@saibolla/ada 0.1.2

package/skills/paper-2-web/references/paper2web.md

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+# Paper2Web: Academic Homepage Generation
+
+## Overview
+
+Paper2Web converts academic papers into interactive, explorable academic homepages. Unlike traditional approaches (direct generation, template-based, or HTML conversion), Paper2Web creates layout-aware, interactive websites through an iterative refinement process.
+
+## Core Capabilities
+
+### 1. Layout-Aware Generation
+- Analyzes paper structure and content organization
+- Creates responsive, multi-section layouts
+- Adapts design based on paper type (research article, review, preprint, etc.)
+
+### 2. Interactive Elements
+- Expandable sections for detailed content
+- Interactive figures and tables
+- Embedded citations and references
+- Navigation menu for easy browsing
+- Mobile-responsive design
+
+### 3. Content Refinement
+The system uses an iterative pipeline:
+1. Initial content extraction and structuring
+2. Layout generation with visual hierarchy
+3. Interactive element integration
+4. Aesthetic refinement
+5. Quality assessment and validation
+
+## Usage
+
+### Basic Website Generation
+
+```bash
+python pipeline_all.py \
+  --input-dir "path/to/papers" \
+  --output-dir "path/to/output" \
+  --model-choice 1
+```
+
+### Parameters
+
+- `--input-dir`: Directory containing paper files (PDF or LaTeX)
+- `--output-dir`: Directory for generated website files
+- `--model-choice`: LLM model selection (1=GPT-4, 2=GPT-4.1)
+- `--enable-logo-search`: Use Google Search API to find institution logos (optional)
+
+### Input Format Requirements
+
+**Supported Input Formats:**
+1. **LaTeX source** (preferred for best results)
+   - Main file: `main.tex`
+   - Include all referenced figures, tables, and bibliography files
+   - Organize in a single directory per paper
+
+2. **PDF files**
+   - High-quality PDF with selectable text
+   - Embedded figures should be high resolution
+   - Proper section headers and structure
+
+**Directory Structure:**
+```
+input/
+└── paper_name/
+    ├── main.tex           # LaTeX source
+    ├── bibliography.bib   # References
+    ├── figures/           # Figure files
+    │   ├── fig1.png
+    │   └── fig2.pdf
+    └── tables/            # Table files
+```
+
+## Output Structure
+
+Generated websites include:
+
+```
+output/paper_name/website/
+├── index.html          # Main webpage
+├── styles.css          # Styling
+├── script.js           # Interactive features
+├── assets/             # Images and media
+│   ├── figures/
+│   └── logos/
+└── data/               # Structured data (optional)
+```
+
+## Customization Options
+
+### Visual Design
+The generated websites automatically include:
+- Professional color schemes based on paper content
+- Typography optimized for readability
+- Consistent spacing and visual hierarchy
+- Dark mode support (optional)
+
+### Content Sections
+Standard sections include:
+- Abstract
+- Key findings/contributions
+- Methodology overview
+- Results and visualizations
+- Discussion and implications
+- References and citations
+- Author information and affiliations
+
+Additional sections are automatically added based on paper content:
+- Code repositories
+- Dataset links
+- Supplementary materials
+- Related publications
+
+## Quality Assessment
+
+Paper2Web includes built-in evaluation:
+
+### Aesthetic Metrics
+- Layout balance and spacing
+- Color harmony
+- Typography consistency
+- Visual hierarchy effectiveness
+
+### Informativeness Metrics
+- Content completeness
+- Key finding clarity
+- Method explanation adequacy
+- Results presentation quality
+
+### Technical Metrics
+- Page load time
+- Mobile responsiveness
+- Browser compatibility
+- Accessibility compliance
+
+## Advanced Features
+
+### Logo Discovery
+When enabled with Google Search API:
+- Automatically finds institution logos
+- Matches author affiliations
+- Downloads and optimizes logo images
+- Integrates into website header
+
+### Citation Integration
+- Interactive reference list
+- Hover previews for citations
+- Links to DOI and external sources
+- Citation count tracking (if available)
+
+### Figure Enhancement
+- High-resolution figure rendering
+- Zoom and pan functionality
+- Caption and description integration
+- Multi-panel figure navigation
+
+## Best Practices
+
+### Input Preparation
+1. **Use LaTeX when possible**: Provides best structure extraction
+2. **Include all assets**: Figures, tables, and bibliography files
+3. **Clean formatting**: Remove compilation artifacts and temporary files
+4. **High-quality figures**: Use vector formats (PDF, SVG) when available
+
+### Model Selection
+- **GPT-4**: Best balance of quality and cost
+- **GPT-4.1**: Latest features, higher cost
+- **GPT-3.5-turbo**: Faster processing, acceptable for simple papers
+
+### Output Optimization
+1. Review generated content for accuracy
+2. Check that all figures render correctly
+3. Test interactive elements functionality
+4. Verify mobile responsiveness
+5. Validate external links
+
+## Limitations
+
+- Complex mathematical equations may require manual review
+- Multi-column layouts in PDF may affect extraction quality
+- Large papers (>50 pages) may require extended processing time
+- Some specialized figure types may need manual adjustment
+
+## Integration with Other Components
+
+Paper2Web can be combined with:
+- **Paper2Video**: Generate companion video for the website
+- **Paper2Poster**: Create matching poster design
+- **AutoPR**: Generate promotional content linking to website

