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Skillsmanuscript-formatting

manuscript-formatting

General & other

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Updated 10-16 06:50

About this skill

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 formats (Word to LaTeX, markdown to LaTeX)
  • Checking compliance with author guidelines
  • Managing references and BibTeX

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)
\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
\documentclass[preprint,12pt]{elsarticle}

LaTeX Essentials

Document Structure

\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

@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

\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

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

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

Word to LaTeX

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

LaTeX to Word (for journals requiring .docx)

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:

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