git clone https://github.com/ywatanabe1989/sciwriter.git my-paper
cd my-paper
./scripts/shell/compile_manuscript.sh

pip install sciwriter
sciwriter compile ./my-paper              # Compile manuscript
sciwriter compile ./my-paper -t suppl     # Compile supplementary
sciwriter status ./my-paper               # Check dependencies

Add to Claude Desktop config (~/.config/claude/claude_desktop_config.json):

{
  "mcpServers": {
    "sciwriter": {
      "command": "python",
      "args": ["-m", "sciwriter.mcp_server"]
    }
  }
}

Tools: compile, status, clean, get_project_info

• Templates - Manuscript, supplementary material, and revision letter
• Modular LaTeX - Section-separated .tex files
• MCP Server - Claude Desktop integration
• Media Support - Figures, tables, and citations
• Citation Management - Multi-file .bib with auto-merge
• Citation Styles - 20+ journal formats (Nature, IEEE, APA, etc.)
• Auto Counts - Words and media per section
• Diff Visualization - Track changes between versions
• Git Friendly - Auto-archive with version history

pip install sciwriter

sudo apt-get install texlive-latex-extra latexdiff parallel imagemagick ghostscript

brew install texlive latexdiff parallel imagemagick ghostscript

# Module system
module load texlive latexdiff parallel

# Docker
docker run -v $(pwd):/work scitex-writer

# Singularity/Apptainer
singularity run scitex-writer.sif

my-paper/
├── 00_shared/              # Shared resources (bibliography, styles)
│   ├── bib_files/          # Multiple .bib files (auto-merged)
│   └── latex_styles/       # Common LaTeX configurations
├── 01_manuscript/          # Main manuscript
│   ├── contents/           # Modular content sections
│   │   ├── abstract.tex
│   │   ├── introduction.tex
│   │   ├── methods.tex
│   │   ├── results.tex
│   │   ├── discussion.tex
│   │   ├── figures/        # Figure captions + media
│   │   └── tables/         # Table captions + CSV data
│   ├── archive/            # Version history (auto-generated)
│   ├── manuscript.tex      # Compiled LaTeX
│   └── manuscript.pdf      # Output PDF
├── 02_supplementary/       # Supplementary materials
├── 03_revision/            # Revision response letter
└── scripts/shell/          # Compilation scripts

./scripts/shell/compile_manuscript.sh          # Manuscript
./scripts/shell/compile_supplementary.sh       # Supplementary
./scripts/shell/compile_revision.sh            # Revision letter

./scripts/shell/compile_manuscript.sh --draft      # Fast single-pass
./scripts/shell/compile_manuscript.sh --no-figs    # Skip figures
./scripts/shell/compile_manuscript.sh --no-tables  # Skip tables
./scripts/shell/compile_manuscript.sh --no-diff    # Skip diff generation

./scripts/shell/compile_manuscript.sh --engine tectonic  # Fastest
./scripts/shell/compile_manuscript.sh --engine latexmk   # Standard
./scripts/shell/compile_manuscript.sh --engine 3pass     # Most compatible

./scripts/shell/compile_manuscript.sh --watch  # Hot-reload on file changes
./scripts/shell/compile_manuscript.sh --clean  # Remove cache

Organize references in multiple .bib files - they auto-merge with deduplication:

00_shared/bib_files/
├── methods_refs.bib      # Method-related references
├── field_background.bib  # Background literature
└── my_papers.bib         # Your own publications

Citation Styles (set in config/config_manuscript.yaml):

• unsrtnat - numbered, order of citation
• plainnat - numbered, alphabetical
• apalike - author-year, APA style
• IEEEtran - IEEE format
• naturemag - Nature style

1. Place media files in 01_manuscript/contents/figures/caption_and_media/:

   01_example_figure.png
   01_example_figure.tex  # Caption file
   

2. Caption file format (01_example_figure.tex):

   %% Figure caption
   \caption{Your figure caption here. Explain panels (A, B, C) if applicable.}
   \label{fig:example_figure_01}
   

3. Supported formats: PNG, JPEG, PDF, SVG, TIFF, Mermaid (.mmd)

1. Place CSV + caption in 01_manuscript/contents/tables/caption_and_media/:

   01_example_table.csv
   01_example_table.tex  # Caption file
   

2. CSV auto-converts to LaTeX table format

3. Caption file format (01_example_table.tex):

   %% Table caption
   \caption{Your table caption. Define abbreviations used.}
   \label{tab:example_table_01}
   

Writing assistance prompts in docs/prompts/:

• abstract.md - Abstract writing guidelines
• introduction.md - Introduction structure
• methods.md - Methods section format
• discussion.md - Discussion framework
• proofreed.md - Proofreading checklist