Quick Start Guide

Fast reference for common tasks and workflows in SciTeX.

Basic Workflow

Edit content files in manuscript/contents/
Add figures to manuscript/contents/figures/contents/
Add tables to manuscript/contents/tables/contents/
Update bibliography in 00_shared/bibliography.bib
Compile with ./compile
View PDF at manuscript/main/manuscript.pdf

Project Structure

SciTeX/
├── 01_manuscript/      # Main manuscript
│   ├── contents/       # Source files
│   │   ├── figures/    # Figure files
│   │   ├── tables/     # Table files
│   │   └── *.tex       # Content (intro, methods, etc.)
├── 02_supplementary/   # Supplementary materials
├── 03_revision/        # Revision responses
├── 00_shared/             # Shared metadata
├── docs/               # Documentation
└── scripts/            # Compilation scripts

Common Commands

# Full compilation
./compile_manuscript

# Compile with figures
./compile_manuscript --figs

# Show changes from previous version
./compile_manuscript --diff

# Debug mode with verbose output
./compile_manuscript --debug

# Launch GUI editor (browser-based)
pip install scitex-writer[editor]   # Install Flask dependency (once)
scitex-writer gui                   # Opens browser with editor + PDF preview

Content Files

Manuscript sections in manuscript/contents/:
- abstract.tex - Abstract
- introduction.tex - Introduction
- methods.tex - Methods
- results.tex - Results
- discussion.tex - Discussion

Shared metadata in 00_shared/:
- authors.tex - Author list
- title.tex - Title
- keywords.tex - Keywords
- bibliography.bib - References

Quick Tasks

Add a Figure

Create PNG/JPG (300 DPI)
Name: .01_description.png
Place in: manuscript/contents/figures/contents/
Create caption: .01_description.tex
Reference in text: Figure~\ref{fig:01}

Add a Table

Create CSV data file
Name: .01_description.csv
Place in: manuscript/contents/tables/contents/
Create caption: .01_description.tex
Reference in text: Table~\ref{tab:01}

Add a Citation

Add to 00_shared/bibliography.bib:

@article{Smith2023,
  author = {Smith, John},
  title = {Title},
  journal = {Journal},
  year = {2023}
}

Cite in text: \cite{Smith2023}

Update Authors

Edit 00_shared/authors.tex:

John Smith\textsuperscript{1,*},
Jane Doe\textsuperscript{1,2}

\textsuperscript{1}Department, University
\textsuperscript{2}Other Department, University

Update Title/Keywords

Title: 00_shared/title.tex
Keywords: 00_shared/keywords.tex

File Naming

Figures: .XX_name.{png|jpg|tif|mmd}
- Example: .01_workflow.png

Tables: .XX_name.csv
- Example: .01_results.csv

Captions: .XX_name.tex
- Example: .01_workflow.tex

Compilation Output

After compilation:
- manuscript.pdf - Final manuscript
- diff.pdf - Changes from previous version
- Debug info in compiled/debug/

Troubleshooting

Figure not appearing:
- Check file exists
- Verify naming (must start with .)
- Both PNG and TEX files must have same name

Bibliography errors:
- Check syntax in .bib file
- Verify all \cite{} keys exist in bibliography

Compilation fails:
- Check for LaTeX errors in content
- Verify all linked files exist
- Review compiler output for details

Best Practices

Version control: Commit changes regularly
bash git add manuscript/contents/ git commit -m "Update results section"
Consistent naming: Use descriptive names
.01_methods_overview.png (good)
.01_Fig.png (bad)
High-quality figures: 300 DPI minimum
Use PNG for screenshots
Use EPS/PDF for diagrams
Clear captions: Explain each figure/table
What is shown
Why it matters
How to interpret
Regular backups: Use git or external storage

More Information

Full content guide: 01_GUIDE_CONTENT_CREATION.md
AI agent guide: G_AGENTS.md
For language-specific standards: to_claude/guidelines/

