Technology
Rxiv-Maker is an automated LaTeX article generation system that transforms scientific writing from chaos to clarity. It converts Markdown manuscripts into professional, publication-ready PDFs with advanced features specifically designed for scientific writing.
The key innovation of Rxiv-Maker is bridging the gap between Markdown's simplicity and LaTeX's professional output quality. It allows researchers to write scientific manuscripts in accessible Markdown format while generating publication-ready PDFs with LaTeX-quality formatting, without requiring LaTeX expertise.
Key Features
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Enhanced Markdown Support: Provides 20+ advanced markdown features for scientific writing, including scientific cross-references, citations, and programmatic figure generation.
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Automated Workflows: Integrates figure generation via Python/R/Mermaid, GitHub Actions for continuous document generation, and supports both cloud and local PDF generation.
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Professional Output: Delivers LaTeX-quality formatting with multiple citation styles, intelligent validation systems, and reproducible scientific workflows.
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Multiple Access Points: Offers three installation options - Google Colab (easiest, browser-based), GitHub Actions (recommended for automated workflows), and local development (maximum control).
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Version Control Integration: Fully compatible with Git workflows, enabling collaborative manuscript development and maintaining computational provenance.
Core Workflow
The Rxiv-Maker workflow consists of five main steps:
- Write manuscript content in enhanced Markdown syntax
- Configure document metadata and properties in YAML
- Create and integrate figures using Python/R/Mermaid
- Validate manuscript for consistency and completeness
- Generate publication-ready PDF output locally or via cloud
Target Applications
Rxiv-Maker is designed for researchers, scientists, and academic writers who need to produce professional scientific documents without the complexity of traditional LaTeX workflows. It's particularly valuable for:
- Computational biology and imaging research workflows
- Collaborative manuscript development
- Reproducible research documentation
- Technical documentation requiring scientific formatting
Reproducible Research Focus
The system addresses reproducibility challenges by treating manuscripts as executable outputs rather than static documents. This approach ensures that visualizations reflect current data and processing algorithms, making it essential for microscopy and image analysis workflows where figures must be programmatically generated and updated.
Rxiv-Maker represents a significant advancement in making scientific publishing more accessible, reproducible, and efficient for researchers worldwide, while maintaining the professional standards expected in academic publishing.
Publications featuring Rxiv-Maker
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Rxiv-Maker: an automated template engine for streamlined scientific publications Bruno M. Saraiva, Guillaume Jacquemet, Ricardo Henriques Preprint published in Zenodo, July 2025 Technologies: Rxiv-Maker () Funded by: CZI, EMBO, ERC, H2021 and H2022 DOI: 10.5281/zenodo.15805470 |
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