# Example code showing how the feature might be used
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from src.new_module import NewFeature
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feature = NewFeature(param1=value1)
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result = feature.compute()
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```
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## Alternative Solutions
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**Have you considered any alternative approaches?**
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Describe any alternative solutions or features you've considered.
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## Use Cases
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**Who would benefit from this feature?**
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- [ ] Clinical educators
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- [ ] Researchers
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- [ ] Hardware integrators
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- [ ] Medical device developers
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- [ ] Students
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- [ ] Other (please specify)
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**Example scenarios where this feature would be useful:**
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1. Scenario 1...
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2. Scenario 2...
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3. Scenario 3...
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## Scientific Justification
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**Literature Support (if applicable):**
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- Does this feature have support in the scientific literature?
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- Are there existing implementations in other software?
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- What are the validation requirements?
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**References:**
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- Author et al. (Year). Title. Journal.
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- [Link to relevant papers or documentation]
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## Implementation Considerations
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**What components would be affected?**
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- [ ] Core models (cardiac, neural, coupling)
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- [ ] Validation framework
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- [ ] Autonomic nervous system
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- [ ] Organ-on-chip platform
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- [ ] Hardware integration
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- [ ] Documentation
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- [ ] Tests
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- [ ] Examples
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**Potential challenges:**
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- Compatibility with existing code
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- Performance considerations
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- Validation requirements
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- Documentation needs
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## Backward Compatibility
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**Would this feature break existing code?**
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- [ ] Yes, breaking change (requires major version bump)
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- [ ] No, fully backward compatible
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- [ ] Unsure
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If breaking, how could the transition be managed?
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## Additional Context
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Add any other context, screenshots, diagrams, or mockups about the feature request here.
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## Willingness to Contribute
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- [ ] I am willing to implement this feature and submit a pull request
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- [ ] I can help with testing and validation
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- [ ] I can provide scientific review
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- [ ] I can help with documentation
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- [ ] I am requesting this feature but cannot contribute implementation
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## Checklist
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- [ ] I have searched existing issues and PRs to avoid duplicates
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- [ ] I have clearly described the motivation and use cases
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- [ ] I have considered alternative approaches
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- [ ] I have thought about backward compatibility
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- [ ] I have included relevant scientific references (if applicable)

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