manuscript-formatting

Manuscript Formatting and Submission Preparation

Format manuscripts to meet journal-specific requirements and prepare submission packages.

When to Use

• Formatting a manuscript for a specific journal
• Preparing a submission package (cover letter, figures, supplementary)
• Converting between Word/DOCX, Markdown, and LaTeX
• Checking compliance with author guidelines
• Managing references and BibTeX

Word Draft Workflow

Use this workflow when the reader needs an editable .docx manuscript draft. The bundled reference document gives a polished, readable starting point with a clear title block, restrained headings, legible body text, page numbers, figure and table captions, and compact table text. It is a review-draft style, not a substitute for a journal's required template.

Create or Customize the Reference DOCX

Set SKILL_DIR to the directory containing this SKILL.md, or replace it with that directory's full path in the commands below. A ready-to-use reference file is at assets/Manuscript_Draft_Reference.docx. Copy it into the manuscript project and pass it to Pandoc with --reference-doc.

To generate a fresh copy or change the sample title, run the bundled helper with Python 3.11 or newer and python-docx available:

uv run --with python-docx python "$SKILL_DIR/scripts/create_docx_template.py" --output manuscript/reference.docx --title "Manuscript Title Goes Here"

Pandoc uses the reference DOCX's styles, page setup, header, and footer; it replaces the sample body with the Markdown manuscript. Keep the reference file in the project so collaborators can reproduce the same Word styling.

Mark Figures and Choose Their Placement

Represent each figure as a top-level fenced Div with the .paper-figure class. Put one standalone image first, then one or more caption paragraphs. The image's alt text is used as accessible alternative text; write it as a concise description of the visual information, separately from the caption.

::: {.paper-figure}
![Scatterplot of response time against device latency, with a positive trend and confidence band.](figures/latency.png){width=95%}
Figure 1. Response time increased with device latency. The shaded band shows the 95% confidence interval.
:::