# Quick Start Guide
Fast reference for common tasks and workflows in SciTeX.
## Basic Workflow
1. Edit content files in `manuscript/contents/`
2. Add figures to `manuscript/contents/figures/contents/`
3. Add tables to `manuscript/contents/tables/contents/`
4. Update bibliography in `00_shared/bibliography.bib`
5. Compile with `./compile`
6. View PDF at `manuscript/main/manuscript.pdf`
## Project Structure
```
SciTeX/
├── 01_manuscript/      # Main manuscript
│   ├── contents/       # Source files
│   │   ├── figures/    # Figure files
│   │   ├── tables/     # Table files
│   │   └── *.tex       # Content (intro, methods, etc.)
├── 02_supplementary/   # Supplementary materials
├── 03_revision/        # Revision responses
├── 00_shared/             # Shared metadata
├── docs/               # Documentation
└── scripts/            # Compilation scripts
```
## Common Commands
```bash
# Full compilation
./compile_manuscript
# Compile with figures
./compile_manuscript --figs
# Show changes from previous version
./compile_manuscript --diff
# Debug mode with verbose output
./compile_manuscript --debug
# Launch GUI editor (browser-based)
pip install scitex-writer[editor]   # Install Flask dependency (once)
scitex-writer gui                   # Opens browser with editor + PDF preview
```
## Content Files
**Manuscript sections** in `manuscript/contents/`:
- `abstract.tex` - Abstract
- `introduction.tex` - Introduction
- `methods.tex` - Methods
- `results.tex` - Results
- `discussion.tex` - Discussion
**Shared metadata** in `00_shared/`:
- `authors.tex` - Author list
- `title.tex` - Title
- `keywords.tex` - Keywords
- `bibliography.bib` - References
## Quick Tasks
### Add a Figure
1. Create PNG/JPG (300 DPI)
2. Name: `.01_description.png`
3. Place in: `manuscript/contents/figures/contents/`
4. Create caption: `.01_description.tex`
5. Reference in text: `Figure~\ref{fig:01}`
### Add a Table
1. Create CSV data file
2. Name: `.01_description.csv`
3. Place in: `manuscript/contents/tables/contents/`
4. Create caption: `.01_description.tex`
5. Reference in text: `Table~\ref{tab:01}`
### Add a Citation
1. Add to `00_shared/bibliography.bib`:
```bibtex
@article{Smith2023,
  author = {Smith, John},
  title = {Title},
  journal = {Journal},
  year = {2023}
}
```
2. Cite in text: `\cite{Smith2023}`
### Update Authors
Edit `00_shared/authors.tex`:
```latex
John Smith\textsuperscript{1,*},
Jane Doe\textsuperscript{1,2}
\textsuperscript{1}Department, University
\textsuperscript{2}Other Department, University
```
### Update Title/Keywords
- Title: `00_shared/title.tex`
- Keywords: `00_shared/keywords.tex`
## File Naming
**Figures**: `.XX_name.{png|jpg|tif|mmd}`
- Example: `.01_workflow.png`
**Tables**: `.XX_name.csv`
- Example: `.01_results.csv`
**Captions**: `.XX_name.tex`
- Example: `.01_workflow.tex`
## Compilation Output
After compilation:
- `manuscript.pdf` - Final manuscript
- `diff.pdf` - Changes from previous version
- Debug info in `compiled/debug/`
## Troubleshooting
**Figure not appearing**:
- Check file exists
- Verify naming (must start with `.`)
- Both PNG and TEX files must have same name
**Bibliography errors**:
- Check syntax in `.bib` file
- Verify all `\cite{}` keys exist in bibliography
**Compilation fails**:
- Check for LaTeX errors in content
- Verify all linked files exist
- Review compiler output for details
## Best Practices
1. **Version control**: Commit changes regularly
   ```bash
   git add manuscript/contents/
   git commit -m "Update results section"
   ```
2. **Consistent naming**: Use descriptive names
   - `.01_methods_overview.png` (good)
   - `.01_Fig.png` (bad)
3. **High-quality figures**: 300 DPI minimum
   - Use PNG for screenshots
   - Use EPS/PDF for diagrams
4. **Clear captions**: Explain each figure/table
   - What is shown
   - Why it matters
   - How to interpret
5. **Regular backups**: Use git or external storage
## More Information
- Full content guide: `01_GUIDE_CONTENT_CREATION.md`
- AI agent guide: `G_AGENTS.md`
- For language-specific standards: `to_claude/guidelines/`