package/skills/paper-2-web/references/usage_examples.md

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+# Usage Examples and Workflows
+
+## Complete Workflow Examples
+
+### Example 1: Conference Presentation Package
+
+**Scenario**: Preparing for a major conference presentation with website, poster, and video.
+
+**User Request**: "I need to create a complete presentation package for my NeurIPS paper submission. Generate a website, poster, and video presentation."
+
+**Workflow**:
+
+```bash
+# Step 1: Organize paper files
+mkdir -p input/neurips2025_paper
+cp main.tex input/neurips2025_paper/
+cp -r figures/ input/neurips2025_paper/
+cp -r tables/ input/neurips2025_paper/
+cp bibliography.bib input/neurips2025_paper/
+
+# Step 2: Generate all components
+python pipeline_all.py \
+  --input-dir input/neurips2025_paper \
+  --output-dir output/ \
+  --model-choice 1 \
+  --generate-website \
+  --generate-poster \
+  --generate-video \
+  --poster-width-inches 48 \
+  --poster-height-inches 36 \
+  --enable-logo-search
+
+# Step 3: Review outputs
+ls -R output/neurips2025_paper/
+# - website/index.html
+# - poster/poster_final.pdf
+# - video/final_video.mp4
+```
+
+**Output**:
+- Interactive website showcasing research
+- 4'×3' conference poster (print-ready)
+- 12-minute presentation video
+- Processing time: ~45 minutes (without talking-head)
+
+---
+
+### Example 2: Quick Website for Preprint
+
+**Scenario**: Creating an explorable homepage for a bioRxiv preprint.
+
+**User Request**: "Convert my genomics preprint to an interactive website to accompany the bioRxiv submission."
+
+**Workflow**:
+
+```bash
+# Using PDF input (LaTeX not available)
+python pipeline_all.py \
+  --input-dir papers/genomics_preprint/ \
+  --output-dir output/genomics_web/ \
+  --model-choice 1 \
+  --generate-website
+
+# Deploy to GitHub Pages or personal server
+cd output/genomics_web/website/
+# Add link to bioRxiv paper, data repositories, code
+# Upload to hosting service
+```
+
+**Tips**:
+- Include links to bioRxiv DOI
+- Add GitHub repository links
+- Include data availability section
+- Embed interactive visualizations if possible
+
+---
+
+### Example 3: Video Abstract for Journal Submission
+
+**Scenario**: Creating a video abstract for a journal that encourages multimedia submissions.
+
+**User Request**: "Generate a 5-minute video abstract for my Nature Communications submission."
+
+**Workflow**:
+
+```bash
+# Generate concise video focusing on key findings
+python pipeline_light.py \
+  --model_name_t gpt-4.1 \
+  --model_name_v gpt-4.1 \
+  --result_dir output/video_abstract/ \
+  --paper_latex_root papers/nature_comms/ \
+  --video-duration 300 \
+  --slides-per-minute 3
+
+# Optional: Add custom intro/outro slides
+# Optional: Include talking-head for introduction
+```
+
+**Output**:
+- 5-minute video abstract
+- Focus on visual results
+- Clear, accessible narration
+- Journal-ready format
+
+---
+
+### Example 4: Multi-Paper Website Generation
+
+**Scenario**: Creating websites for multiple papers from a research group.
+
+**User Request**: "Generate websites for all 5 papers our lab published this year."
+
+**Workflow**:
+
+```bash
+# Organize papers
+mkdir -p batch_input/
+# Create subdirectories: paper1/, paper2/, paper3/, paper4/, paper5/
+# Each with their LaTeX sources
+
+# Batch process
+python pipeline_all.py \
+  --input-dir batch_input/ \
+  --output-dir batch_output/ \
+  --model-choice 1 \
+  --generate-website \
+  --enable-logo-search
+
+# Creates:
+# batch_output/paper1/website/
+# batch_output/paper2/website/
+# batch_output/paper3/website/
+# batch_output/paper4/website/
+# batch_output/paper5/website/
+```
+
+**Best Practice**:
+- Use consistent naming conventions
+- Process overnight for large batches
+- Review each website for accuracy
+- Deploy to unified lab website
+
+---
+
+### Example 5: Poster for Virtual Conference
+
+**Scenario**: Creating a digital poster for a virtual conference with interactive elements.
+
+**User Request**: "Create a poster for the virtual ISMB conference with clickable links to code and data."
