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:

bashCopy code
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.

markdownCopy code
::: {.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.
:::

Run the conversion with the bundled figure-placement filter. The default is inline, which keeps each figure at its Markdown location. Set figure-placement to end to gather marked figures in a Figures section immediately before References, or at the end when no References heading is present.

bashCopy code
pandoc manuscript.md --output manuscript.docx --reference-doc manuscript/reference.docx --lua-filter="$SKILL_DIR/scripts/figure-placement.lua" --metadata figure-placement=inline --citeproc --bibliography=references.bib --csl=journal.csl

For end-of-document figures, change the metadata value to figure-placement=end.

Keep a textual callout such as Figure 1 in the surrounding prose so readers can find the figure in either layout. Use figure-placement=inline for the normal in-place draft. The filter rejects malformed .paper-figure blocks and images without alt text instead of silently dropping content.

Review the Generated DOCX

Open the result in Word or LibreOffice and inspect page breaks, long captions, table widths, equations, cross-references, and the rendered bibliography. Journal submission rules override this generic draft styling; apply the journal's actual template and figure-placement requirements before submission.

Common Journal Formats

IEEE

• Template: IEEEtran class
• Columns: Two-column
• References: Numbered, [1] style
• Figures: Fit within column or span both columns
• Page limit: Varies (typically 6-8 for conference, 12-14 for journal)

latexCopy code
\documentclass[journal]{IEEEtran}
\usepackage{cite}
\usepackage{amsmath}
\usepackage{graphicx}

Nature/Science

• Format: Single column, specific heading hierarchy
• References: Superscript numbered
• Word limit: ~3000-5000 words (main text)
• Figures: Max 6-8, submitted as separate files
• Methods: Often separate section with no word limit

PNAS

• Template: pnas-new class
• Columns: Two-column in print, single for review
• Word limit: ~4500 words
• References: Numbered
• Significance statement: Required, 120 words max

PLoS ONE

• Format: No specific template required
• References: Numbered, Vancouver style
• No length restriction
• Data availability: Statement required

Elsevier

• Template: elsarticle class
• Multiple formats: preprint, review, final

latexCopy code
\documentclass[preprint,12pt]{elsarticle}

LaTeX Essentials

Document Structure

latexCopy code
\documentclass[options]{class}
\usepackage{packages}

\title{Title}
\author{Authors}

\begin{document}
\maketitle
\begin{abstract}
\end{abstract}

\section{Introduction}
\section{Methods}
\section{Results}
\section{Discussion}

\bibliography{references}
\end{document}

BibTeX Management

bibtexCopy code
@article{smith2024,
  author  = {Smith, John and Doe, Jane},
  title   = {Title of the Paper},
  journal = {Journal Name},
  year    = {2024},
  volume  = {10},
  pages   = {1--15},
  doi     = {10.1000/example}
}

Common BibTeX styles:

• plain - numbered, sorted alphabetically
• unsrt - numbered, order of citation
• ieeetr - IEEE transactions style
• apalike - APA-like author-year

Cross-references

latexCopy code
\label{fig:results}   % Label a figure
\ref{fig:results}     % Reference by number
Figure~\ref{fig:results}  % Standard format

Submission Checklist

Before Submission

• Manuscript formatted per journal template
• Title page: title, authors, affiliations, corresponding author, ORCID
• Abstract within word limit
• Keywords provided (if required)
• Main text within page/word limit
• Figures as separate high-resolution files (typically 300+ DPI)
• Figure captions in a separate list
• Tables formatted per journal style
• References complete and consistently formatted
• Supplementary materials prepared separately
• Cover letter drafted (run manuscript:humanizer on it; cover letters are particularly prone to AI-tell phrasing)
• manuscript:humanizer natural-writing pass applied to all narrative sections, then journal house style (title case, citation format, etc.) re-applied where it overrides humanizer defaults
• Conflict of interest statement
• Data availability statement
• Ethics approval statement (if applicable)
• Author contributions (CRediT format if required)
• Suggested reviewers (if required)

Cover Letter Template

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Dear Editor,

We submit our manuscript titled "{TITLE}" for consideration
in {JOURNAL}.

{1-2 sentences: what the study did and found}

{1-2 sentences: why this matters to the journal's readership}

{1 sentence: confirmation of originality and no concurrent submission}

We suggest the following reviewers:
1. {Name, Affiliation, Email}
2. {Name, Affiliation, Email}

Sincerely,
{Corresponding Author}

Format Conversion

Markdown to LaTeX

bashCopy code
pandoc manuscript.md -o manuscript.tex --template=journal-template.tex --bibliography=refs.bib --citeproc

Word to LaTeX

bashCopy code
pandoc manuscript.docx -o manuscript.tex --extract-media=figures/

LaTeX to Word (for journals requiring .docx)

bashCopy code
pandoc manuscript.tex -o manuscript.docx --bibliography=refs.bib --citeproc

Semantic Line Breaks

Semantic line breaks put each substantial unit of thought on its own source line, so a small prose edit produces a small, reviewable diff. The SemBr specification requires that this formatting not alter the rendered document. The sembr CLI supports Markdown, plain text, and LaTeX and can be installed portably with uv tool install sembr.

Raw SemBr output is reasonable for ordinary Markdown after review. Do not trust raw output on LaTeX: line breaks can change comment scope or corrupt commands and escape sequences. Use the bundled safety wrapper for LaTeX:

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uv run python plugins/manuscript/skills/manuscript-formatting/scripts/semantic_breaks.py \
  manuscript.tex manuscript-semantic.tex \
  --compile-command latexmk -pdf -interaction=nonstopmode \
  -outdir '{build_dir}' '{source}'

The wrapper performs these gates before writing the destination:

1. It replaces \\begin{verbatim}...\\end{verbatim} blocks and full-line % comments with atomic placeholders, then restores them after SemBr.
2. It aligns whitespace-delimited tokens with Python's difflib.SequenceMatcher. If any token content diverges, it restores the original paragraph containing that divergence; whitespace-only changes in other paragraphs remain available as semantic breaks. A whitespace-collapsed string comparison alone is unsafe because it misses % comment truncation.
3. When --compile-command is supplied, it compiles the original and guarded versions separately, runs pdftotext on both PDFs, and refuses to write the result unless the extracted bytes are identical. The compiler command must use {source} for its input and route generated files into {build_dir}; arguments after --compile-command are consumed by the wrapper.

Inspect the resulting diff and keep the compiled-output check in the workflow; matching extracted text is a safety gate, not a substitute for reviewing the source and the rendered PDF.

Additional Resources

• Reference: references/journal-requirements.md - Detailed requirements for major journals
• Reference: references/latex-troubleshooting.md - Common LaTeX issues and fixes