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update documentation for the main template [ci skip]
Signed-off-by: Abhinav Sharma <[email protected]>
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‎.gitignore‎

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template/.idea
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template/template.iml
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docs/presentations/academic-template/output/src/template-presentation_files
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docs/presentations/academic-template/output/template-presentation_files
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template-presentation_files
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/docs/presentations/output/src/template-presentation.html

‎docs/README.md‎

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# Documentation Structure
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This documentation system supports multiple types of academic and technical content with a modular, scalable structure.
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## Directory Structure
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```
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docs/
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├── presentations/ # Academic and technical presentations
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│ ├── academic-template/ # Main academic presentation
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│ └── shared/ # Shared presentation resources
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├── manuscript/ # Scientific manuscripts and papers
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│ ├── src/ # Source manuscript files
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│ ├── assets/ # Manuscript-specific assets
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│ └── output/ # Generated manuscript outputs
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├── website/ # Website content and documentation
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│ ├── src/ # Website source files
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│ ├── assets/ # Website assets
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│ ├── walkthroughs/ # Step-by-step guides
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│ ├── case-studies/ # Real-world examples
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│ └── output/ # Generated website files
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└── shared/ # Shared resources across all content
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├── assets/ # Common images, logos, etc.
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├── styles/ # Common CSS/SCSS files
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└── references/ # Shared bibliography files
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```
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## Content Types
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### 📊 Presentations
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- **Academic presentations** for conferences and seminars
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- **Technical presentations** for workshops and training
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- **Multiple format support**: HTML slides, PDF, PowerPoint
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- **Shared styling** and assets for consistency
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### 📝 Manuscripts
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- **Scientific papers** and research articles
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- **Technical reports** and documentation
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- **Multiple formats**: PDF, HTML, Word
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- **Citation management** and bibliography support
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### 🌐 Website
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- **Project documentation** and guides
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- **Interactive walkthroughs** for complex processes
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- **Case studies** with real-world examples
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- **Static site generation** for easy deployment
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## Getting Started
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1. **Choose your content type** and navigate to the appropriate directory
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2. **Read the specific README** in each directory for detailed instructions
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3. **Use the provided templates** as starting points
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4. **Leverage shared resources** for consistency across content types
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## Tools and Technologies
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- **Quarto**: Primary authoring system for all content types
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- **Markdown/QMD**: Source format for writing
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- **SCSS**: Styling and theming
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- **BibTeX**: Citation management
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- **Git**: Version control for all content
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## Build and Deployment
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Each content type has its own build process:
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```bash
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# Presentations
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cd presentations/academic-template && quarto render
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# Manuscripts
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cd manuscript && quarto render
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# Website
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cd website && quarto render
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```
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## Contributing
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- Follow the established directory structure
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- Use shared resources when possible
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- Maintain consistent styling and formatting
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- Update documentation when adding new content types

‎docs/manuscript/README.md‎

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# Scientific Manuscript
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This section contains scientific manuscripts and research papers related to the project.
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## Structure
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```
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manuscript/
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├── src/ # Source manuscript files
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│ ├── manuscript.qmd # Main manuscript (to be created)
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│ ├── abstract.qmd # Abstract section
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│ ├── introduction.qmd # Introduction section
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│ ├── methods.qmd # Methods section
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│ ├── results.qmd # Results section
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│ ├── discussion.qmd # Discussion section
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│ └── conclusion.qmd # Conclusion section
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├── assets/ # Manuscript-specific assets
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│ ├── figures/ # Figures and charts
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│ ├── tables/ # Data tables
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│ ├── references.bib # Bibliography
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│ └── manuscript.css # Custom styling
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└── output/ # Generated manuscript outputs
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```
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## Manuscript Types
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### Research Paper
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- Full-length research articles
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- Conference papers
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- Technical reports
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### Format Support
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- **PDF**: Camera-ready publication format
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- **HTML**: Web-friendly format with interactivity
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- **Word**: Collaborative editing format
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- **LaTeX**: High-quality typesetting
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## Building the Manuscript
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### Single File Approach
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```bash
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# Create and render main manuscript
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quarto render src/manuscript.qmd
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# Multiple formats
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quarto render src/manuscript.qmd --to pdf
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quarto render src/manuscript.qmd --to html
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quarto render src/manuscript.qmd --to docx
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```
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### Modular Approach
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```bash
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# Render individual sections
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quarto render src/introduction.qmd
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quarto render src/methods.qmd
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# ... etc
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```
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## Getting Started
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1. **Create your manuscript structure**:
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```bash
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cd manuscript/src
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# Create main manuscript file
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touch manuscript.qmd
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```
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2. **Set up bibliography**:
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```bash
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# Add references to assets/references.bib
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```
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3. **Add figures and tables**:
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```bash
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# Place images in assets/figures/
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# Place data tables in assets/tables/
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```
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4. **Customize styling**:
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```bash
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# Edit assets/manuscript.css for custom styling
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```
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## Manuscript Template
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A typical manuscript includes:
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- Title page with author information
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- Abstract (structured or unstructured)
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- Keywords
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- Introduction with literature review
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- Methods/Methodology
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- Results with figures and tables
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- Discussion
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- Conclusions
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- References
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- Appendices (if needed)
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## Citation Management
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- Use BibTeX format in `assets/references.bib`
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- Reference using `@key` syntax in Quarto
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- Automatic bibliography generation
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- Multiple citation styles supported
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## Collaborative Workflows
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- Version control with Git
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- Word output for reviewer comments
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- Track changes and revisions
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- Merge feedback efficiently
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## Quality Assurance
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- Spell check and grammar review
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- Reference validation
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- Figure and table numbering
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- Cross-reference checking
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- Reproducible code execution
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## Submission Ready
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- Journal-specific formatting
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- Supplementary materials
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- Cover letter template
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- Compliance with submission guidelines