+
+**Workflow**:
+
+```bash
+# Generate poster with QR codes and links
+python pipeline_all.py \
+  --input-dir papers/ismb_submission/ \
+  --output-dir output/ismb_poster/ \
+  --model-choice 1 \
+  --generate-poster \
+  --poster-width-inches 48 \
+  --poster-height-inches 36 \
+  --enable-qr-codes
+
+# Manually add QR codes to:
+# - GitHub repository
+# - Interactive results dashboard
+# - Supplementary data
+# - Video presentation
+```
+
+**Digital Enhancements**:
+- PDF with embedded hyperlinks
+- High-resolution PNG for virtual platform
+- Separate PDF with video links for download
+
+---
+
+### Example 6: Promotional Video Clip
+
+**Scenario**: Creating a short promotional video for social media.
+
+**User Request**: "Generate a 2-minute highlight video of our Cell paper for Twitter."
+
+**Workflow**:
+
+```bash
+# Generate short, engaging video
+python pipeline_light.py \
+  --model_name_t gpt-4.1 \
+  --model_name_v gpt-4.1 \
+  --result_dir output/promo_video/ \
+  --paper_latex_root papers/cell_paper/ \
+  --video-duration 120 \
+  --presentation-style public
+
+# Post-process:
+# - Extract key 30-second clip for Twitter
+# - Add captions for sound-off viewing
+# - Optimize file size for social media
+```
+
+**Social Media Optimization**:
+- Square format (1:1) for Instagram
+- Horizontal format (16:9) for Twitter/LinkedIn
+- Vertical format (9:16) for TikTok/Stories
+- Add text overlays for key findings
+
+---
+
+## Common Use Case Patterns
+
+### Pattern 1: LaTeX Paper → Full Package
+
+**Input**: LaTeX source with all assets
+**Output**: Website + Poster + Video
+**Time**: 45-90 minutes
+**Best for**: Major publications, conference presentations
+
+```bash
+python pipeline_all.py \
+  --input-dir [latex_dir] \
+  --output-dir [output_dir] \
+  --model-choice 1 \
+  --generate-website \
+  --generate-poster \
+  --generate-video
+```
+
+---
+
+### Pattern 2: PDF → Interactive Website
+
+**Input**: Published PDF paper
+**Output**: Explorable website
+**Time**: 15-30 minutes
+**Best for**: Post-publication promotion, preprint enhancement
+
+```bash
+python pipeline_all.py \
+  --input-dir [pdf_dir] \
+  --output-dir [output_dir] \
+  --model-choice 1 \
+  --generate-website
+```
+
+---
+
+### Pattern 3: LaTeX → Conference Poster
+
+**Input**: LaTeX paper
+**Output**: Print-ready poster (custom size)
+**Time**: 10-20 minutes
+**Best for**: Conference poster sessions
+
+```bash
+python pipeline_all.py \
+  --input-dir [latex_dir] \
+  --output-dir [output_dir] \
+  --model-choice 1 \
+  --generate-poster \
+  --poster-width-inches [width] \
+  --poster-height-inches [height]
+```
+
+---
+
+### Pattern 4: LaTeX → Presentation Video
+
+**Input**: LaTeX paper
+**Output**: Narrated presentation video
+**Time**: 20-60 minutes (without talking-head)
+**Best for**: Video abstracts, online presentations, course materials
+
+```bash
+python pipeline_light.py \
+  --model_name_t gpt-4.1 \
+  --model_name_v gpt-4.1 \
+  --result_dir [output_dir] \
+  --paper_latex_root [latex_dir]
+```
+
+---
+
+## Platform-Specific Outputs
+
+### Twitter/X Promotional Content
+
+The system auto-detects Twitter targeting for numeric folder names:
+
+```bash
+# Create Twitter-optimized content
+mkdir -p input/001_twitter_post/
+# System generates English promotional content
+```
+
+**Generated Output**:
+- Short, engaging summary
+- Key figure highlights
+- Hashtag recommendations
+- Thread-ready format
+
+---
+
+### Xiaohongshu (小红书) Content
+
+For Chinese social media, use alphanumeric folder names:
+
+```bash
+# Create Xiaohongshu-optimized content
+mkdir -p input/xhs_genomics/
+# System generates Chinese promotional content
+```
+
+**Generated Output**:
+- Chinese language content
+- Platform-appropriate formatting
+- Visual-first presentation
+- Engagement optimizations
+
+---
+
+## Troubleshooting Common Scenarios
+
+### Scenario: Large Paper (>50 pages)
+
+**Challenge**: Processing time and content selection
+**Solution**:
+```bash
+# Option 1: Focus on key sections
+# Edit LaTeX to comment out less critical sections
+
+# Option 2: Process in parts
+# Generate website for overview
+# Generate separate detailed videos for methods/results
+
+# Option 3: Use faster model for initial pass
+# Review and regenerate critical components with better model
+```
+
+---
+
+### Scenario: Complex Mathematical Content
+
+**Challenge**: Equations may not render perfectly
+**Solution**:
+- Use LaTeX input (not PDF) for best equation handling
+- Review generated content for equation accuracy
+- Manually adjust complex equations if needed
+- Consider using figure screenshots for critical equations
+
+---
+
+### Scenario: Non-Standard Paper Structure
+
+**Challenge**: Paper doesn't follow standard IMRAD format
+**Solution**:
+- Provide custom section guidance in paper metadata
+- Review generated structure and adjust
+- Use more powerful model (GPT-4.1) for better adaptation
+- Consider manual section annotation in LaTeX comments
+
+---
+
+### Scenario: Limited API Budget
+
+**Challenge**: Reducing costs while maintaining quality
+**Solution**:
+```bash
+# Use GPT-3.5-turbo for simple papers
+python pipeline_all.py \
+  --input-dir [paper_dir] \
+  --output-dir [output_dir] \
+  --model-choice 3
+
+# Generate only needed components
+# Website-only (cheapest)
+# Poster-only (moderate)
+# Video without talking-head (moderate)
+```
+
+---
+
+### Scenario: Tight Deadline
+
+**Challenge**: Need outputs quickly
+**Solution**:
+```bash
+# Parallel processing if multiple papers
+# Use faster models (GPT-3.5-turbo)
+# Generate only essential component first
+# Skip optional features (logo search, talking-head)
+
+python pipeline_light.py \
+  --model_name_t gpt-3.5-turbo \
+  --model_name_v gpt-3.5-turbo \
+  --result_dir [output_dir] \
+  --paper_latex_root [latex_dir]
+```
+
+**Priority Order**:
+1. Website (fastest, most versatile)
+2. Poster (moderate speed, print deadline)
+3. Video (slowest, can be generated later)
+
+---
+
+## Quality Optimization Tips
+
+### For Best Website Results
+1. Use LaTeX input with all assets
+2. Include high-resolution figures
+3. Ensure paper has clear section structure
+4. Enable logo search for professional appearance
+5. Review and test all interactive elements
+
+### For Best Poster Results
+1. Provide high-resolution figures (300+ DPI)
+2. Specify exact poster dimensions needed
+3. Include institution branding information
+4. Use professional color scheme
+5. Test print small preview before full poster
+
+### For Best Video Results
+1. Use LaTeX for clearest content extraction
+2. Specify target duration appropriately
+3. Review script before video generation
+4. Choose appropriate presentation style
+5. Test audio quality and pacing
+
+### For Best Overall Results
+1. Start with clean, well-organized LaTeX source
+2. Use GPT-4 or GPT-4.1 for highest quality
+3. Review all outputs before finalizing
+4. Iterate on any component that needs adjustment
+5. Combine components for cohesive presentation package

package/skills/paper-code-audit/SKILL.md

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+---
+name: paper-code-audit
+description: Compare a paper's claims against its public codebase. Use when the user asks to audit a paper, check code-claim consistency, verify reproducibility of a specific paper, or find mismatches between a paper and its implementation.
+---
+
+# Paper-Code Audit
+
+Run the `/audit` workflow. Read the prompt template at `prompts/audit.md` for the full procedure.
+
+Agents used: `researcher`, `verifier`
+
+Output: audit report in `outputs/`.

package/skills/paper-writing/SKILL.md

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+---
+name: paper-writing
+description: Turn research findings into a polished paper-style draft with sections, equations, and citations. Use when the user asks to write a paper, draft a report, write up findings, or produce a technical document from collected research.
+---
+
+# Paper Writing
+
+Run the `/draft` workflow. Read the prompt template at `prompts/draft.md` for the full procedure.
+
+Agents used: `writer`, `verifier`
+
+Output: paper draft in `papers/`.