‎docs/presentations/README.md‎

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# Presentations
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This folder contains all presentations related to the project.
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## Structure
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- **academic-template/**: Main template for academic presentations.
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- **shared/**: Common resources and styles for presentations.
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## Usage
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1. Navigate to the desired presentation folder.
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2. Use the provided Quarto files as starting points.
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3. Build using Quarto:
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```bash
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quarto render
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```

‎docs/presentations/academic-template/.gitignore‎

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/.quarto/

‎docs/presentations/academic-template/README.md‎

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# Academic Template Presentation
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This presentation showcases the integrated research template system for academic workflows.
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## Files Structure
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```
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academic-template/
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├── src/
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│ └── template-presentation.qmd # Main presentation source
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├── assets/
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│ ├── custom.scss # Custom styling
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│ ├── references.bib # Bibliography
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│ └── .gitkeep # Placeholder for additional assets
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└── output/ # Generated presentation files
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```
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## Building the Presentation
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### Prerequisites
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- Quarto installed
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- Modern web browser for HTML output
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### Available Formats
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```bash
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# HTML slides (default)
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quarto render src/template-presentation.qmd
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# PDF slides
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quarto render src/template-presentation.qmd --to beamer
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# PowerPoint
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quarto render src/template-presentation.qmd --to pptx
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# All formats
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quarto render src/template-presentation.qmd --to all
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```
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### Customization
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1. **Content**: Edit `src/template-presentation.qmd`
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2. **Styling**: Modify `assets/custom.scss`
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3. **References**: Update `assets/references.bib`
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4. **Assets**: Add images/logos to `assets/`
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## Presentation Overview
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This presentation covers:
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- Academic research workflow challenges
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- Integrated template solution
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- Data architecture and management
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- Multi-language development support
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- Pipeline automation with Nextflow/Snakemake
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- Quality assurance and reproducibility
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- Real-world use cases and success stories
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## Usage Tips
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- Use speaker notes for detailed explanations
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- Customize the color scheme in `custom.scss`
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- Add your organization's logo to `assets/`
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- Update contact information in the presentation
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- Adapt content for your specific audience
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## Output Location
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Rendered presentations are saved to the `output/` directory automatically.

‎docs/presentations/academic-template/_quarto.yml‎

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project:
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type: default
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output-dir: ../output
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format:
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revealjs:
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theme: [default, assets/custom.scss]
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slide-number: true
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chalkboard: true
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preview-links: auto
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logo: assets/logo.png
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footer: "Comprehensive Academic Research Template"
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transition: fade
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background-transition: fade
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highlight-style: github
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code-line-numbers: true
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code-overflow: wrap
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pptx:
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reference-doc: assets/template.pptx
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pdf:
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documentclass: beamer
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theme: metropolis
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bibliography: assets/references.bib
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execute:
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echo: true
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eval: false

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‎docs/presentations/academic-template/assets/logo.png.placeholder‎

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# Logo Placeholder
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Place your organization's logo here as `logo.png`.
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## Requirements:
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- Format: PNG
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- Recommended size: 200x200 pixels or similar square ratio
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- Transparent background preferred
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- High resolution for crisp display
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## Usage:
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The logo will appear in the top-right corner of RevealJS slides and be used in other presentation formats as specified in the template.

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